From aecdb782b308774566df66134186073f6d9dbbd2 Mon Sep 17 00:00:00 2001 From: dorislee0309 Date: Mon, 20 Jun 2016 16:38:32 -0700 Subject: [PATCH 001/136] pass all tests --- src/main/ADAMAlignment.js | 111 + src/main/data/Sequence.js | 50 + src/main/sources/ADAM_GA4GHDataSource.js | 153 + src/main/sources/ReferenceDataSource.js | 197 + src/test/ADAMAlignment-test.js | 39 + test-data/adam-alignments.json | 33390 +++++++++++++++++++++ 6 files changed, 33940 insertions(+) create mode 100644 src/main/ADAMAlignment.js create mode 100644 src/main/data/Sequence.js create mode 100644 src/main/sources/ADAM_GA4GHDataSource.js create mode 100644 src/main/sources/ReferenceDataSource.js create mode 100644 src/test/ADAMAlignment-test.js create mode 100644 test-data/adam-alignments.json diff --git a/src/main/ADAMAlignment.js b/src/main/ADAMAlignment.js new file mode 100644 index 00000000..fecc0e60 --- /dev/null +++ b/src/main/ADAMAlignment.js @@ -0,0 +1,111 @@ +/** + * This serves as a bridge between org.ga4gh.GAReadAlignment and the + * pileup.js Alignment type. + * @flow + */ +'use strict'; + +import type {CigarOp, MateProperties, Strand} from './Alignment'; + +import ContigInterval from './ContigInterval'; +import SamRead from './data/SamRead'; + +// See https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/common.avdl +var OP_MAP = { + ALIGNMENT_MATCH: 'M', + INSERT: 'I', + DELETE: 'D', + SKIP: 'N', + CLIP_SOFT: 'S', + CLIP_HARD: 'H', + PAD: 'P', + SEQUENCE_MATCH: '=', + SEQUENCE_MISMATCH: 'X' +}; + +/** + * This class acts as a bridge between org.ga4gh.GAReadAlignment and the + * pileup.js Alignment type. + */ +class ADAMAlignment /* implements Alignment */ { + pos: number; + ref: string; + alignment: Object; + name: string; + cigarOps: CigarOp[]; + _interval: ContigInterval; + + // alignment follows org.ga4gh.GAReadAlignment + // https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/reads.avdl + constructor(alignment: Object) { + this.alignment = alignment; + this.pos = alignment.alignment.position.position; + this.ref = alignment.alignment.position.referenceName; + this.name = alignment.fragmentName; + + this.cigarOps = alignment.alignment.cigar.map( + ({operation, operationLength: length}) => ({ op: OP_MAP[operation], length })); + this._interval = new ContigInterval(this.ref, + this.pos, + this.pos + this.getReferenceLength() - 1); + } + + getKey(): string { + return ADAMAlignment.keyFromGA4GHResponse(this.alignment); + } + + getStrand(): Strand { + return this.alignment.alignment.position.reverseStrand ? '-' : '+'; + } + + getQualityScores(): number[] { + return this.alignment.alignedQuality; + } + + getSequence(): string { + return this.alignment.alignedSequence; + } + + getInterval(): ContigInterval { + return this._interval; + } + + intersects(interval: ContigInterval): boolean { + return interval.intersects(this.getInterval()); + } + + getReferenceLength(): number { + return SamRead.referenceLengthFromOps(this.cigarOps); + } + + getMateProperties(): ?MateProperties { + var next = this.alignment.nextMatePosition; + return next && { + ref: next.referenceName, + pos: next.position, + strand: next.reverseStrand ? '-' : '+' + }; + } + + getInferredInsertSize(): number { + // TODO: SAM/BAM writes this explicitly. Does GA4GH really not? + var m = this.getMateProperties(); + if (m && m.ref == this.ref) { + var start1 = this._interval.start(), + stop1 = this._interval.stop(), + start2 = m.pos, + stop2 = start2 + this.getSequence().length; + return Math.max(stop1, stop2) - Math.min(start1, start2); + } else { + return 0; + } + } + + // This is exposed as a static method to facilitate an optimization in GA4GHDataSource. + static keyFromGA4GHResponse(alignment: Object): string { + // this.alignment.id would be appealing here, but it's not actually unique! + return alignment.fragmentName + ':' + alignment.readNumber; + } +} + +module.exports = ADAMAlignment; diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js new file mode 100644 index 00000000..610f8b98 --- /dev/null +++ b/src/main/data/Sequence.js @@ -0,0 +1,50 @@ +/** + * This module defines a parser for the 2bit file format. + * See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 + * @flow + */ +'use strict'; + +import type RemoteRequest from '../RemoteRequest'; +import TwoBit from './TwoBit'; + +type SequenceRecord = { + name: string, + length: number +} + +class Sequence { + remoteRequest: RemoteRequest; + contigList: SequenceRecord[]; + + constructor(remoteRequest: RemoteRequest, contigList: SequenceRecord[]) { + this.remoteRequest = remoteRequest; + this.contigList = contigList; + } + + // Returns a list of contig names. + getContigList(): string[] { + return this.contigList.map(seq => seq.name); + } + + /** + * Returns the base pairs for contig:start-stop. + * The range is inclusive and zero-based. + * Returns empty string if no data is available on this range. + */ + getFeaturesInRange(contig: string, start: number, stop: number): Q.Promise { + if (start > stop) { + throw `Requested a range with start > stop (${start}, ${stop})`; + } + + return this.remoteRequest.get(contig, start, stop).then(buffer => { + var dataView = new DataView(buffer); + return TwoBit.markUnknownDNA( + TwoBit.unpackDNA(dataView, start % 4, stop - start + 1), start) + .join(''); + }); + } + +} + +module.exports = Sequence; diff --git a/src/main/sources/ADAM_GA4GHDataSource.js b/src/main/sources/ADAM_GA4GHDataSource.js new file mode 100644 index 00000000..2c9199f3 --- /dev/null +++ b/src/main/sources/ADAM_GA4GHDataSource.js @@ -0,0 +1,153 @@ +/** + * A data source which implements the GA4GH protocol. + * Currently only used to load alignments. + * @flow + */ +'use strict'; + +import type {Alignment, AlignmentDataSource} from '../Alignment'; + +import _ from 'underscore'; +import {Events} from 'backbone'; + +import ContigInterval from '../ContigInterval'; +import ADAMAlignment from '../ADAMAlignment'; + +var ALIGNMENTS_PER_REQUEST = 200; // TODO: explain this choice. + + +// Genome ranges are rounded to multiples of this for fetching. +// This reduces network activity while fetching. +// TODO: tune this value -- setting it close to the read length will result in +// lots of reads being fetched twice, but setting it too large will result in +// bulkier requests. +var BASE_PAIRS_PER_FETCH = 100; + +function expandRange(range: ContigInterval) { + var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; + var newStart = Math.max(1, roundDown(range.start())), + newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); + + return new ContigInterval(range.contig, newStart, newStop); +} + +type GA4GHSpec = { + endpoint: string; + readGroupId: string; + // HACK if set, strips "chr" from reference names. + // See https://github.com/ga4gh/schemas/issues/362 + killChr: boolean; +}; + +function create(spec: GA4GHSpec): AlignmentDataSource { + if (spec.endpoint.slice(-6) != 'v0.5.1') { + throw new Error('Only v0.5.1 of the GA4GH API is supported by pileup.js'); + } + + var url = spec.endpoint + '/reads/search'; + + var reads: {[key:string]: Alignment} = {}; + + // Ranges for which we have complete information -- no need to hit network. + var coveredRanges: ContigInterval[] = []; + + function addReadsFromResponse(response: Object) { + response.alignments.forEach(alignment => { + // optimization: don't bother constructing a ADAMAlignment unless it's new. + var key = ADAMAlignment.keyFromGA4GHResponse(alignment); + if (key in reads) return; + + var ga4ghAlignment = new ADAMAlignment(alignment); + reads[key] = ga4ghAlignment; + }); + } + + function rangeChanged(newRange: GenomeRange) { + // HACK FOR DEMO + var contig = spec.killChr ? newRange.contig.replace(/^chr/, '') : newRange.contig; + var interval = new ContigInterval(contig, newRange.start, newRange.stop); + if (interval.isCoveredBy(coveredRanges)) return; + + interval = expandRange(interval); + + // We "cover" the interval immediately (before the reads have arrived) to + // prevent duplicate network requests. + coveredRanges.push(interval); + coveredRanges = ContigInterval.coalesce(coveredRanges); + fetchAlignmentsForInterval(interval, null, 1 /* first request */); + } + + function notifyFailure(message: string) { + o.trigger('networkfailure', message); + o.trigger('networkdone'); + console.warn(message); + } + + function fetchAlignmentsForInterval(range: ContigInterval, + pageToken: ?string, + numRequests: number) { + var xhr = new XMLHttpRequest(); + xhr.open('POST', url); + xhr.responseType = 'json'; + xhr.setRequestHeader('Content-Type', 'application/json'); + + xhr.addEventListener('load', function(e) { + var response = this.response; + if (this.status >= 400) { + notifyFailure(this.status + ' ' + this.statusText + ' ' + JSON.stringify(response)); + } else { + if (response.errorCode) { + notifyFailure('Error from GA4GH endpoint: ' + JSON.stringify(response)); + } else { + addReadsFromResponse(response); + o.trigger('newdata', range); // display data as it comes in. + if (response.nextPageToken) { + fetchAlignmentsForInterval(range, response.nextPageToken, numRequests + 1); + } else { + o.trigger('networkdone'); + } + } + } + }); + xhr.addEventListener('error', function(e) { + notifyFailure('Request failed with status: ' + this.status); + }); + + o.trigger('networkprogress', {numRequests}); + xhr.send(JSON.stringify({ + pageToken: pageToken, + pageSize: ALIGNMENTS_PER_REQUEST, + readGroupIds: [spec.readGroupId], + referenceName: range.contig, + start: range.start(), + end: range.stop() + })); + } + + function getAlignmentsInRange(range: ContigInterval): Alignment[] { + if (!range) return []; + + // HACK FOR DEMO + if (spec.killChr) { + range = new ContigInterval(range.contig.replace(/^chr/, ''), range.start(), range.stop()); + } + return _.filter(reads, read => read.intersects(range)); + } + + var o = { + rangeChanged, + getAlignmentsInRange, + + // These are here to make Flow happy. + on: () => {}, + once: () => {}, + off: () => {}, + trigger: () => {} + }; + _.extend(o, Events); // Make this an event emitter + return o; +} + +module.exports = { + create +}; diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js new file mode 100644 index 00000000..2246f170 --- /dev/null +++ b/src/main/sources/ReferenceDataSource.js @@ -0,0 +1,197 @@ +/** + * The "glue" between TwoBit.js and GenomeTrack.js. + * + * GenomeTrack is pure view code -- it renders data which is already in-memory + * in the browser. + * + * TwoBit is purely for data parsing and fetching. It only knows how to return + * promises for various genome features. + * + * This code acts as a bridge between the two. It maintains a local version of + * the data, fetching remote data and informing the view when it becomes + * available. + * + * + */ +'use strict';Object.defineProperty(exports, '__esModule', { value: true });function _interopRequireDefault(obj) {return obj && obj.__esModule ? obj : { 'default': obj };}var _q = require( + +'q');var _q2 = _interopRequireDefault(_q);var _underscore = require( +'underscore');var _underscore2 = _interopRequireDefault(_underscore);var _backbone = require( +'backbone');var _RemoteRequest = require( + +'../RemoteRequest');var _RemoteRequest2 = _interopRequireDefault(_RemoteRequest);var _ContigInterval = require( +'../ContigInterval');var _ContigInterval2 = _interopRequireDefault(_ContigInterval);var _dataSequence = require( +'../data/Sequence');var _dataSequence2 = _interopRequireDefault(_dataSequence);var _SequenceStore = require( +'../SequenceStore');var _SequenceStore2 = _interopRequireDefault(_SequenceStore);var _utils = require( +'../utils');var _utils2 = _interopRequireDefault(_utils); + + +// Requests for 2bit ranges are expanded to begin & end at multiples of this +// constant. Doing this means that panning typically won't require +// additional network requests. +var BASE_PAIRS_PER_FETCH = 10000; + +var MAX_BASE_PAIRS_TO_FETCH = 100000; + + +// Flow type for export. + + + + + + + + + + + + +// Expand range to begin and end on multiples of BASE_PAIRS_PER_FETCH. +function expandRange(range) { + var roundDown = function roundDown(x) {return x - x % BASE_PAIRS_PER_FETCH;}; + var newStart = Math.max(0, roundDown(range.start())), + newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); + + return new _ContigInterval2['default'](range.contig, newStart, newStop);} + + + +var createFromReferenceUrl = function createFromReferenceUrl(remoteRequest) { + // Local cache of genomic data. + var contigList = []; + var store = new _SequenceStore2['default'](); + + // Ranges for which we have complete information -- no need to hit network. + var coveredRanges = []; + + function fetch(range) { + var span = range.length(); + if (span > MAX_BASE_PAIRS_TO_FETCH) { + return _q2['default'].when(); // empty promise + } + + // TODO: fetch JSON from file + var letters = "AAAAAAA"; + + store.setRange(range, letters); + o.trigger('newdata', range);} + + + function fetch(range) { + var span = range.length(); + if (span > MAX_BASE_PAIRS_TO_FETCH) { + return _q2['default'].when(); // empty promise + } + + console.log('Fetching ' + span + ' base pairs'); + remoteRequest.getFeaturesInRange(range.contig, range.start(), range.stop()). + then(function (letters) { + if (!letters) return; + if (letters.length < range.length()) { + // Probably at EOF + range = new _ContigInterval2['default'](range.contig, + range.start(), + range.start() + letters.length - 1);} + + store.setRange(range, letters);}). + then(function () { + o.trigger('newdata', range);}). + done();} + + + function normalizeRange(range) { + return contigPromise.then(function () {return normalizeRangeSync(range);});} + + + // Returns a {"chr12:123" -> "[ATCG]"} mapping for the range. + function getRange(range) { + return store.getAsObjects(_ContigInterval2['default'].fromGenomeRange(range));} + + + // Returns a string of base pairs for this range. + function getRangeAsString(range) { + if (!range) return ''; + return store.getAsString(_ContigInterval2['default'].fromGenomeRange(range));} + + + // This either adds or removes a 'chr' as needed. + function normalizeRangeSync(range) { + if (contigList.indexOf(range.contig) >= 0) { + return range;} + + var altContig = _utils2['default'].altContigName(range.contig); + if (contigList.indexOf(altContig) >= 0) { + return { + contig: altContig, + start: range.start, + stop: range.stop };} + + + return range; // let it fail with the original contig + } + + // Fetch the contig list immediately. + var contigList = remoteRequest.getContigList(); + o.trigger('contigs', contigList); + + var o = { + // The range here is 0-based, inclusive + rangeChanged: function rangeChanged(newRange) { + normalizeRange(newRange).then(function (r) { + var range = new _ContigInterval2['default'](r.contig, r.start, r.stop); + + // Check if this interval is already in the cache. + if (range.isCoveredBy(coveredRanges)) { + return;} + + + range = expandRange(range); + var newRanges = range.complementIntervals(coveredRanges); + coveredRanges.push(range); + coveredRanges = _ContigInterval2['default'].coalesce(coveredRanges);var _iteratorNormalCompletion = true;var _didIteratorError = false;var _iteratorError = undefined;try { + + for (var _iterator = newRanges[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true) {var newRange = _step.value; + fetch(newRange);}} catch (err) {_didIteratorError = true;_iteratorError = err;} finally {try {if (!_iteratorNormalCompletion && _iterator['return']) {_iterator['return']();}} finally {if (_didIteratorError) {throw _iteratorError;}}}}). + + done();}, + + // The ranges passed to these methods are 0-based + getRange: getRange, + getRangeAsString: getRangeAsString, + contigList: (function (_contigList) {function contigList() {return _contigList.apply(this, arguments);}contigList.toString = function () {return _contigList.toString();};return contigList;})(function () {return contigList;}), + normalizeRange: normalizeRange, + + // These are here to make Flow happy. + on: function on() {}, + once: function once() {}, + off: function off() {}, + trigger: function trigger() {} }; + + _underscore2['default'].extend(o, _backbone.Events); // Make this an event emitter + + return o;}; + + +function create(data) { + var urlPrefix = data.prefix; + var contigList = data.contigList; + + // verify data was correctly set + if (!urlPrefix) { + throw new Error('Missing URL from track: ' + JSON.stringify(data));} + + if (!contigList) { + throw new Error('Missing Contig List from track: ' + JSON.stringify(data));} + + + // create request with url prefix + var remoteRequest = new _RemoteRequest2['default'](urlPrefix); + var sequence = new _dataSequence2['default'](remoteRequest, contigList); + + return createFromReferenceUrl(sequence);} + + +module.exports = { + create: create, + createFromReferenceUrl: createFromReferenceUrl }; \ No newline at end of file diff --git a/src/test/ADAMAlignment-test.js b/src/test/ADAMAlignment-test.js new file mode 100644 index 00000000..f07884a5 --- /dev/null +++ b/src/test/ADAMAlignment-test.js @@ -0,0 +1,39 @@ +/** @flow */ +'use strict'; + +import {expect} from 'chai'; + +import GA4GHAlignment from '../main/GA4GHAlignment'; +import RemoteFile from '../main/RemoteFile'; +import Bam from '../main/data/bam'; + +describe('ADAM_Alignment', function() { + var sampleAlignments = []; + + before(function() { + return new RemoteFile('/test-data/adam-alignments.json').getAllString().then(data => { + // console.log("data: "+ JSON.parse(data).alignments); + sampleAlignments = JSON.parse(data).alignments; + // console.log("sampleAlignments: " + sampleAlignments); + // console.log("sampleAlignments length: " +sampleAlignments.length); + }); + }); + + it('should read the sample alignments', function() { + // console.log("sampleAlignments length: " +sampleAlignments.length); + expect(sampleAlignments).to.have.length(1046); + }); + + it('should provide basic accessors', function() { + var a = new GA4GHAlignment(sampleAlignments[0]); + expect(a.name).to.equal('613F0AAXX100423:5:47:2891:8862'); + expect(a.getSequence()).to.equal('GTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATCATTGTATCCCATAAACACAAAGTTTTGGTCCTGGCCTTATAATTACTTAG'); + expect(a.getQualityScores()).to.deep.equal([17, 28, 10, 23, 27, 28, 17, 31, 22, 10, 16, 19, 9, 15, 16, 22, 15, 14, 15, 20, 15, 9, 15, 15, 9, 32, 32, 25, 27, 9, 21, 25, 32, 28, 28, 31, 31, 23, 22, 22, 9, 17, 22, 12, 25, 24, 14, 10, 26, 26, 10, 32, 26, 30, 32, 31, 25, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]); + expect(a.getStrand()).to.equal('+'); + expect(a.getInterval().toString()).to.equal('chrM:0-58'); // 0-based + expect(a.cigarOps).to.deep.equal([ + {length:59, op: 'M'},{length: 42,op:'S'} + ]); + }); + // Can not check with SamReads because we don't have the corresponding BAM file +}); diff --git a/test-data/adam-alignments.json b/test-data/adam-alignments.json new file mode 100644 index 00000000..2448fc1d --- /dev/null +++ b/test-data/adam-alignments.json @@ -0,0 +1,33390 @@ +{ + "alignments": [{ + "id": null, + "readGroupId": "613F0.5", + "fragmentName": "613F0AAXX100423:5:47:2891:8862", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 175, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 0, + "reverseStrand": false + }, + "mappingQuality": 29, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 59, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 42, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "GTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATCATTGTATCCCATAAACACAAAGTTTTGGTCCTGGCCTTATAATTACTTAG", + "alignedQuality": [17, 28, 10, 23, 27, 28, 17, 31, 22, 10, 16, 19, 9, 15, 16, 22, 15, 14, 15, 20, 15, 9, 15, 15, 9, 32, 32, 25, 27, 9, 21, 25, 32, 28, 28, 31, 31, 23, 22, 22, 9, 17, 22, 12, 25, 24, 14, 10, 26, 26, 10, 32, 26, 30, 32, 31, 25, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.7", + "fragmentName": "613F1AAXX100423:7:40:17115:17222", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 154, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 1, + "reverseStrand": false + }, + "mappingQuality": 29, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 31, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 70, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TTCATGTAGCTTGATAACAGCGCAAAGAACTCCAAATGCTTAGATGGATAATTGTATCCCATAAAAACAAAGGATTGGGCCTGGCCTTATAANTATTTTGA", + "alignedQuality": [31, 31, 7, 30, 7, 11, 31, 7, 31, 7, 7, 11, 6, 28, 11, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.4", + "fragmentName": "613F1AAXX100423:4:27:8808:3060", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 171, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 2, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATNAATTAGAG", + "alignedQuality": [38, 38, 38, 38, 35, 37, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 38, 37, 38, 38, 38, 38, 38, 38, 30, 37, 35, 38, 37, 37, 37, 37, 38, 38, 38, 35, 36, 37, 37, 36, 38, 38, 38, 35, 38, 36, 37, 36, 38, 36, 37, 36, 36, 37, 33, 33, 34, 35, 36, 36, 34, 35, 35, 35, 35, 35, 36, 25, 35, 36, 30, 35, 32, 25, 26, 0, 26, 6, 29, 26, 29, 28, 22, 32], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F0.3", + "fragmentName": "613F0AAXX100423:3:93:11085:15551", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 138, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 2, + "reverseStrand": false + }, + "mappingQuality": 29, + "cigar": [{ + "operation": "CLIP_SOFT", + "operationLength": 47, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + "operationLength": 54, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "AACCAAAACTCTAATCATACTCTATTACGCAATAAACATTAACAAGATAATGTAGCTTAATAACAAAGCAAAGCACTGCATATGCTTAGATGGGTAATTGT", + "alignedQuality": [23, 18, 23, 29, 18, 30, 27, 30, 24, 27, 26, 21, 21, 11, 18, 30, 29, 23, 11, 24, 29, 18, 23, 27, 27, 30, 23, 27, 30, 27, 24, 29, 32, 24, 29, 29, 31, 31, 32, 31, 33, 33, 28, 33, 33, 27, 7, 23, 23, 23, 32, 33, 33, 27, 31, 32, 25, 33, 33, 28, 31, 24, 29, 33, 31, 16, 32, 31, 31, 19, 16, 16, 27, 29, 17, 27, 30, 29, 10, 25, 9, 29, 29, 30, 29, 31, 21, 33, 18, 31, 33, 31, 10, 18, 31, 33, 32, 32, 19, 32, 25], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F0.2", + "fragmentName": "613F0AAXX100423:2:2:14636:7280", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 182, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 2, + "reverseStrand": false + }, + "mappingQuality": 29, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 35, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 66, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": 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"fragmentName": "6141AAAXX100423:6:54:18839:9717", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 169, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 35, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 88, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 13, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "AATGCTTAGATGGATAATTGTATCCCATAAACACGAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTACATAGAACGA", + "alignedQuality": [38, 38, 38, 35, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 37, 38, 38, 36, 37, 37, 35, 38, 32, 38, 38, 38, 38, 37, 38, 36, 38, 38, 38, 38, 25, 37, 37, 37, 36, 28, 36, 36, 36, 36, 25, 35, 37, 32, 35, 32, 37, 33, 36, 36, 36, 37, 35, 36, 32, 38, 34, 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"fragmentName": "6141AAAXX100423:2:102:13963:2305", + "properPlacement": false, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": null, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 133, + "reverseStrand": false + }, + "mappingQuality": 37, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 52, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 49, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CGGTGGAAAATCCCTTAAACATTTACTTAAAATTTATGGAGAGGGTATCAAGTACATTAAAATAGCTTAAGACAACTTGCCTAGCCACACCAGCAACGACC", + "alignedQuality": [17, 22, 20, 17, 17, 17, 26, 22, 28, 23, 21, 11, 27, 22, 21, 11, 27, 28, 31, 7, 21, 15, 14, 21, 8, 21, 21, 21, 28, 13, 8, 32, 17, 15, 21, 32, 9, 21, 26, 32, 27, 33, 17, 10, 17, 33, 30, 27, 16, 32, 21, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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"fragmentName": "6141AAAXX100423:4:58:19645:7588", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 179, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 583, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 75, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 26, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAAACCCGCTCTACCTCACCATCTCTTGCTAATTCTACATCTCGTC", + "alignedQuality": [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 32, 32, 30, 32, 35, 33, 23, 29, 28, 29, 17, 31, 29, 29, 28, 34, 20, 31, 31, 32, 35, 28, 34, 20, 34, 28, 29, 26, 31, 21, 28, 18, 28, 15, 30, 30, 20, 30, 29, 30, 30, 34, 33, 9, 30, 34, 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false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 592, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 70, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 31, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATAGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATTATCACTATTT", + "alignedQuality": [35, 33, 28, 35, 35, 35, 33, 35, 28, 35, 35, 35, 28, 35, 32, 35, 35, 25, 35, 32, 25, 34, 30, 34, 32, 29, 12, 10, 25, 20, 32, 34, 32, 30, 34, 35, 35, 28, 35, 28, 32, 34, 11, 25, 28, 34, 34, 20, 34, 34, 35, 28, 34, 11, 26, 7, 33, 25, 26, 29, 12, 32, 34, 34, 34, 34, 25, 34, 32, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F0.4", + "fragmentName": "613F0AAXX100423:4:10:14689:13457", + "properPlacement": false, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 98, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 592, + "reverseStrand": false + }, + "mappingQuality": 37, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATAGA", + "alignedQuality": [37, 38, 38, 38, 38, 38, 37, 35, 38, 36, 38, 36, 38, 38, 37, 38, 38, 35, 33, 37, 37, 38, 38, 38, 38, 37, 35, 30, 36, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 28, 38, 38, 37, 35, 38, 36, 35, 37, 30, 33, 38, 37, 36, 37, 38, 34, 30, 37, 37, 36, 36, 36, 35, 36, 36, 33, 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"secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "GTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCANACTTCAGC", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 36, 38, 37, 38, 36, 36, 36, 37, 36, 37, 36, 36, 36, 37, 36, 36, 36, 36, 35, 36, 36, 35, 36, 35, 35, 36, 36, 36, 36, 36, 36, 33, 34, 35, 29, 24, 0, 6, 27, 21, 26, 23, 19, 23, 34], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.3", + "fragmentName": "613F1AAXX100423:3:56:16917:3099", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 173, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 597, + 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"duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 181, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 600, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCACAC", + "alignedQuality": [38, 38, 38, 35, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 35, 37, 35, 35, 34, 37, 35, 37, 35, 35, 36, 33, 30, 35, 35, 36, 34, 32, 32, 35, 34, 31, 34, 32, 34, 28, 20, 32, 35, 34, 32, 35, 34, 35, 35, 35, 35, 20, 32, 32, 34, 32, 32, 31, 30, 30, 32, 25, 32, 32, 32, 8, 32, 30], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.6", + "fragmentName": "613F1AAXX100423:6:37:15714:21079", + "properPlacement": false, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 94, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 603, + "reverseStrand": false + }, + "mappingQuality": 37, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAGATCGG", + "alignedQuality": [38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 36, 36, 36, 36, 36, 37, 36, 36, 36, 36, 35, 35, 37, 36, 36, 36, 36, 34, 31, 35, 34, 36, 35, 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"alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 36, 12, 36, 35, 34, 34, 35, 35, 33, 38, 37, 38, 36, 37, 38, 38, 38, 36, 37, 37, 35, 37, 38, 37, 38, 37, 35, 37, 35, 31, 35, 33, 36, 25, 33, 32, 36, 35, 36, 35, 37, 33, 25, 36, 37, 33, 38, 31, 33, 35, 33, 33, 36, 35, 33, 35, 31, 36, 35, 36, 33, 33, 35, 36, 32, 28, 33, 32, 25, 32, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.3", + "fragmentName": "613F1AAXX100423:3:45:3029:17994", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 190, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 604, + "reverseStrand": false + }, + "mappingQuality": 17, + "cigar": [{ + "operation": "CLIP_SOFT", + "operationLength": 1, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + 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"duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 152, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 606, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 92, + "referenceSequence": null + }, { + "operation": "INSERT", + "operationLength": 1, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + "operationLength": 8, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "ATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCANAACCCTAA", + "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 38, 37, 37, 36, 37, 34, 38, 36, 36, 37, 37, 37, 36, 33, 36, 36, 36, 30, 36, 33, 33, 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"properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 186, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 628, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 95, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 6, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TATAATCGATAAACTCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAG", + "alignedQuality": [37, 37, 37, 37, 37, 32, 37, 37, 37, 37, 37, 37, 37, 36, 20, 36, 36, 36, 36, 36, 37, 37, 37, 36, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 35, 37, 33, 37, 35, 37, 35, 36, 36, 37, 37, 37, 37, 37, 37, 36, 20, 35, 32, 36, 37, 36, 37, 35, 33, 33, 28, 36, 36, 33, 37, 37, 36, 36, 36, 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"fragmentLength": 174, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 640, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "ACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTAAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAA", + "alignedQuality": [37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 37, 38, 38, 35, 37, 36, 38, 35, 36, 33, 37, 37, 38, 37, 36, 35, 36, 37, 36, 36, 37, 36, 36, 36, 35, 35, 36, 35, 36, 34, 35, 34, 35, 35, 34, 35, 36, 34, 28, 27, 30, 32, 34, 33, 30, 33, 35, 34, 36, 35, 34, 34, 34, 34, 34, 34, 33, 32, 36, 35, 35, 34, 34, 34, 34, 32, 35, 34, 34, 34, 34, 34, 34, 35, 34, 35, 31, 33, 35, 28, 26, 34, 32, 35, 35, 35, 35], + "nextMatePosition": null, + "info": {} + }, { + "id": 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null, + "readGroupId": "6141A.1", + "fragmentName": "6141AAAXX100423:1:50:13981:3364", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 134, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 644, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 90, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 11, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATNTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAAC", + "alignedQuality": [35, 32, 35, 33, 36, 33, 36, 35, 36, 33, 32, 32, 36, 36, 36, 32, 32, 36, 36, 33, 29, 25, 34, 32, 34, 36, 30, 35, 33, 35, 28, 30, 35, 35, 32, 35, 30, 35, 35, 12, 35, 30, 34, 34, 33, 24, 0, 22, 26, 33, 29, 28, 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"alignment": { + "position": { + "referenceName": "chrM", + "position": 648, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 73, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 28, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAACAAGTGATTAAAGTAAGCAAAAGACTCAAACATAAAAACGTTA", + "alignedQuality": [26, 23, 18, 26, 9, 21, 17, 17, 17, 17, 31, 22, 21, 17, 15, 17, 17, 15, 31, 30, 10, 15, 19, 14, 22, 33, 33, 26, 23, 30, 17, 26, 15, 26, 15, 27, 25, 33, 33, 16, 33, 24, 33, 33, 33, 20, 16, 17, 33, 33, 14, 33, 22, 17, 33, 33, 14, 9, 22, 33, 17, 17, 5, 14, 14, 25, 32, 9, 18, 32, 32, 33, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": 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"referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAACGNATAGGTCA", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 34, 38, 38, 38, 38, 36, 37, 38, 37, 38, 38, 36, 38, 33, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 30, 38, 37, 35, 26, 31, 0, 20, 29, 29, 20, 22, 16, 29, 36], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F0.4", + "fragmentName": "613F0AAXX100423:4:61:19310:6422", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 176, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + 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"properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 176, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 883, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 65, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 36, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TGAGCAATGAAGTACGCACACACCGCCCGTCACCCTCATCAAATTAAATTAAACTTCACATAATTAATTTCTACACATCAGTTTCTGAGAGTAGATAAGTC", + "alignedQuality": [25, 28, 20, 33, 30, 25, 30, 25, 29, 20, 34, 28, 34, 26, 28, 31, 29, 29, 29, 28, 24, 12, 24, 26, 24, 34, 34, 34, 26, 20, 34, 29, 28, 26, 29, 20, 8, 8, 25, 32, 34, 32, 34, 21, 12, 26, 29, 33, 21, 22, 24, 31, 30, 7, 27, 14, 10, 27, 8, 31, 28, 33, 31, 26, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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"613F1AAXX100423:2:1:9402:7081", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 127, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 996, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "GCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACNCTGAACTA", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 35, 38, 36, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 37, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 36, 37, 37, 38, 38, 37, 37, 37, 37, 38, 35, 37, 35, 37, 37, 35, 29, 29, 0, 30, 23, 23, 23, 26, 20, 17, 30], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F0.3", + "fragmentName": "613F0AAXX100423:3:55:10727:9120", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 177, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 996, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "GCATACTGGAAAGTGTGCTTTGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTCTGAACTA", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 38, 36, 36, 38, 36, 37, 33, 38, 36, 36, 36, 36, 36, 36, 36, 37, 37, 36, 37, 36, 35, 36, 35, 35, 36, 33, 36, 36, 35, 36, 35, 34, 35, 35, 31, 36, 35, 36, 36], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.1", + "fragmentName": "613F1AAXX100423:1:104:16417:14423", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 190, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 997, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 93, + "referenceSequence": null + }, { + "operation": "INSERT", + "operationLength": 1, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + "operationLength": 7, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTNTTGAACTA", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 38, 38, 38, 37, 35, 37, 37, 38, 38, 38, 38, 38, 38, 38, 37, 37, 35, 37, 37, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 37, 37, 35, 36, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 37, 38, 37, 38, 37, 38, 38, 38, 38, 36, 35, 37, 38, 37, 37, 36, 36, 37, 36, 35, 37, 37, 37, 36, 36, 36, 36, 33, 35, 37, 37, 37, 30, 33, 0, 22, 30, 14, 23, 14, 17, 18, 30], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "6141A.8", + "fragmentName": "6141AAAXX100423:8:82:11001:10820", + "properPlacement": false, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": null, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 997, + "reverseStrand": false + }, + "mappingQuality": 37, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 84, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 17, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CATACTGGGAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTTGCCTACACCCAGAAGATTTCATGACCAATGAACACCTTTCAGCTT", + "alignedQuality": [26, 26, 25, 33, 33, 34, 34, 26, 12, 28, 28, 13, 29, 25, 28, 20, 12, 26, 25, 25, 27, 29, 32, 26, 32, 34, 28, 26, 26, 33, 20, 26, 24, 26, 27, 12, 33, 32, 33, 32, 33, 28, 34, 34, 28, 34, 28, 33, 28, 34, 26, 32, 12, 21, 32, 12, 26, 11, 26, 26, 12, 26, 32, 30, 17, 34, 26, 34, 25, 33, 32, 34, 23, 34, 34, 17, 31, 26, 11, 24, 17, 34, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "6141A.8", + "fragmentName": "6141AAAXX100423:8:82:11001:10820", + "properPlacement": false, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": null, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": null, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CATACTGGAAAGGGTTCATTGGTCATGAAATCTTCTGGGTGTAGGCCAGATGCTTTAATATTAAGCTACACTATGATTATTCCAAGCACACTTTCTACTTC", + "alignedQuality": [31, 13, 26, 21, 26, 29, 13, 29, 31, 31, 25, 28, 12, 24, 26, 29, 28, 13, 28, 27, 34, 34, 12, 34, 34, 34, 30, 34, 30, 34, 29, 13, 28, 31, 12, 28, 25, 30, 33, 17, 24, 23, 31, 26, 26, 13, 31, 28, 26, 29, 30, 32, 21, 32, 32, 33, 18, 34, 26, 12, 10, 26, 26, 26, 11, 28, 31, 26, 28, 25, 26, 26, 29, 21, 34, 34, 34, 30, 12, 28, 34, 17, 12, 16, 30, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }], + "nextPageToken": null +} \ No newline at end of file From 01d8da0ded2f3bc6ce4b38ab6595a2da923e824c Mon Sep 17 00:00:00 2001 From: dorislee0309 Date: Mon, 20 Jun 2016 16:40:07 -0700 Subject: [PATCH 002/136] pass all tests --- examples/data.js | 86 +++-------- src/main/sources/ReferenceDataSource.js | 197 ------------------------ 2 files changed, 21 insertions(+), 262 deletions(-) delete mode 100644 src/main/sources/ReferenceDataSource.js diff --git a/examples/data.js b/examples/data.js index 77d16e35..ccbb1329 100644 --- a/examples/data.js +++ b/examples/data.js @@ -1,68 +1,24 @@ -// Some data for the demo. - -// We are going to use the same data source for multiple tracks -var bamSource = pileup.formats.bam({ - url: '/test-data/synth3.normal.17.7500000-7515000.bam', - indexUrl: '/test-data/synth3.normal.17.7500000-7515000.bam.bai' -}); - var sources = [ - { - viz: pileup.viz.genome(), - isReference: true, - data: pileup.formats.twoBit({ - url: 'http://www.biodalliance.org/datasets/hg19.2bit' - }), - name: 'Reference' - }, - { - viz: pileup.viz.scale(), - name: 'Scale' - }, - { - viz: pileup.viz.location(), - name: 'Location' - }, - { - viz: pileup.viz.variants(), - data: pileup.formats.vcf({ - url: '/test-data/snv.chr17.vcf' - }), - name: 'Variants' - }, - { - viz: pileup.viz.genes(), - data: pileup.formats.bigBed({ - url: 'http://www.biodalliance.org/datasets/ensGene.bb' - }), - name: 'Genes' - }, - { - viz: pileup.viz.coverage(), - data: bamSource, - cssClass: 'normal', - name: 'Coverage' - }, - { - viz: pileup.viz.pileup(), - data: bamSource, - cssClass: 'normal', - name: 'Alignments' - }, - { - viz: pileup.viz.coverage(), - data: bamSource, - cssClass: 'tumor', - name: 'Coverage' - }, - { - viz: pileup.viz.pileup({ - viewAsPairs: true - }), - data: bamSource, - cssClass: 'tumor', - name: 'Alignments' - } + + { viz: pileup.viz.genome(), + data: pileup.formats.ADAMAlignment({ + { + // endpoint:"/test-data/adam-alignments.json", + endpoint: '/v0.5.1', + readGroupId: 'some-group-set:some-read-group', + killChr: false + } + }), + name: 'Alignments' + }, + { + viz: pileup.viz.location(), + name: 'Location' + }, + { + viz: pileup.viz.scale(), + name: 'Scale' + } ]; -var range = {contig: 'chr17', start: 7512284, stop: 7512644}; +var range = {contig: 'chrM', start: 0, stop: 7512644}; diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js deleted file mode 100644 index 2246f170..00000000 --- a/src/main/sources/ReferenceDataSource.js +++ /dev/null @@ -1,197 +0,0 @@ -/** - * The "glue" between TwoBit.js and GenomeTrack.js. - * - * GenomeTrack is pure view code -- it renders data which is already in-memory - * in the browser. - * - * TwoBit is purely for data parsing and fetching. It only knows how to return - * promises for various genome features. - * - * This code acts as a bridge between the two. It maintains a local version of - * the data, fetching remote data and informing the view when it becomes - * available. - * - * - */ -'use strict';Object.defineProperty(exports, '__esModule', { value: true });function _interopRequireDefault(obj) {return obj && obj.__esModule ? obj : { 'default': obj };}var _q = require( - -'q');var _q2 = _interopRequireDefault(_q);var _underscore = require( -'underscore');var _underscore2 = _interopRequireDefault(_underscore);var _backbone = require( -'backbone');var _RemoteRequest = require( - -'../RemoteRequest');var _RemoteRequest2 = _interopRequireDefault(_RemoteRequest);var _ContigInterval = require( -'../ContigInterval');var _ContigInterval2 = _interopRequireDefault(_ContigInterval);var _dataSequence = require( -'../data/Sequence');var _dataSequence2 = _interopRequireDefault(_dataSequence);var _SequenceStore = require( -'../SequenceStore');var _SequenceStore2 = _interopRequireDefault(_SequenceStore);var _utils = require( -'../utils');var _utils2 = _interopRequireDefault(_utils); - - -// Requests for 2bit ranges are expanded to begin & end at multiples of this -// constant. Doing this means that panning typically won't require -// additional network requests. -var BASE_PAIRS_PER_FETCH = 10000; - -var MAX_BASE_PAIRS_TO_FETCH = 100000; - - -// Flow type for export. - - - - - - - - - - - - -// Expand range to begin and end on multiples of BASE_PAIRS_PER_FETCH. -function expandRange(range) { - var roundDown = function roundDown(x) {return x - x % BASE_PAIRS_PER_FETCH;}; - var newStart = Math.max(0, roundDown(range.start())), - newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); - - return new _ContigInterval2['default'](range.contig, newStart, newStop);} - - - -var createFromReferenceUrl = function createFromReferenceUrl(remoteRequest) { - // Local cache of genomic data. - var contigList = []; - var store = new _SequenceStore2['default'](); - - // Ranges for which we have complete information -- no need to hit network. - var coveredRanges = []; - - function fetch(range) { - var span = range.length(); - if (span > MAX_BASE_PAIRS_TO_FETCH) { - return _q2['default'].when(); // empty promise - } - - // TODO: fetch JSON from file - var letters = "AAAAAAA"; - - store.setRange(range, letters); - o.trigger('newdata', range);} - - - function fetch(range) { - var span = range.length(); - if (span > MAX_BASE_PAIRS_TO_FETCH) { - return _q2['default'].when(); // empty promise - } - - console.log('Fetching ' + span + ' base pairs'); - remoteRequest.getFeaturesInRange(range.contig, range.start(), range.stop()). - then(function (letters) { - if (!letters) return; - if (letters.length < range.length()) { - // Probably at EOF - range = new _ContigInterval2['default'](range.contig, - range.start(), - range.start() + letters.length - 1);} - - store.setRange(range, letters);}). - then(function () { - o.trigger('newdata', range);}). - done();} - - - function normalizeRange(range) { - return contigPromise.then(function () {return normalizeRangeSync(range);});} - - - // Returns a {"chr12:123" -> "[ATCG]"} mapping for the range. - function getRange(range) { - return store.getAsObjects(_ContigInterval2['default'].fromGenomeRange(range));} - - - // Returns a string of base pairs for this range. - function getRangeAsString(range) { - if (!range) return ''; - return store.getAsString(_ContigInterval2['default'].fromGenomeRange(range));} - - - // This either adds or removes a 'chr' as needed. - function normalizeRangeSync(range) { - if (contigList.indexOf(range.contig) >= 0) { - return range;} - - var altContig = _utils2['default'].altContigName(range.contig); - if (contigList.indexOf(altContig) >= 0) { - return { - contig: altContig, - start: range.start, - stop: range.stop };} - - - return range; // let it fail with the original contig - } - - // Fetch the contig list immediately. - var contigList = remoteRequest.getContigList(); - o.trigger('contigs', contigList); - - var o = { - // The range here is 0-based, inclusive - rangeChanged: function rangeChanged(newRange) { - normalizeRange(newRange).then(function (r) { - var range = new _ContigInterval2['default'](r.contig, r.start, r.stop); - - // Check if this interval is already in the cache. - if (range.isCoveredBy(coveredRanges)) { - return;} - - - range = expandRange(range); - var newRanges = range.complementIntervals(coveredRanges); - coveredRanges.push(range); - coveredRanges = _ContigInterval2['default'].coalesce(coveredRanges);var _iteratorNormalCompletion = true;var _didIteratorError = false;var _iteratorError = undefined;try { - - for (var _iterator = newRanges[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true) {var newRange = _step.value; - fetch(newRange);}} catch (err) {_didIteratorError = true;_iteratorError = err;} finally {try {if (!_iteratorNormalCompletion && _iterator['return']) {_iterator['return']();}} finally {if (_didIteratorError) {throw _iteratorError;}}}}). - - done();}, - - // The ranges passed to these methods are 0-based - getRange: getRange, - getRangeAsString: getRangeAsString, - contigList: (function (_contigList) {function contigList() {return _contigList.apply(this, arguments);}contigList.toString = function () {return _contigList.toString();};return contigList;})(function () {return contigList;}), - normalizeRange: normalizeRange, - - // These are here to make Flow happy. - on: function on() {}, - once: function once() {}, - off: function off() {}, - trigger: function trigger() {} }; - - _underscore2['default'].extend(o, _backbone.Events); // Make this an event emitter - - return o;}; - - -function create(data) { - var urlPrefix = data.prefix; - var contigList = data.contigList; - - // verify data was correctly set - if (!urlPrefix) { - throw new Error('Missing URL from track: ' + JSON.stringify(data));} - - if (!contigList) { - throw new Error('Missing Contig List from track: ' + JSON.stringify(data));} - - - // create request with url prefix - var remoteRequest = new _RemoteRequest2['default'](urlPrefix); - var sequence = new _dataSequence2['default'](remoteRequest, contigList); - - return createFromReferenceUrl(sequence);} - - -module.exports = { - create: create, - createFromReferenceUrl: createFromReferenceUrl }; \ No newline at end of file From c69cfaf6b850ab622838760607b56d39e25c28a1 Mon Sep 17 00:00:00 2001 From: dorislee0309 Date: Sat, 25 Jun 2016 15:13:47 -0700 Subject: [PATCH 003/136] ga4gh data source loaded in, compatible with mango, no error --- examples/data.js | 101 ++++++++--- examples/json/reference.json | 8 + scripts/quick-build.sh | 19 +++ scripts/test.sh | 5 +- src/main/ADAMAlignment.js | 111 ------------ src/main/GA4GHAlignment.js | 11 +- src/main/sources/ADAM_GA4GHDataSource.js | 153 ----------------- src/main/sources/GA4GHDataSource.js | 27 +-- src/main/sources/ReferenceDataSource.js | 169 +++++++++++++++++++ src/main/viz/pileuputils.js | 7 +- src/test/sources/ReferenceDataSource-test.js | 148 ++++++++++++++++ test-data/adam-alignments.json | 2 +- test-data/features_chrM_0_2000.json | 18 ++ test-data/reference-chrM-0-1000.json | 1 + 14 files changed, 475 insertions(+), 305 deletions(-) create mode 100644 examples/json/reference.json create mode 100755 scripts/quick-build.sh delete mode 100644 src/main/ADAMAlignment.js delete mode 100644 src/main/sources/ADAM_GA4GHDataSource.js create mode 100644 src/main/sources/ReferenceDataSource.js create mode 100644 src/test/sources/ReferenceDataSource-test.js create mode 100644 test-data/features_chrM_0_2000.json create mode 100644 test-data/reference-chrM-0-1000.json diff --git a/examples/data.js b/examples/data.js index ccbb1329..86b0f074 100644 --- a/examples/data.js +++ b/examples/data.js @@ -1,24 +1,83 @@ -var sources = [ +// Some data for the demo. + +//// We are going to use the same data source for multiple tracks +//var bamSource = pileup.formats.bam({ +// url: '/test-data/synth3.normal.17.7500000-7515000.bam', +// indexUrl: '/test-data/synth3.normal.17.7500000-7515000.bam.bai' +//}); - { viz: pileup.viz.genome(), - data: pileup.formats.ADAMAlignment({ - { - // endpoint:"/test-data/adam-alignments.json", - endpoint: '/v0.5.1', - readGroupId: 'some-group-set:some-read-group', - killChr: false - } - }), - name: 'Alignments' - }, - { - viz: pileup.viz.location(), - name: 'Location' - }, - { - viz: pileup.viz.scale(), - name: 'Scale' - } +var sources = [ + { + viz: pileup.viz.genome(), + isReference: true, + data: pileup.formats.reference({ + url: '/reference', + contigList: [{ + name:"chrM", + length: 1000 + },{ + name:"22", + length: 1000 + }] + }), + name: 'Reference' + } +// { +// viz: pileup.viz.genome(), +// isReference: true, +// data: pileup.formats.reference({ +// prefix:"../json/" +// }), +// name: 'Reference' +// } +// { +// viz: pileup.viz.scale(), +// name: 'Scale' +// }, +// { +// viz: pileup.viz.location(), +// name: 'Location' +// }, +// { +// viz: pileup.viz.variants(), +// data: pileup.formats.vcf({ +// url: '/test-data/snv.chr17.vcf' +// }), +// name: 'Variants' +// }, +// { +// viz: pileup.viz.genes(), +// data: pileup.formats.bigBed({ +// url: 'http://www.biodalliance.org/datasets/ensGene.bb' +// }), +// name: 'Genes' +// }, +// { +// viz: pileup.viz.coverage(), +// data: bamSource, +// cssClass: 'normal', +// name: 'Coverage' +// }, +// { +// viz: pileup.viz.pileup(), +// data: bamSource, +// cssClass: 'normal', +// name: 'Alignments' +// }, +// { +// viz: pileup.viz.coverage(), +// data: bamSource, +// cssClass: 'tumor', +// name: 'Coverage' +// }, +// { +// viz: pileup.viz.pileup({ +// viewAsPairs: true +// }), +// data: bamSource, +// cssClass: 'tumor', +// name: 'Alignments' +// } ]; -var range = {contig: 'chrM', start: 0, stop: 7512644}; +var range = {contig: 'chrM', start: 0, stop: 10}; diff --git a/examples/json/reference.json b/examples/json/reference.json new file mode 100644 index 00000000..f36ca060 --- /dev/null +++ b/examples/json/reference.json @@ -0,0 +1,8 @@ +{ + "region": { + "contig": "chrM", + "start": "0", + "stop": "500" + }, + "sequence": "GTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAAATATTAAGCAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATTAAAATCCAACTTATATGTGAAAATTCATTGTTAGGACCTAAACTCAATAACGAAAGTAATTCTAGTCATTTATAATACACGACAGCTAAGACCCAAACTGGGATTAGATA" +} \ No newline at end of file diff --git a/scripts/quick-build.sh b/scripts/quick-build.sh new file mode 100755 index 00000000..1c617c78 --- /dev/null +++ b/scripts/quick-build.sh @@ -0,0 +1,19 @@ +#!/bin/bash +# Build require-ale and minified assets for distribution. +set -o errexit +# ./scripts/make-mini-d3.sh # TODO: remove + +# Transpile individual files. This is useful if another module, +# e.g. cycledash, wants to require('pileup'). +# The dist/test files are required for code coverage +mkdir -p dist/test/{data,source,viz} +babel src --retain-lines --ignore src/lib --out-dir dist +cp -r src/lib dist/ + +# Create dist/tests +browserify \ + -v \ + -t [ babelify --ignore src/lib ] \ + --debug \ + -o dist/tests.js \ + $(find src/test -name '*.js') diff --git a/scripts/test.sh b/scripts/test.sh index 6dd937d2..2b734566 100755 --- a/scripts/test.sh +++ b/scripts/test.sh @@ -3,6 +3,9 @@ # Note that you must run `npm run build` or `npm run watch` before running this. set -o errexit +# compile files for test +./scripts/quick-build.sh + # Run http-server and save its PID http-server -p 8081 > /dev/null & SERVER_PID=$! @@ -18,4 +21,4 @@ trap finish EXIT sleep 1 # Start the tests -mocha-phantomjs http://localhost:8081/src/test/runner.html "$@" +mocha-phantomjs http://localhost:8081/src/test/runner.html diff --git a/src/main/ADAMAlignment.js b/src/main/ADAMAlignment.js deleted file mode 100644 index fecc0e60..00000000 --- a/src/main/ADAMAlignment.js +++ /dev/null @@ -1,111 +0,0 @@ -/** - * This serves as a bridge between org.ga4gh.GAReadAlignment and the - * pileup.js Alignment type. - * @flow - */ -'use strict'; - -import type {CigarOp, MateProperties, Strand} from './Alignment'; - -import ContigInterval from './ContigInterval'; -import SamRead from './data/SamRead'; - -// See https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/common.avdl -var OP_MAP = { - ALIGNMENT_MATCH: 'M', - INSERT: 'I', - DELETE: 'D', - SKIP: 'N', - CLIP_SOFT: 'S', - CLIP_HARD: 'H', - PAD: 'P', - SEQUENCE_MATCH: '=', - SEQUENCE_MISMATCH: 'X' -}; - -/** - * This class acts as a bridge between org.ga4gh.GAReadAlignment and the - * pileup.js Alignment type. - */ -class ADAMAlignment /* implements Alignment */ { - pos: number; - ref: string; - alignment: Object; - name: string; - cigarOps: CigarOp[]; - _interval: ContigInterval; - - // alignment follows org.ga4gh.GAReadAlignment - // https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/reads.avdl - constructor(alignment: Object) { - this.alignment = alignment; - this.pos = alignment.alignment.position.position; - this.ref = alignment.alignment.position.referenceName; - this.name = alignment.fragmentName; - - this.cigarOps = alignment.alignment.cigar.map( - ({operation, operationLength: length}) => ({ op: OP_MAP[operation], length })); - this._interval = new ContigInterval(this.ref, - this.pos, - this.pos + this.getReferenceLength() - 1); - } - - getKey(): string { - return ADAMAlignment.keyFromGA4GHResponse(this.alignment); - } - - getStrand(): Strand { - return this.alignment.alignment.position.reverseStrand ? '-' : '+'; - } - - getQualityScores(): number[] { - return this.alignment.alignedQuality; - } - - getSequence(): string { - return this.alignment.alignedSequence; - } - - getInterval(): ContigInterval { - return this._interval; - } - - intersects(interval: ContigInterval): boolean { - return interval.intersects(this.getInterval()); - } - - getReferenceLength(): number { - return SamRead.referenceLengthFromOps(this.cigarOps); - } - - getMateProperties(): ?MateProperties { - var next = this.alignment.nextMatePosition; - return next && { - ref: next.referenceName, - pos: next.position, - strand: next.reverseStrand ? '-' : '+' - }; - } - - getInferredInsertSize(): number { - // TODO: SAM/BAM writes this explicitly. Does GA4GH really not? - var m = this.getMateProperties(); - if (m && m.ref == this.ref) { - var start1 = this._interval.start(), - stop1 = this._interval.stop(), - start2 = m.pos, - stop2 = start2 + this.getSequence().length; - return Math.max(stop1, stop2) - Math.min(start1, start2); - } else { - return 0; - } - } - - // This is exposed as a static method to facilitate an optimization in GA4GHDataSource. - static keyFromGA4GHResponse(alignment: Object): string { - // this.alignment.id would be appealing here, but it's not actually unique! - return alignment.fragmentName + ':' + alignment.readNumber; - } -} - -module.exports = ADAMAlignment; diff --git a/src/main/GA4GHAlignment.js b/src/main/GA4GHAlignment.js index abdc0adf..6287c643 100644 --- a/src/main/GA4GHAlignment.js +++ b/src/main/GA4GHAlignment.js @@ -39,11 +39,12 @@ class GA4GHAlignment /* implements Alignment */ { // https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/reads.avdl constructor(alignment: Object) { this.alignment = alignment; - this.pos = alignment.alignment.position.position; - this.ref = alignment.alignment.position.referenceName; - this.name = alignment.fragmentName; + // console.log(alignment) + this.pos = alignment.alignment.position.position; + this.ref = alignment.alignment.position.referenceName; + this.name = alignment.fragmentName; - this.cigarOps = alignment.alignment.cigar.map( + this.cigarOps = alignment.alignment.cigar.map( ({operation, operationLength: length}) => ({ op: OP_MAP[operation], length })); this._interval = new ContigInterval(this.ref, this.pos, @@ -79,7 +80,7 @@ class GA4GHAlignment /* implements Alignment */ { } getMateProperties(): ?MateProperties { - var next = this.alignment.nextMatePosition; + var next = this.nextMatePosition; return next && { ref: next.referenceName, pos: next.position, diff --git a/src/main/sources/ADAM_GA4GHDataSource.js b/src/main/sources/ADAM_GA4GHDataSource.js deleted file mode 100644 index 2c9199f3..00000000 --- a/src/main/sources/ADAM_GA4GHDataSource.js +++ /dev/null @@ -1,153 +0,0 @@ -/** - * A data source which implements the GA4GH protocol. - * Currently only used to load alignments. - * @flow - */ -'use strict'; - -import type {Alignment, AlignmentDataSource} from '../Alignment'; - -import _ from 'underscore'; -import {Events} from 'backbone'; - -import ContigInterval from '../ContigInterval'; -import ADAMAlignment from '../ADAMAlignment'; - -var ALIGNMENTS_PER_REQUEST = 200; // TODO: explain this choice. - - -// Genome ranges are rounded to multiples of this for fetching. -// This reduces network activity while fetching. -// TODO: tune this value -- setting it close to the read length will result in -// lots of reads being fetched twice, but setting it too large will result in -// bulkier requests. -var BASE_PAIRS_PER_FETCH = 100; - -function expandRange(range: ContigInterval) { - var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; - var newStart = Math.max(1, roundDown(range.start())), - newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); - - return new ContigInterval(range.contig, newStart, newStop); -} - -type GA4GHSpec = { - endpoint: string; - readGroupId: string; - // HACK if set, strips "chr" from reference names. - // See https://github.com/ga4gh/schemas/issues/362 - killChr: boolean; -}; - -function create(spec: GA4GHSpec): AlignmentDataSource { - if (spec.endpoint.slice(-6) != 'v0.5.1') { - throw new Error('Only v0.5.1 of the GA4GH API is supported by pileup.js'); - } - - var url = spec.endpoint + '/reads/search'; - - var reads: {[key:string]: Alignment} = {}; - - // Ranges for which we have complete information -- no need to hit network. - var coveredRanges: ContigInterval[] = []; - - function addReadsFromResponse(response: Object) { - response.alignments.forEach(alignment => { - // optimization: don't bother constructing a ADAMAlignment unless it's new. - var key = ADAMAlignment.keyFromGA4GHResponse(alignment); - if (key in reads) return; - - var ga4ghAlignment = new ADAMAlignment(alignment); - reads[key] = ga4ghAlignment; - }); - } - - function rangeChanged(newRange: GenomeRange) { - // HACK FOR DEMO - var contig = spec.killChr ? newRange.contig.replace(/^chr/, '') : newRange.contig; - var interval = new ContigInterval(contig, newRange.start, newRange.stop); - if (interval.isCoveredBy(coveredRanges)) return; - - interval = expandRange(interval); - - // We "cover" the interval immediately (before the reads have arrived) to - // prevent duplicate network requests. - coveredRanges.push(interval); - coveredRanges = ContigInterval.coalesce(coveredRanges); - fetchAlignmentsForInterval(interval, null, 1 /* first request */); - } - - function notifyFailure(message: string) { - o.trigger('networkfailure', message); - o.trigger('networkdone'); - console.warn(message); - } - - function fetchAlignmentsForInterval(range: ContigInterval, - pageToken: ?string, - numRequests: number) { - var xhr = new XMLHttpRequest(); - xhr.open('POST', url); - xhr.responseType = 'json'; - xhr.setRequestHeader('Content-Type', 'application/json'); - - xhr.addEventListener('load', function(e) { - var response = this.response; - if (this.status >= 400) { - notifyFailure(this.status + ' ' + this.statusText + ' ' + JSON.stringify(response)); - } else { - if (response.errorCode) { - notifyFailure('Error from GA4GH endpoint: ' + JSON.stringify(response)); - } else { - addReadsFromResponse(response); - o.trigger('newdata', range); // display data as it comes in. - if (response.nextPageToken) { - fetchAlignmentsForInterval(range, response.nextPageToken, numRequests + 1); - } else { - o.trigger('networkdone'); - } - } - } - }); - xhr.addEventListener('error', function(e) { - notifyFailure('Request failed with status: ' + this.status); - }); - - o.trigger('networkprogress', {numRequests}); - xhr.send(JSON.stringify({ - pageToken: pageToken, - pageSize: ALIGNMENTS_PER_REQUEST, - readGroupIds: [spec.readGroupId], - referenceName: range.contig, - start: range.start(), - end: range.stop() - })); - } - - function getAlignmentsInRange(range: ContigInterval): Alignment[] { - if (!range) return []; - - // HACK FOR DEMO - if (spec.killChr) { - range = new ContigInterval(range.contig.replace(/^chr/, ''), range.start(), range.stop()); - } - return _.filter(reads, read => read.intersects(range)); - } - - var o = { - rangeChanged, - getAlignmentsInRange, - - // These are here to make Flow happy. - on: () => {}, - once: () => {}, - off: () => {}, - trigger: () => {} - }; - _.extend(o, Events); // Make this an event emitter - return o; -} - -module.exports = { - create -}; diff --git a/src/main/sources/GA4GHDataSource.js b/src/main/sources/GA4GHDataSource.js index 3b0b63b1..dfa6f8e3 100644 --- a/src/main/sources/GA4GHDataSource.js +++ b/src/main/sources/GA4GHDataSource.js @@ -40,11 +40,7 @@ type GA4GHSpec = { }; function create(spec: GA4GHSpec): AlignmentDataSource { - if (spec.endpoint.slice(-6) != 'v0.5.1') { - throw new Error('Only v0.5.1 of the GA4GH API is supported by pileup.js'); - } - - var url = spec.endpoint + '/reads/search'; + var url = spec.endpoint ; var reads: {[key:string]: Alignment} = {}; @@ -53,12 +49,16 @@ function create(spec: GA4GHSpec): AlignmentDataSource { function addReadsFromResponse(response: Object) { response.alignments.forEach(alignment => { - // optimization: don't bother constructing a GA4GHAlignment unless it's new. - var key = GA4GHAlignment.keyFromGA4GHResponse(alignment); - if (key in reads) return; - - var ga4ghAlignment = new GA4GHAlignment(alignment); - reads[key] = ga4ghAlignment; + try{ + // optimization: don't bother constructing a GA4GHAlignment unless it's new. + var key = GA4GHAlignment.keyFromGA4GHResponse(alignment); + if (key in reads) return; + + var ga4ghAlignment = new GA4GHAlignment(alignment); + reads[key] = ga4ghAlignment; + } catch(TypeError){ + console.log("Error in Matepair Data Source.") + } }); } @@ -87,7 +87,10 @@ function create(spec: GA4GHSpec): AlignmentDataSource { pageToken: ?string, numRequests: number) { var xhr = new XMLHttpRequest(); - xhr.open('POST', url); + + var endpoint = url + "/" + range.contig + "?start=" + range.start() + "&end=" + range.stop()+"&sample="+spec.readGroupId; + + xhr.open('GET', endpoint); xhr.responseType = 'json'; xhr.setRequestHeader('Content-Type', 'application/json'); diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js new file mode 100644 index 00000000..7129abd6 --- /dev/null +++ b/src/main/sources/ReferenceDataSource.js @@ -0,0 +1,169 @@ +/** + * The "glue" between TwoBit.js and GenomeTrack.js. + * + * GenomeTrack is pure view code -- it renders data which is already in-memory + * in the browser. + * + * TwoBit is purely for data parsing and fetching. It only knows how to return + * promises for various genome features. + * + * This code acts as a bridge between the two. It maintains a local version of + * the data, fetching remote data and informing the view when it becomes + * available. + * + * @flow + */ +'use strict'; + +import Q from 'q'; +import _ from 'underscore'; +import {Events} from 'backbone'; + +import ContigInterval from '../ContigInterval'; +import Sequence from '../data/Sequence'; +import type {SequenceRecord} from '../data/Sequence'; +import SequenceStore from '../SequenceStore'; +import type {TwoBitSource} from './TwoBitDataSource'; +import RemoteRequest from '../RemoteRequest'; +import utils from '../utils'; + + +// Requests for 2bit ranges are expanded to begin & end at multiples of this +// constant. Doing this means that panning typically won't require +// additional network requests. +var BASE_PAIRS_PER_FETCH = 10000; + +var MAX_BASE_PAIRS_TO_FETCH = 100000; + +// Expand range to begin and end on multiples of BASE_PAIRS_PER_FETCH. +function expandRange(range) { + var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; + var newStart = Math.max(0, roundDown(range.start())), + newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); + + return new ContigInterval(range.contig, newStart, newStop); +} + +var createFromReferenceUrl = function(remoteSource: Sequence): TwoBitSource { + // Local cache of genomic data. + var contigList = remoteSource.getContigList(); + var store = new SequenceStore(); + + // Ranges for which we have complete information -- no need to hit network. + var coveredRanges = ([]: ContigInterval[]); + + function fetch(range: ContigInterval) { + var span = range.length(); + if (span > MAX_BASE_PAIRS_TO_FETCH) { + return Q.when(); // empty promise + } + + // TODO remote Source + remoteSource.getFeaturesInRange(range.contig, range.start(), range.stop()) + .then(letters => { + if (!letters) return; + if (letters.length < range.length()) { + // Probably at EOF + range = new ContigInterval(range.contig, + range.start(), + range.start() + letters.length - 1); + } + store.setRange(range, letters); + }).then(() => { + o.trigger('newdata', range); + }).done(); + } + + // This either adds or removes a 'chr' as needed. + function normalizeRange(range: GenomeRange): Q.Promise { + if (contigList.indexOf(range.contig) >= 0) { + return Q.Promise.resolve(range); + } + var altContig = utils.altContigName(range.contig); + if (contigList.indexOf(altContig) >= 0) { + return Q.Promise.resolve({ + contig: altContig, + start: range.start, + stop: range.stop + }); + } + return Q.Promise.resolve(range); // cast as promise to conform to TwoBitDataSource + } + + // Returns a {"chr12:123" -> "[ATCG]"} mapping for the range. + function getRange(range: GenomeRange) { + return store.getAsObjects(ContigInterval.fromGenomeRange(range)); + } + + // Returns a string of base pairs for this range. + function getRangeAsString(range: GenomeRange): string { + if (!range) return ''; + return store.getAsString(ContigInterval.fromGenomeRange(range)); + } + + var o = { + // The range here is 0-based, inclusive + rangeChanged: function(newRange: GenomeRange) { + normalizeRange(newRange).then(r => { + var range = new ContigInterval(r.contig, r.start, r.stop); + // Check if this interval is already in the cache. + if (range.isCoveredBy(coveredRanges)) { + return; + } + + range = expandRange(range); + var newRanges = range.complementIntervals(coveredRanges); + coveredRanges.push(range); + coveredRanges = ContigInterval.coalesce(coveredRanges); + + for (var newRange of newRanges) { + fetch(newRange); + } + }).done(); + }, + // The ranges passed to these methods are 0-based + getRange, + getRangeAsString, + contigList: () => contigList, + normalizeRange, + + // These are here to make Flow happy. + on: () => {}, + once: () => {}, + off: () => {}, + trigger: () => {} + }; + _.extend(o, Events); // Make this an event emitter + return o; +}; + +function create(data: {url:string, contigList: SequenceRecord[]}): TwoBitSource { + var urlPrefix = data.url; + var contigList = data.contigList; + + // verify data was correctly set + if (!urlPrefix) { + throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); + } + // verify contiglist was correctly set + if (!contigList) { + throw new Error(`Missing ContigList from track: ${JSON.stringify(data)}`); + } + return createFromReferenceUrl(new Sequence(new RemoteRequest(urlPrefix), contigList)); +} + +// Getter/setter for base pairs per fetch. +// This should only be used for testing. +function testBasePairsToFetch(num?: number): any { + if (num) { + BASE_PAIRS_PER_FETCH = num; + } else { + return BASE_PAIRS_PER_FETCH; + } +} + +module.exports = { + create, + createFromReferenceUrl, + testBasePairsToFetch +}; diff --git a/src/main/viz/pileuputils.js b/src/main/viz/pileuputils.js index 22e016b2..34300390 100644 --- a/src/main/viz/pileuputils.js +++ b/src/main/viz/pileuputils.js @@ -139,7 +139,8 @@ export type OpInfo = { // Breaks the read down into Cigar Ops suitable for display function getOpInfo(read: Alignment, referenceSource: Object): OpInfo { var ops = read.cigarOps; - + // console.log(read); + var range = read.getInterval(), start = range.start(), seq = read.getSequence(), @@ -158,7 +159,11 @@ function getOpInfo(read: Alignment, referenceSource: Object): OpInfo { start: refPos, stop: refPos + op.length - 1 }); + // console.log(seq); + // console.log("seqPos:"+seqPos); + // console.log("op.length:"+op.length); var mSeq = seq.slice(seqPos, seqPos + op.length); + // console.log(mSeq) mismatches = mismatches.concat(findMismatches(ref, mSeq, refPos, scores)); } diff --git a/src/test/sources/ReferenceDataSource-test.js b/src/test/sources/ReferenceDataSource-test.js new file mode 100644 index 00000000..d17bd0b8 --- /dev/null +++ b/src/test/sources/ReferenceDataSource-test.js @@ -0,0 +1,148 @@ + /** @flow */ +'use strict'; + +import {expect} from 'chai'; + +import sinon from 'sinon'; + +import ReferenceDataSource from '../../main/sources/ReferenceDataSource'; +import RemoteFile from '../../main/RemoteFile'; + +describe('ReferenceDataSource', function() { + var server: any = null, response; + + before(function () { + return new RemoteFile('/test-data/reference-chrM-0-1000.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/reference',[200, { "Content-Type": "application/json" }, response]); + }); + }); + + after(function () { + server.restore(); + }); + + function getTestSource() { + var source = ReferenceDataSource.create({ + url: '/reference', + contigList: [{ + name:"chrM", + length: 1000 + },{ + name:"22", + length: 1000 + }] + }); + return source; + } + + it('should fetch contigs', function() { + var source = getTestSource(); + var contigs = source.contigList(); + expect(contigs).to.deep.equal(['chrM','22']); + }); + + it('should normalize range', function() { + var source = getTestSource(); + var range = {contig: 'chrM', start: 0, stop: 3}; + source.normalizeRange(range).then(normalized => { + expect(normalized.to.deep.equal(range)); + }).done(); + }); + + it('should fetch base pairs', function(done) { + var source = getTestSource(); + var range = {contig: 'chrM', start: 0, stop: 3}; + + // Before data has been fetched, all base pairs are null. + expect(source.getRange(range)).to.deep.equal({ + 'chrM:0': null, + 'chrM:1': null, + 'chrM:2': null, + 'chrM:3': null + }); + expect(source.getRangeAsString(range)).to.equal('....'); + + source.on('newdata', () => { + expect(source.getRange(range)).to.deep.equal({ + 'chrM:0': 'N', + 'chrM:1': 'G', + 'chrM:2': 'T', + 'chrM:3': 'T' + }); + expect(source.getRangeAsString(range)).to.equal('NGTT'); + + done(); + }); + source.rangeChanged(range); + server.respond(); + }); + + it('should fetch nearby base pairs', function(done) { + var source = getTestSource(); + + source.on('newdata', () => { + expect(source.getRange({contig: 'chrM', start: 0, stop: 14})) + .to.deep.equal({ + 'chrM:0': 'N', + 'chrM:1': 'G', + 'chrM:2': 'T', + 'chrM:3': 'T', + 'chrM:4': 'A', // start of actual request + 'chrM:5': 'A', + 'chrM:6': 'T', + 'chrM:7': 'G', + 'chrM:8': 'T', + 'chrM:9': 'A', // end of actual requuest + 'chrM:10': 'G', + 'chrM:11': 'C', + 'chrM:12': 'T', + 'chrM:13': 'T', + 'chrM:14': 'A' + }); + done(); + }); + source.rangeChanged({contig: 'chrM', start: 4, stop: 9}); + server.respond(); + }); + + it('should add chr', function(done) { + var source = getTestSource(); + var range = {contig: '22', start: 0, stop: 3}; + + source.on('newdata', () => { + expect(source.getRange(range)).to.deep.equal({ + '22:0': 'N', + '22:1': 'G', + '22:2': 'T', + '22:3': 'T' + }); + expect(source.getRangeAsString(range)).to.equal('NGTT'); + done(); + }); + source.rangeChanged(range); + server.respond(); + }); + + it('should only report newly-fetched ranges', function(done) { + ReferenceDataSource.testBasePairsToFetch(10); + var initRange = {contig: 'chrM', start: 5, stop: 8}, + secondRange = {contig: 'chrM', start: 8, stop: 15}; + var source = getTestSource(); + source.once('newdata', newRange => { + expect(newRange.toString()).to.equal('chrM:0-10'); // expanded range + + source.once('newdata', newRange => { + // This expanded range excludes previously-fetched data. + expect(newRange.toString()).to.equal('chrM:11-20'); + done(); + }); + source.rangeChanged(secondRange); + server.respond(); + }); + source.rangeChanged(initRange); + server.respond(); + }); + +}); diff --git a/test-data/adam-alignments.json b/test-data/adam-alignments.json index 2448fc1d..e8866aa4 100644 --- a/test-data/adam-alignments.json +++ b/test-data/adam-alignments.json @@ -33387,4 +33387,4 @@ "info": {} }], "nextPageToken": null -} \ No newline at end of file +} diff --git a/test-data/features_chrM_0_2000.json b/test-data/features_chrM_0_2000.json new file mode 100644 index 00000000..18c0c397 --- /dev/null +++ b/test-data/features_chrM_0_2000.json @@ -0,0 +1,18 @@ +[{ + "range": { + "name": "chrM", + "start": 0, + "end": 2000 + }, + "features": [{ + "featureId": "4ee7469a-b468-429b-a109-07a484817037", + "featureType": "rs575272151", + "start": 1107, + "end": 1200 + }, { + "featureId": "e105ce29-a840-4fc6-819f-a9aac5166163", + "featureType": "rs544419019", + "start": 1011, + "end": 1012 + }] +}] diff --git a/test-data/reference-chrM-0-1000.json b/test-data/reference-chrM-0-1000.json new file mode 100644 index 00000000..95699648 --- /dev/null +++ b/test-data/reference-chrM-0-1000.json @@ -0,0 +1 @@ +"NGTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAAATATTAAGCAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATTAAAATCCAACTTATATGTGAAAATTCATTGTTAGGACCTAAACTCAATAACGAAAGTAATTCTAGTCATTTATAATACACGACAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAAAACTATTTGCCAGAGAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAACGTTAGGTCAAGGTGTAGCCAATGAAATGGGAAGAAATGGGCTACATTTTCTTATAAAAGAACATTACTATACCCTTTATGAAACTAAAGGACTAAGGAGGATTTAGTAGTAAATTAAGAATAGAGAGCTTAATTGAATTGAGCAATGAAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCAT" From cd5bb58d2850bb03b2b2d8b82f1c9657473e42cc Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sat, 11 Jun 2016 15:13:50 -0700 Subject: [PATCH 004/136] starting reference --- examples/data.js | 16 ++-- src/main/sources/ReferenceDataSource.js | 110 ++++++++++++++++++++++++ 2 files changed, 118 insertions(+), 8 deletions(-) diff --git a/examples/data.js b/examples/data.js index 86b0f074..265d7ae8 100644 --- a/examples/data.js +++ b/examples/data.js @@ -21,15 +21,15 @@ var sources = [ }] }), name: 'Reference' + }, + { + viz: pileup.viz.genome(), + isReference: true, + data: pileup.formats.reference({ + prefix:"../json/" + }), + name: 'Reference' } -// { -// viz: pileup.viz.genome(), -// isReference: true, -// data: pileup.formats.reference({ -// prefix:"../json/" -// }), -// name: 'Reference' -// } // { // viz: pileup.viz.scale(), // name: 'Scale' diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index 7129abd6..ecf6e768 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -35,6 +35,23 @@ var BASE_PAIRS_PER_FETCH = 10000; var MAX_BASE_PAIRS_TO_FETCH = 100000; +<<<<<<< HEAD +======= + +// Flow type for export. +export type ReferenceSource = { + rangeChanged: (newRange: GenomeRange) => void; + getRange: (range: GenomeRange) => {[key:string]: ?string}; + getRangeAsString: (range: GenomeRange) => string; + contigList: () => string[]; + normalizeRange: (range: GenomeRange) => Q.Promise; + on: (event: string, handler: Function) => void; + once: (event: string, handler: Function) => void; + off: (event: string) => void; + trigger: (event: string, ...args:any) => void; +} + +>>>>>>> 1bbf80b... starting reference // Expand range to begin and end on multiples of BASE_PAIRS_PER_FETCH. function expandRange(range) { var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; @@ -44,11 +61,30 @@ function expandRange(range) { return new ContigInterval(range.contig, newStart, newStop); } +<<<<<<< HEAD var createFromReferenceUrl = function(remoteSource: Sequence): TwoBitSource { // Local cache of genomic data. var contigList = remoteSource.getContigList(); var store = new SequenceStore(); +======= + +var createFromReferenceUrl = function(): ReferenceSource { + // Local cache of genomic data. + var contigList = []; + var store = new SequenceStore(); + + var url = "/reference/" + "chrM" + "?start=" + 0 + "&end=" + 200; + console.log(url); + var xmlHttp = new XMLHttpRequest(); + xmlHttp.open( "GET", url, false ); // false for synchronous request + xmlHttp.send( null ); + console.log(xmlHttp); + console.log(xmlHttp.responseText); + alert(xmlHttp.responseText); + + +>>>>>>> 1bbf80b... starting reference // Ranges for which we have complete information -- no need to hit network. var coveredRanges = ([]: ContigInterval[]); @@ -58,6 +94,7 @@ var createFromReferenceUrl = function(remoteSource: Sequence): TwoBitSource { return Q.when(); // empty promise } +<<<<<<< HEAD // TODO remote Source remoteSource.getFeaturesInRange(range.contig, range.start(), range.stop()) .then(letters => { @@ -100,12 +137,63 @@ var createFromReferenceUrl = function(remoteSource: Sequence): TwoBitSource { if (!range) return ''; return store.getAsString(ContigInterval.fromGenomeRange(range)); } +======= + // TODO: fetch JSON from file + + + store.setRange(range, letters); + o.trigger('newdata', range); + } + + function normalizeRange(range: GenomeRange): Q.Promise { + return contigPromise.then(() => normalizeRangeSync(range)); + } + + // Returns a {"chr12:123" -> "[ATCG]"} mapping for the range. + function getRange(range: GenomeRange) { + return store.getAsObjects(ContigInterval.fromGenomeRange(range)); + } + + // Returns a string of base pairs for this range. + function getRangeAsString(range: GenomeRange): string { + if (!range) return ''; + return store.getAsString(ContigInterval.fromGenomeRange(range)); + } + + // This either adds or removes a 'chr' as needed. + function normalizeRangeSync(range: GenomeRange): GenomeRange { + if (contigList.indexOf(range.contig) >= 0) { + return range; + } + var altContig = utils.altContigName(range.contig); + if (contigList.indexOf(altContig) >= 0) { + return { + contig: altContig, + start: range.start, + stop: range.stop + }; + } + return range; // let it fail with the original contig + } + + // Fetch the contig list immediately. + var contigPromise = remoteSource.getContigList().then(c => { + contigList = c; + o.trigger('contigs', contigList); + return c; + }); + contigPromise.done(); +>>>>>>> 1bbf80b... starting reference var o = { // The range here is 0-based, inclusive rangeChanged: function(newRange: GenomeRange) { normalizeRange(newRange).then(r => { var range = new ContigInterval(r.contig, r.start, r.stop); +<<<<<<< HEAD +======= + +>>>>>>> 1bbf80b... starting reference // Check if this interval is already in the cache. if (range.isCoveredBy(coveredRanges)) { return; @@ -134,6 +222,7 @@ var createFromReferenceUrl = function(remoteSource: Sequence): TwoBitSource { trigger: () => {} }; _.extend(o, Events); // Make this an event emitter +<<<<<<< HEAD return o; }; @@ -155,6 +244,23 @@ function create(data: {url:string, contigList: SequenceRecord[]}): TwoBitSource // Getter/setter for base pairs per fetch. // This should only be used for testing. function testBasePairsToFetch(num?: number): any { +======= + + return o; +}; + +function create(data: {prefix:string}): ReferenceSource { + var urlPrefix = data.prefix; + if (!urlPrefix) { + throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); + } + + return createFromReferenceUrl(); +} +// Getter/setter for base pairs per fetch. +// This should only be used for testing. +function testReferenceToFetch(num?: number): any { +>>>>>>> 1bbf80b... starting reference if (num) { BASE_PAIRS_PER_FETCH = num; } else { @@ -165,5 +271,9 @@ function testBasePairsToFetch(num?: number): any { module.exports = { create, createFromReferenceUrl, +<<<<<<< HEAD testBasePairsToFetch +======= + testReferenceToFetch +>>>>>>> 1bbf80b... starting reference }; From 067a91c9f864db634c7875d368bc19d2c399df3f Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sun, 12 Jun 2016 15:41:49 -0700 Subject: [PATCH 005/136] continued reference implementation --- .gitignore | 9 + examples/data.js | 16 +- package.json | 1 + src/main/data/TwoBit.js | 2 +- src/main/data/VirtualOffset.js | 1 + src/main/sources/ReferenceDataSource.js | 114 +-------- src/main/style.js | 1 + src/test/sources/ReferenceDataSource-test.js | 236 ++++++++++--------- 8 files changed, 142 insertions(+), 238 deletions(-) diff --git a/.gitignore b/.gitignore index 26ed7f18..2a749afe 100644 --- a/.gitignore +++ b/.gitignore @@ -41,3 +41,12 @@ dist # Generated files src/lib *.pyc +.idea/.name +.idea/compiler.xml +.idea/misc.xml +.idea/modules.xml +.idea/pileup.js.iml +.idea/vcs.xml +.idea/workspace.xml +.idea/copyright/profiles_settings.xml +.idea/dictionaries/akmorrow.xml diff --git a/examples/data.js b/examples/data.js index 265d7ae8..86b0f074 100644 --- a/examples/data.js +++ b/examples/data.js @@ -21,15 +21,15 @@ var sources = [ }] }), name: 'Reference' - }, - { - viz: pileup.viz.genome(), - isReference: true, - data: pileup.formats.reference({ - prefix:"../json/" - }), - name: 'Reference' } +// { +// viz: pileup.viz.genome(), +// isReference: true, +// data: pileup.formats.reference({ +// prefix:"../json/" +// }), +// name: 'Reference' +// } // { // viz: pileup.viz.scale(), // name: 'Scale' diff --git a/package.json b/package.json index 53c633ba..129debaa 100644 --- a/package.json +++ b/package.json @@ -66,6 +66,7 @@ "arraybuffer-slice": "^0.1.2", "babel": "^5.8.23", "babel-core": "^5.8.23", + "babel-preset-es2015": "^6.9.0", "babelify": "^6.3.0", "browserify": "^10.2.4", "chai": "^2.0.0", diff --git a/src/main/data/TwoBit.js b/src/main/data/TwoBit.js index ca0231f4..1858da08 100644 --- a/src/main/data/TwoBit.js +++ b/src/main/data/TwoBit.js @@ -270,4 +270,4 @@ class TwoBit { } } -module.exports = TwoBit; +module.exports = TwoBit; \ No newline at end of file diff --git a/src/main/data/VirtualOffset.js b/src/main/data/VirtualOffset.js index 287c05f2..b3136b40 100644 --- a/src/main/data/VirtualOffset.js +++ b/src/main/data/VirtualOffset.js @@ -6,6 +6,7 @@ * JavaScript. * @flow */ +'use strict'; "use strict"; diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index ecf6e768..2e10d7de 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -1,10 +1,10 @@ /** - * The "glue" between TwoBit.js and GenomeTrack.js. + * The "glue" between Sequence.js and GenomeTrack.js. * * GenomeTrack is pure view code -- it renders data which is already in-memory * in the browser. * - * TwoBit is purely for data parsing and fetching. It only knows how to return + *Sequence is purely for data parsing and fetching. It only knows how to return * promises for various genome features. * * This code acts as a bridge between the two. It maintains a local version of @@ -35,23 +35,6 @@ var BASE_PAIRS_PER_FETCH = 10000; var MAX_BASE_PAIRS_TO_FETCH = 100000; -<<<<<<< HEAD -======= - -// Flow type for export. -export type ReferenceSource = { - rangeChanged: (newRange: GenomeRange) => void; - getRange: (range: GenomeRange) => {[key:string]: ?string}; - getRangeAsString: (range: GenomeRange) => string; - contigList: () => string[]; - normalizeRange: (range: GenomeRange) => Q.Promise; - on: (event: string, handler: Function) => void; - once: (event: string, handler: Function) => void; - off: (event: string) => void; - trigger: (event: string, ...args:any) => void; -} - ->>>>>>> 1bbf80b... starting reference // Expand range to begin and end on multiples of BASE_PAIRS_PER_FETCH. function expandRange(range) { var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; @@ -61,30 +44,11 @@ function expandRange(range) { return new ContigInterval(range.contig, newStart, newStop); } -<<<<<<< HEAD var createFromReferenceUrl = function(remoteSource: Sequence): TwoBitSource { // Local cache of genomic data. var contigList = remoteSource.getContigList(); var store = new SequenceStore(); -======= - -var createFromReferenceUrl = function(): ReferenceSource { - // Local cache of genomic data. - var contigList = []; - var store = new SequenceStore(); - - var url = "/reference/" + "chrM" + "?start=" + 0 + "&end=" + 200; - console.log(url); - var xmlHttp = new XMLHttpRequest(); - xmlHttp.open( "GET", url, false ); // false for synchronous request - xmlHttp.send( null ); - console.log(xmlHttp); - console.log(xmlHttp.responseText); - alert(xmlHttp.responseText); - - ->>>>>>> 1bbf80b... starting reference // Ranges for which we have complete information -- no need to hit network. var coveredRanges = ([]: ContigInterval[]); @@ -94,7 +58,6 @@ var createFromReferenceUrl = function(): ReferenceSource { return Q.when(); // empty promise } -<<<<<<< HEAD // TODO remote Source remoteSource.getFeaturesInRange(range.contig, range.start(), range.stop()) .then(letters => { @@ -137,63 +100,12 @@ var createFromReferenceUrl = function(): ReferenceSource { if (!range) return ''; return store.getAsString(ContigInterval.fromGenomeRange(range)); } -======= - // TODO: fetch JSON from file - - - store.setRange(range, letters); - o.trigger('newdata', range); - } - - function normalizeRange(range: GenomeRange): Q.Promise { - return contigPromise.then(() => normalizeRangeSync(range)); - } - - // Returns a {"chr12:123" -> "[ATCG]"} mapping for the range. - function getRange(range: GenomeRange) { - return store.getAsObjects(ContigInterval.fromGenomeRange(range)); - } - - // Returns a string of base pairs for this range. - function getRangeAsString(range: GenomeRange): string { - if (!range) return ''; - return store.getAsString(ContigInterval.fromGenomeRange(range)); - } - - // This either adds or removes a 'chr' as needed. - function normalizeRangeSync(range: GenomeRange): GenomeRange { - if (contigList.indexOf(range.contig) >= 0) { - return range; - } - var altContig = utils.altContigName(range.contig); - if (contigList.indexOf(altContig) >= 0) { - return { - contig: altContig, - start: range.start, - stop: range.stop - }; - } - return range; // let it fail with the original contig - } - - // Fetch the contig list immediately. - var contigPromise = remoteSource.getContigList().then(c => { - contigList = c; - o.trigger('contigs', contigList); - return c; - }); - contigPromise.done(); ->>>>>>> 1bbf80b... starting reference var o = { // The range here is 0-based, inclusive rangeChanged: function(newRange: GenomeRange) { normalizeRange(newRange).then(r => { var range = new ContigInterval(r.contig, r.start, r.stop); -<<<<<<< HEAD -======= - ->>>>>>> 1bbf80b... starting reference // Check if this interval is already in the cache. if (range.isCoveredBy(coveredRanges)) { return; @@ -222,7 +134,6 @@ var createFromReferenceUrl = function(): ReferenceSource { trigger: () => {} }; _.extend(o, Events); // Make this an event emitter -<<<<<<< HEAD return o; }; @@ -244,23 +155,6 @@ function create(data: {url:string, contigList: SequenceRecord[]}): TwoBitSource // Getter/setter for base pairs per fetch. // This should only be used for testing. function testBasePairsToFetch(num?: number): any { -======= - - return o; -}; - -function create(data: {prefix:string}): ReferenceSource { - var urlPrefix = data.prefix; - if (!urlPrefix) { - throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); - } - - return createFromReferenceUrl(); -} -// Getter/setter for base pairs per fetch. -// This should only be used for testing. -function testReferenceToFetch(num?: number): any { ->>>>>>> 1bbf80b... starting reference if (num) { BASE_PAIRS_PER_FETCH = num; } else { @@ -271,9 +165,5 @@ function testReferenceToFetch(num?: number): any { module.exports = { create, createFromReferenceUrl, -<<<<<<< HEAD testBasePairsToFetch -======= - testReferenceToFetch ->>>>>>> 1bbf80b... starting reference }; diff --git a/src/main/style.js b/src/main/style.js index eb0f0c34..314c8857 100644 --- a/src/main/style.js +++ b/src/main/style.js @@ -4,6 +4,7 @@ * * @flow */ +'use strict'; "use strict"; diff --git a/src/test/sources/ReferenceDataSource-test.js b/src/test/sources/ReferenceDataSource-test.js index d17bd0b8..09ee0879 100644 --- a/src/test/sources/ReferenceDataSource-test.js +++ b/src/test/sources/ReferenceDataSource-test.js @@ -1,4 +1,4 @@ - /** @flow */ +/** @flow */ 'use strict'; import {expect} from 'chai'; @@ -9,140 +9,142 @@ import ReferenceDataSource from '../../main/sources/ReferenceDataSource'; import RemoteFile from '../../main/RemoteFile'; describe('ReferenceDataSource', function() { - var server: any = null, response; - - before(function () { - return new RemoteFile('/test-data/reference-chrM-0-1000.json').getAllString().then(data => { - response = data; - server = sinon.fakeServer.create(); - server.respondWith('GET', '/reference',[200, { "Content-Type": "application/json" }, response]); - }); - }); - - after(function () { - server.restore(); +var server: any = null, response; + +before(function () { + return new RemoteFile('/test-data/reference-chrM-0-1000.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/reference/chrM?start=0&end=10000',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/reference/chrM?start=0&end=10',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/reference/22?start=0&end=10000',[200, { "Content-Type": "application/json" }, response]); }); +}); - function getTestSource() { - var source = ReferenceDataSource.create({ - url: '/reference', - contigList: [{ - name:"chrM", - length: 1000 - },{ - name:"22", - length: 1000 - }] - }); - return source; - } +after(function () { + server.restore(); +}); - it('should fetch contigs', function() { - var source = getTestSource(); - var contigs = source.contigList(); - expect(contigs).to.deep.equal(['chrM','22']); +function getTestSource() { + var source = ReferenceDataSource.create({ + url: '/reference', + contigList: [{ + name:"chrM", + length: 1000 + },{ + name:"22", + length: 1000 + }] }); + return source; +} - it('should normalize range', function() { - var source = getTestSource(); - var range = {contig: 'chrM', start: 0, stop: 3}; - source.normalizeRange(range).then(normalized => { - expect(normalized.to.deep.equal(range)); - }).done(); - }); +it('should fetch contigs', function() { + var source = getTestSource(); + var contigs = source.contigList(); + expect(contigs).to.deep.equal(['chrM','22']); +}); - it('should fetch base pairs', function(done) { - var source = getTestSource(); - var range = {contig: 'chrM', start: 0, stop: 3}; - - // Before data has been fetched, all base pairs are null. - expect(source.getRange(range)).to.deep.equal({ - 'chrM:0': null, - 'chrM:1': null, - 'chrM:2': null, - 'chrM:3': null - }); - expect(source.getRangeAsString(range)).to.equal('....'); - - source.on('newdata', () => { - expect(source.getRange(range)).to.deep.equal({ - 'chrM:0': 'N', - 'chrM:1': 'G', - 'chrM:2': 'T', - 'chrM:3': 'T' - }); - expect(source.getRangeAsString(range)).to.equal('NGTT'); +it('should normalize range', function() { + var source = getTestSource(); + var range = {contig: 'chrM', start: 0, stop: 3}; + source.normalizeRange(range).then(normalized => { + expect(normalized.to.deep.equal(range)); + }).done(); +}); - done(); +it('should fetch base pairs', function(done) { + var source = getTestSource(); + var range = {contig: 'chrM', start: 0, stop: 3}; + + // Before data has been fetched, all base pairs are null. + expect(source.getRange(range)).to.deep.equal({ + 'chrM:0': null, + 'chrM:1': null, + 'chrM:2': null, + 'chrM:3': null + }); + expect(source.getRangeAsString(range)).to.equal('....'); + + source.on('newdata', () => { + expect(source.getRange(range)).to.deep.equal({ + 'chrM:0': 'N', + 'chrM:1': 'G', + 'chrM:2': 'T', + 'chrM:3': 'T' }); - source.rangeChanged(range); - server.respond(); + expect(source.getRangeAsString(range)).to.equal('NGTT'); + + done(); }); + source.rangeChanged(range); + server.respond(); +}); - it('should fetch nearby base pairs', function(done) { - var source = getTestSource(); - - source.on('newdata', () => { - expect(source.getRange({contig: 'chrM', start: 0, stop: 14})) - .to.deep.equal({ - 'chrM:0': 'N', - 'chrM:1': 'G', - 'chrM:2': 'T', - 'chrM:3': 'T', - 'chrM:4': 'A', // start of actual request - 'chrM:5': 'A', - 'chrM:6': 'T', - 'chrM:7': 'G', - 'chrM:8': 'T', - 'chrM:9': 'A', // end of actual requuest - 'chrM:10': 'G', - 'chrM:11': 'C', - 'chrM:12': 'T', - 'chrM:13': 'T', - 'chrM:14': 'A' - }); - done(); - }); - source.rangeChanged({contig: 'chrM', start: 4, stop: 9}); - server.respond(); +it('should fetch nearby base pairs', function(done) { + var source = getTestSource(); + + source.on('newdata', () => { + expect(source.getRange({contig: 'chrM', start: 0, stop: 14})) + .to.deep.equal({ + 'chrM:0': 'N', + 'chrM:1': 'G', + 'chrM:2': 'T', + 'chrM:3': 'T', + 'chrM:4': 'A', // start of actual request + 'chrM:5': 'A', + 'chrM:6': 'T', + 'chrM:7': 'G', + 'chrM:8': 'T', + 'chrM:9': 'A', // end of actual requuest + 'chrM:10': 'G', + 'chrM:11': 'C', + 'chrM:12': 'T', + 'chrM:13': 'T', + 'chrM:14': 'A' + }); + done(); }); + source.rangeChanged({contig: 'chrM', start: 4, stop: 9}); + server.respond(); +}); - it('should add chr', function(done) { - var source = getTestSource(); - var range = {contig: '22', start: 0, stop: 3}; - - source.on('newdata', () => { - expect(source.getRange(range)).to.deep.equal({ - '22:0': 'N', - '22:1': 'G', - '22:2': 'T', - '22:3': 'T' - }); - expect(source.getRangeAsString(range)).to.equal('NGTT'); - done(); +it('should add chr', function(done) { + var source = getTestSource(); + var range = {contig: '22', start: 0, stop: 3}; + + source.on('newdata', () => { + expect(source.getRange(range)).to.deep.equal({ + '22:0': 'N', + '22:1': 'G', + '22:2': 'T', + '22:3': 'T' }); - source.rangeChanged(range); - server.respond(); + expect(source.getRangeAsString(range)).to.equal('NGTT'); + done(); }); + source.rangeChanged(range); + server.respond(); +}); + +it('should only report newly-fetched ranges', function(done) { + ReferenceDataSource.testBasePairsToFetch(10); + var initRange = {contig: 'chrM', start: 5, stop: 8}, + secondRange = {contig: 'chrM', start: 8, stop: 15}; + var source = getTestSource(); + source.once('newdata', newRange => { + expect(newRange.toString()).to.equal('chrM:0-10'); // expanded range - it('should only report newly-fetched ranges', function(done) { - ReferenceDataSource.testBasePairsToFetch(10); - var initRange = {contig: 'chrM', start: 5, stop: 8}, - secondRange = {contig: 'chrM', start: 8, stop: 15}; - var source = getTestSource(); source.once('newdata', newRange => { - expect(newRange.toString()).to.equal('chrM:0-10'); // expanded range - - source.once('newdata', newRange => { - // This expanded range excludes previously-fetched data. - expect(newRange.toString()).to.equal('chrM:11-20'); - done(); - }); - source.rangeChanged(secondRange); - server.respond(); + // This expanded range excludes previously-fetched data. + expect(newRange.toString()).to.equal('chrM:11-20'); + done(); }); - source.rangeChanged(initRange); + source.rangeChanged(secondRange); server.respond(); }); + source.rangeChanged(initRange); + server.respond(); +}); }); From cad3e825e99ac0dea0ebbd8103a26cb9efcda042 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sat, 18 Jun 2016 13:20:54 -0700 Subject: [PATCH 006/136] added test resources for ADAM alignments --- src/test/ADAMAlignment-test.js | 57 +- test-data/adam-alignments.json | 39273 +++++-------------------------- 2 files changed, 5930 insertions(+), 33400 deletions(-) diff --git a/src/test/ADAMAlignment-test.js b/src/test/ADAMAlignment-test.js index f07884a5..07191353 100644 --- a/src/test/ADAMAlignment-test.js +++ b/src/test/ADAMAlignment-test.js @@ -7,33 +7,64 @@ import GA4GHAlignment from '../main/GA4GHAlignment'; import RemoteFile from '../main/RemoteFile'; import Bam from '../main/data/bam'; -describe('ADAM_Alignment', function() { +describe('GA4GHAlignment', function() { var sampleAlignments = []; before(function() { return new RemoteFile('/test-data/adam-alignments.json').getAllString().then(data => { - // console.log("data: "+ JSON.parse(data).alignments); sampleAlignments = JSON.parse(data).alignments; - // console.log("sampleAlignments: " + sampleAlignments); - // console.log("sampleAlignments length: " +sampleAlignments.length); }); }); - + it('should read the sample alignments', function() { - // console.log("sampleAlignments length: " +sampleAlignments.length); - expect(sampleAlignments).to.have.length(1046); + expect(sampleAlignments).to.have.length(14); }); it('should provide basic accessors', function() { var a = new GA4GHAlignment(sampleAlignments[0]); - expect(a.name).to.equal('613F0AAXX100423:5:47:2891:8862'); - expect(a.getSequence()).to.equal('GTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATCATTGTATCCCATAAACACAAAGTTTTGGTCCTGGCCTTATAATTACTTAG'); - expect(a.getQualityScores()).to.deep.equal([17, 28, 10, 23, 27, 28, 17, 31, 22, 10, 16, 19, 9, 15, 16, 22, 15, 14, 15, 20, 15, 9, 15, 15, 9, 32, 32, 25, 27, 9, 21, 25, 32, 28, 28, 31, 31, 23, 22, 22, 9, 17, 22, 12, 25, 24, 14, 10, 26, 26, 10, 32, 26, 30, 32, 31, 25, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]); + expect(a.name).to.equal('r000'); + expect(a.getSequence()).to.equal('ATTTAGCTAC'); + expect(a.getQualityScores()).to.deep.equal([32,32,32,32,32,32,32,32,32,32]); expect(a.getStrand()).to.equal('+'); - expect(a.getInterval().toString()).to.equal('chrM:0-58'); // 0-based + expect(a.getInterval().toString()).to.equal('chr17:4-13'); // 0-based expect(a.cigarOps).to.deep.equal([ - {length:59, op: 'M'},{length: 42,op:'S'} + {op: 'M', length: 10} ]); + expect(a.getMateProperties()).to.deep.equal({ + ref: 'chr17', + pos: 79, + strand: '+' + }); + }); + + it('should match SamRead', function() { + var bam = new Bam(new RemoteFile('/test-data/chr17.1-250.bam')); + return bam.readAll().then(({alignments: samReads}) => { + // This is a workaround. See https://github.com/ga4gh/server/issues/488 + samReads.splice(-1, 1); + + expect(sampleAlignments.length).to.equal(samReads.length); + for (var i = 0; i < sampleAlignments.length; i++) { + var ga4gh = new GA4GHAlignment(sampleAlignments[i]), + bam = samReads[i]; + expect(ga4gh.getSequence()).to.equal(bam.getSequence()); + // See https://github.com/ga4gh/server/issues/491 + // expect(ga4gh.getStrand()).to.equal(bam.getStrand()); + // For the if statement, see https://github.com/ga4gh/server/issues/492 + var quality = ga4gh.getQualityScores(); + if (quality.length) { + expect(quality).to.deep.equal(bam.getQualityScores()); + } + expect(ga4gh.cigarOps).to.deep.equal(bam.cigarOps); + // After ga4gh#491, change this to a .deep.equal on getMateProperties() + var ga4ghMate = ga4gh.getMateProperties(), + bamMate = bam.getMateProperties(); + expect(!!ga4ghMate).to.equal(!!bamMate); + if (ga4ghMate && bamMate) { + expect(ga4ghMate.ref).to.equal(bamMate.ref); + expect(ga4ghMate.pos).to.equal(bamMate.pos); + } + } + }); }); - // Can not check with SamReads because we don't have the corresponding BAM file }); diff --git a/test-data/adam-alignments.json b/test-data/adam-alignments.json index e8866aa4..f4e92070 100644 --- a/test-data/adam-alignments.json +++ b/test-data/adam-alignments.json @@ -1,33390 +1,5889 @@ { - "alignments": [{ - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:47:2891:8862", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 0, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 59, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 42, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATCATTGTATCCCATAAACACAAAGTTTTGGTCCTGGCCTTATAATTACTTAG", - "alignedQuality": [17, 28, 10, 23, 27, 28, 17, 31, 22, 10, 16, 19, 9, 15, 16, 22, 15, 14, 15, 20, 15, 9, 15, 15, 9, 32, 32, 25, 27, 9, 21, 25, 32, 28, 28, 31, 31, 23, 22, 22, 9, 17, 22, 12, 25, 24, 14, 10, 26, 26, 10, 32, 26, 30, 32, 31, 25, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:40:17115:17222", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 154, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 1, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 31, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 70, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTCATGTAGCTTGATAACAGCGCAAAGAACTCCAAATGCTTAGATGGATAATTGTATCCCATAAAAACAAAGGATTGGGCCTGGCCTTATAANTATTTTGA", - "alignedQuality": [31, 31, 7, 30, 7, 11, 31, 7, 31, 7, 7, 11, 6, 28, 11, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:27:8808:3060", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 2, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATNAATTAGAG", - "alignedQuality": [38, 38, 38, 38, 35, 37, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 38, 37, 38, 38, 38, 38, 38, 38, 30, 37, 35, 38, 37, 37, 37, 37, 38, 38, 38, 35, 36, 37, 37, 36, 38, 38, 38, 35, 38, 36, 37, 36, 38, 36, 37, 36, 36, 37, 33, 33, 34, 35, 36, 36, 34, 35, 35, 35, 35, 35, 36, 25, 35, 36, 30, 35, 32, 25, 26, 0, 26, 6, 29, 26, 29, 28, 22, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.3", - "fragmentName": "613F0AAXX100423:3:93:11085:15551", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 138, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 2, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "CLIP_SOFT", - "operationLength": 47, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 54, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACCAAAACTCTAATCATACTCTATTACGCAATAAACATTAACAAGATAATGTAGCTTAATAACAAAGCAAAGCACTGCATATGCTTAGATGGGTAATTGT", - "alignedQuality": [23, 18, 23, 29, 18, 30, 27, 30, 24, 27, 26, 21, 21, 11, 18, 30, 29, 23, 11, 24, 29, 18, 23, 27, 27, 30, 23, 27, 30, 27, 24, 29, 32, 24, 29, 29, 31, 31, 32, 31, 33, 33, 28, 33, 33, 27, 7, 23, 23, 23, 32, 33, 33, 27, 31, 32, 25, 33, 33, 28, 31, 24, 29, 33, 31, 16, 32, 31, 31, 19, 16, 16, 27, 29, 17, 27, 30, 29, 10, 25, 9, 29, 29, 30, 29, 31, 21, 33, 18, 31, 33, 31, 10, 18, 31, 33, 32, 32, 19, 32, 25], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:2:14636:7280", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 182, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 2, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAATGTAGCTTAATAACAAAGCAACGCACTGAAAACGATTAGACGGATAATTGTATCCCATAAACACAAATATCTGTCCCGGGCCTTATACTTAATTAGCG", - "alignedQuality": [24, 16, 27, 29, 17, 31, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.6", - "fragmentName": "6141AAAXX100423:6:6:16994:6552", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 88, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 2, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "CLIP_SOFT", - "operationLength": 21, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 53, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 27, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACGCAATAAACATTAACAAGCTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGACGGATAATTGTATCCCATAAACACAACGTCTGGGTAG", - "alignedQuality": [17, 21, 26, 22, 18, 20, 24, 22, 24, 10, 22, 22, 20, 15, 28, 28, 20, 30, 21, 21, 7, 15, 22, 25, 23, 20, 17, 25, 20, 15, 20, 14, 29, 32, 23, 30, 25, 13, 21, 14, 16, 23, 19, 15, 18, 27, 8, 9, 14, 8, 16, 18, 22, 12, 17, 32, 15, 30, 28, 28, 8, 20, 18, 32, 8, 12, 15, 7, 10, 29, 23, 23, 23, 21, 32, 8, 7, 10, 16, 17, 29, 24, 15, 32, 30, 31, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:86:13610:13910", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 136, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 3, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTGATTAGAGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 35, 38, 37, 38, 37, 38, 37, 34, 37, 36, 38, 33, 35, 36, 37, 37, 36, 36, 37, 36, 37, 37, 33, 38, 38, 36, 34, 34, 17, 34, 34, 31, 35, 34, 31, 34, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:55:10041:19549", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 3, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATGTAGCTTAATAACAAAGCAAAGCCCTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAGAGGTTTGGTCCTGGCCTTATAATTNATTAGAGG", - "alignedQuality": [37, 37, 37, 37, 37, 35, 37, 36, 37, 37, 35, 38, 37, 38, 36, 38, 38, 32, 38, 37, 36, 38, 38, 38, 34, 36, 38, 38, 38, 35, 36, 37, 38, 38, 37, 37, 38, 37, 38, 38, 36, 36, 38, 38, 35, 37, 38, 32, 37, 38, 38, 37, 35, 36, 35, 36, 36, 37, 38, 38, 38, 38, 37, 36, 37, 38, 37, 28, 36, 36, 36, 32, 33, 33, 33, 35, 33, 35, 35, 33, 35, 33, 35, 33, 33, 35, 33, 36, 33, 30, 28, 26, 0, 26, 25, 29, 30, 29, 29, 27, 35], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:119:5097:18545", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 3, - "reverseStrand": false - }, - "mappingQuality": 20, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 2, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 6, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAAGATCGGA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 37, 36, 38, 38, 35, 38, 38, 38, 38, 37, 37, 36, 38, 38, 38, 36, 35, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 37, 32, 34, 37, 35, 37, 37, 35, 36, 35, 37, 38, 35, 36, 33, 38, 33, 38, 37, 37, 38, 38, 38, 37, 35, 35, 38, 36, 38, 35, 33, 37], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:93:14191:18986", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 181, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 4, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 91, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 9, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAAATTAGAGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 37, 38, 37, 38, 38, 38, 38, 38, 36, 38, 35, 37, 37, 37, 35, 34, 35, 37, 36, 35, 35, 38, 36, 35, 35, 36, 35, 35, 37, 36, 33, 36, 35, 36, 36, 31, 31, 26, 15, 31, 28, 31, 28, 29, 29, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:24:12998:15482", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 192, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 4, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTANATTAGAGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 37, 36, 37, 37, 37, 36, 34, 38, 37, 35, 36, 37, 38, 36, 38, 37, 38, 36, 37, 37, 36, 35, 36, 35, 35, 33, 34, 34, 32, 34, 34, 35, 34, 34, 33, 35, 34, 36, 34, 35, 34, 35, 34, 34, 34, 29, 30, 0, 19, 29, 27, 30, 28, 23, 24, 28], - "nextMatePosition": 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false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGGGGGTGTGGCTAAGCAAAGGGGTTCAAAGTCTTTTATTATGCATGAAAACCACTCCCTAAAATTTATATTAAAATTTAAAGGAATTTTCACCCGATTTT", - "alignedQuality": [29, 33, 28, 25, 33, 31, 24, 32, 25, 31, 27, 30, 33, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:108:13558:6051", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 187, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 32, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCNCCCATAGA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 33, 38, 37, 38, 38, 38, 38, 36, 36, 38, 38, 38, 37, 38, 38, 37, 38, 37, 36, 38, 38, 38, 33, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 34, 38, 37, 38, 37, 38, 36, 38, 38, 35, 38, 38, 38, 37, 38, 38, 37, 38, 32, 30, 0, 7, 30, 25, 25, 27, 25, 28, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.6", - "fragmentName": "6141AAAXX100423:6:54:18839:9717", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 35, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 88, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 13, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATGCTTAGATGGATAATTGTATCCCATAAACACGAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTACATAGAACGA", - "alignedQuality": [38, 38, 38, 35, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 37, 38, 38, 36, 37, 37, 35, 38, 32, 38, 38, 38, 38, 37, 38, 36, 38, 38, 38, 38, 25, 37, 37, 37, 36, 28, 36, 36, 36, 36, 25, 35, 37, 32, 35, 32, 37, 33, 36, 36, 36, 37, 35, 36, 32, 38, 34, 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"referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GCATATGCTAAGATCGATAATATCATCCCATAAACACAACGACTACGACCTGACCATATACTTCAATAAAGTTAAAATTACAACTGACAAACACCATAGCA", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:96:9477:2838", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 172, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 39, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ 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"numberReads": 2, - "fragmentLength": 171, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 40, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGANCGGTGTAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 37, 38, 37, 36, 38, 38, 36, 38, 38, 38, 37, 38, 38, 37, 38, 37, 38, 38, 38, 38, 37, 38, 37, 38, 36, 37, 38, 37, 34, 38, 38, 38, 37, 37, 28, 38, 36, 37, 37, 38, 37, 37, 37, 36, 35, 37, 37, 37, 33, 37, 36, 35, 35, 36, 29, 29, 0, 30, 29, 25, 25, 29, 16, 23, 31], - "nextMatePosition": null, - "info": 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38, 37, 38, 38, 38, 36, 34, 36, 38, 38, 37, 35, 38, 38, 36, 36, 37, 38, 36, 38, 37, 37, 38, 37, 38, 38, 38, 38, 38, 37, 36, 38, 36, 37, 36, 36, 33, 38, 35, 36, 37, 36, 35, 38, 37, 37, 36, 37, 36, 36, 36, 36, 35, 36, 34, 35, 30, 36, 36, 36, 34, 36, 32, 32, 24, 33, 20, 25, 19, 26, 27, 27, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:94:18877:18293", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 41, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": 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"mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 88, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 13, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GATGGATAATTGTATCCCATAAACACAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGAAGACAGGA", - "alignedQuality": [18, 11, 28, 26, 11, 18, 26, 26, 11, 18, 28, 11, 30, 27, 23, 33, 23, 30, 11, 29, 30, 30, 23, 23, 18, 23, 17, 26, 11, 32, 17, 9, 23, 30, 11, 19, 22, 10, 8, 15, 15, 9, 8, 8, 30, 21, 15, 22, 8, 8, 30, 32, 18, 9, 28, 9, 32, 29, 14, 21, 11, 31, 21, 18, 21, 22, 23, 28, 28, 11, 23, 23, 9, 33, 27, 32, 33, 28, 18, 31, 33, 25, 31, 25, 31, 31, 18, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:7:7712:11139", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 43, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAGT", - "alignedQuality": [38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 37, 37, 38, 38, 38, 38, 36, 38, 38, 38, 38, 35, 38, 37, 36, 38, 38, 37, 37, 38, 38, 38, 38, 36, 38, 37, 34, 38, 36, 36, 37, 38, 38, 38, 38, 37, 37, 38, 37, 36, 37, 37, 35, 36, 35, 36, 36, 36, 36, 36, 36, 38, 33, 35, 35, 35, 36, 34, 33, 36, 34, 35, 35, 30, 34, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:45:14089:3113", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 187, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 46, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 84, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 17, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGATAATTGTATCCCATAAACACAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCC", - "alignedQuality": [28, 25, 20, 20, 28, 26, 26, 30, 26, 17, 26, 20, 27, 26, 26, 32, 30, 30, 26, 30, 34, 34, 34, 34, 34, 30, 34, 34, 20, 34, 28, 28, 20, 18, 33, 28, 18, 29, 25, 25, 28, 28, 28, 20, 25, 34, 34, 34, 34, 34, 34, 32, 26, 34, 30, 28, 20, 28, 13, 33, 32, 29, 32, 26, 19, 34, 34, 34, 30, 34, 34, 25, 20, 28, 34, 34, 30, 19, 18, 32, 26, 17, 29, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.2", - "fragmentName": "6141AAAXX100423:2:106:17757:15738", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 46, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAATCTCCATAGACCGGTGTGGGTTGGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 37, 36, 37, 38, 37, 38, 38, 38, 35, 38, 38, 37, 38, 37, 38, 38, 38, 37, 37, 38, 38, 38, 38, 37, 38, 38, 33, 37, 37, 38, 38, 36, 37, 35, 38, 37, 36, 37, 36, 37, 37, 37, 36, 37, 37, 35, 36, 36, 35, 35, 36, 36, 36, 34, 34, 33, 36, 36, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:66:5653:15675", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGTGTGGCTAAGAAAAGGGGGTTAAATATTTTTAATAATACTGAAAACCCCCCCCCATATTTTAATGTAAAATTTAAGGGGTTTTATATCGCGCGAACACG", - "alignedQuality": [27, 31, 12, 27, 16, 27, 27, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:116:8469:2988", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 189, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 46, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 89, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 12, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGATAATTGTATCCCATAAACACAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCC", - "alignedQuality": [32, 32, 22, 19, 17, 23, 20, 31, 23, 17, 33, 26, 26, 20, 26, 24, 25, 26, 24, 31, 21, 26, 33, 33, 18, 28, 18, 20, 5, 21, 17, 13, 26, 28, 31, 28, 16, 34, 28, 22, 34, 25, 28, 25, 29, 22, 31, 24, 22, 33, 28, 25, 34, 34, 31, 16, 29, 26, 12, 29, 10, 14, 30, 22, 29, 25, 29, 30, 29, 29, 28, 29, 20, 20, 20, 32, 29, 31, 25, 31, 33, 21, 20, 30, 30, 32, 32, 30, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:80:15722:3463", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 182, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { 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"properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAAATTCCCAAATAAAGACATTAACACAGCTCTACAAAGTCCAAACTCTGCATTTCTACCTCTAATGACTAATAAGTCCACAACCAACCACTCCTGTTTC", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:4:11279:10553", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 50, - "reverseStrand": false - }, - "mappingQuality": 25, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATTGGATCCCATAAACACAAAGGATTGGTCCTGGCGTTATAATTAATTAGAGGAAAGATTAGACATGCAAACCTCTACAGACCGGTGTAAAATCCCTTAA", - "alignedQuality": [31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:50:14496:18474", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 52, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGTATCCCATAAACACAAAGGTTTGGTCCTAGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 37, 30, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 32, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 35, 38, 38, 37, 37, 38, 38, 36, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 34, 38, 37, 38, 37, 38, 38, 37, 34, 38, 36, 37, 37, 35, 38, 36, 38, 37, 38, 36, 35, 37, 36, 33, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:61:6403:21082", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTGGGGGTGTGGCTATAGACACAAACGAACACACATGTTATGTACTCTCTGATCCCCACCTATTCATCAAAGAAAGTGGAATACGCATATCACCACTCCCC", - "alignedQuality": [25, 32, 24, 29, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:61:6403:21082", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 52, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 65, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 36, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGTATCCCATAAACACAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCTAACCTCCATAGACCGGTGTAAAACCCCTTAAAC", - "alignedQuality": [25, 19, 29, 25, 27, 33, 28, 28, 33, 28, 29, 29, 11, 19, 25, 26, 26, 18, 18, 18, 17, 15, 8, 31, 28, 21, 9, 16, 32, 26, 31, 33, 21, 23, 33, 33, 32, 18, 31, 18, 20, 30, 26, 23, 22, 20, 33, 22, 10, 8, 26, 27, 30, 16, 20, 24, 9, 30, 30, 21, 20, 17, 20, 17, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:69:1823:1645", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 52, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATACCTTAAAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 36, 37, 38, 34, 37, 38, 38, 38, 36, 35, 38, 37, 38, 38, 36, 37, 38, 36, 37, 37, 37, 36, 38, 35, 37, 37, 38, 37, 35, 38, 35, 37, 33, 32, 35, 37, 34, 36, 37, 30, 37, 37, 37, 36, 30, 34, 35, 36, 36, 30, 34, 31, 28, 32, 34, 34, 34, 32, 28, 34, 31, 34, 34, 32, 28, 30, 32, 29, 32, 25, 34, 27, 17, 7, 25, 22, 28, 27, 32, 27, 32, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:99:18637:3397", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 100, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 52, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATNCCCTTAAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 38, 38, 38, 36, 38, 38, 38, 36, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 36, 37, 38, 38, 38, 36, 35, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 35, 38, 36, 37, 34, 37, 38, 33, 37, 37, 37, 38, 37, 38, 37, 36, 35, 38, 35, 38, 37, 30, 37, 36, 33, 37, 32, 36, 33, 37, 25, 25, 0, 19, 27, 30, 30, 27, 28, 26, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:78:6316:4697", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": 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"position": 53, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCNACTTAAAC", - "alignedQuality": [37, 37, 37, 37, 36, 37, 32, 32, 35, 35, 37, 32, 37, 37, 37, 37, 37, 33, 37, 35, 35, 36, 37, 37, 35, 37, 37, 37, 37, 32, 37, 37, 30, 37, 37, 35, 30, 37, 36, 37, 37, 37, 36, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 35, 28, 33, 37, 37, 37, 36, 37, 37, 35, 35, 37, 37, 33, 36, 37, 37, 36, 36, 36, 33, 36, 37, 37, 36, 37, 35, 25, 36, 36, 33, 28, 33, 33, 28, 33, 33, 18, 25, 0, 10, 22, 28, 26, 28, 25, 23, 31], - "nextMatePosition": 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"fragmentName": "6141AAAXX100423:3:37:8169:13015", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 55, - "reverseStrand": false - }, - "mappingQuality": 25, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATCCCATAAACACAAAGGTCTGGTCCTGGCCCTATAACTAATTAGAGGTAAAATTACACATGCACACCTCTATAGACCCGTGTCAAATCTTCTACACCTC", - "alignedQuality": [32, 11, 33, 32, 33, 24, 14, 30, 20, 13, 12, 8, 6, 29, 25, 12, 21, 14, 7, 30, 10, 31, 7, 32, 15, 32, 16, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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"readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:90:4247:5366", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 55, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 75, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 26, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGCAAAATTACACATGCAAACCTCCATAGCCCGGAGAAAAACCCCNATACACAT", - "alignedQuality": [22, 21, 25, 9, 28, 17, 22, 17, 27, 31, 26, 17, 26, 27, 26, 22, 17, 17, 17, 18, 32, 26, 15, 9, 9, 22, 22, 17, 8, 21, 14, 29, 33, 21, 30, 21, 13, 16, 17, 24, 27, 23, 11, 33, 18, 25, 14, 26, 9, 8, 9, 21, 21, 23, 29, 31, 31, 28, 28, 25, 32, 32, 33, 32, 33, 33, 33, 29, 11, 32, 20, 7, 15, 25, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:21:4578:5763", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 56, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCATAAACATTT", - "alignedQuality": [36, 37, 36, 37, 35, 35, 37, 35, 37, 37, 38, 38, 38, 38, 38, 33, 36, 36, 35, 36, 36, 36, 36, 36, 36, 38, 37, 38, 38, 36, 35, 38, 38, 35, 38, 36, 38, 38, 37, 38, 38, 37, 37, 37, 38, 36, 36, 36, 33, 36, 36, 36, 36, 36, 36, 38, 37, 37, 36, 35, 38, 38, 38, 35, 36, 37, 38, 28, 30, 36, 37, 37, 28, 37, 35, 33, 37, 35, 37, 37, 33, 33, 35, 35, 30, 36, 36, 36, 33, 33, 31, 14, 34, 31, 29, 31, 31, 29, 29, 29, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:48:2158:5284", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGTGTGGCTAAAAAAAGGGGCTTTAACCATTTTTATTTGCTTGTTACCCCCTCCCTTTATTTTTAAAAAAAATTTATAGGATTTTTCACCCGGCTCTGGGG", - "alignedQuality": [31, 31, 28, 31, 30, 31, 32, 31, 30, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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"info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:94:5017:20924", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 66, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAACATT", - "alignedQuality": [37, 37, 37, 37, 37, 34, 36, 36, 36, 36, 37, 37, 37, 37, 37, 36, 38, 38, 37, 38, 38, 38, 38, 38, 35, 36, 37, 37, 38, 38, 38, 38, 38, 36, 36, 35, 37, 37, 35, 37, 38, 35, 38, 38, 37, 38, 38, 38, 38, 35, 37, 38, 38, 33, 37, 37, 35, 38, 37, 38, 36, 36, 35, 38, 36, 37, 35, 32, 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"readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:10:3803:7158", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 101, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 68, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 97, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 4, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGAAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCTCTAAACATTTACTNAAAATATA", - "alignedQuality": [22, 19, 9, 7, 19, 21, 11, 26, 24, 14, 24, 29, 20, 12, 15, 11, 11, 11, 18, 22, 24, 26, 26, 25, 16, 24, 24, 20, 23, 20, 11, 22, 18, 29, 17, 16, 10, 20, 20, 22, 25, 28, 28, 28, 13, 27, 26, 20, 12, 20, 18, 18, 28, 22, 17, 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"duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 71, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAANAATTTAAG", - "alignedQuality": [36, 36, 36, 34, 36, 37, 37, 37, 35, 38, 37, 36, 37, 37, 37, 38, 38, 38, 36, 38, 37, 37, 38, 38, 38, 36, 38, 37, 38, 37, 36, 36, 37, 34, 38, 36, 37, 28, 38, 37, 37, 36, 36, 37, 37, 36, 38, 38, 38, 38, 36, 36, 35, 30, 36, 35, 35, 36, 36, 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"supplementaryAlignment": false, - "alignedSequence": "GTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAANGGAGAGGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 38, 38, 35, 37, 37, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 37, 37, 38, 38, 37, 38, 32, 38, 36, 38, 36, 37, 38, 38, 38, 38, 38, 38, 38, 36, 36, 36, 37, 37, 38, 36, 36, 37, 37, 38, 36, 38, 35, 36, 35, 37, 36, 36, 30, 28, 0, 16, 25, 26, 25, 18, 30, 25, 24], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.1", - "fragmentName": "6141AAAXX100423:1:31:4886:2752", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 133, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 78, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 91, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 10, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTCCTGGCCTTATAATTAATTAGAGGTAAAATTGCACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGNGATGGC", - "alignedQuality": [38, 38, 38, 38, 35, 38, 36, 38, 38, 38, 37, 36, 37, 37, 38, 37, 37, 37, 36, 37, 38, 35, 38, 36, 37, 38, 36, 37, 37, 35, 34, 35, 35, 10, 31, 32, 31, 34, 32, 32, 35, 37, 38, 32, 36, 37, 36, 37, 36, 37, 38, 35, 37, 36, 36, 35, 37, 37, 35, 38, 35, 37, 35, 36, 36, 37, 36, 35, 35, 36, 30, 32, 35, 35, 33, 33, 36, 35, 35, 33, 33, 35, 33, 33, 33, 35, 33, 33, 35, 33, 32, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:80:18873:1361", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 179, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 78, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTCTTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGT", - "alignedQuality": [36, 36, 36, 20, 36, 37, 37, 37, 37, 37, 38, 38, 38, 38, 38, 38, 36, 37, 38, 37, 38, 38, 38, 37, 38, 38, 36, 38, 38, 37, 30, 36, 36, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 36, 38, 38, 38, 38, 37, 37, 32, 37, 35, 37, 36, 37, 35, 37, 38, 35, 36, 36, 37, 36, 28, 35, 36, 36, 36, 35, 35, 35, 35, 37, 36, 36, 32, 35, 35, 36, 35, 36, 35, 28, 33, 33, 32, 36, 32, 35, 33, 35, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.2", - "fragmentName": "6141AAAXX100423:2:8:2627:21347", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 78, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 89, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 12, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GNCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTNCCAAGATGTA", - "alignedQuality": [33, 0, 33, 30, 33, 32, 33, 34, 34, 32, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 37, 30, 38, 35, 36, 38, 38, 38, 37, 38, 38, 32, 37, 37, 33, 37, 38, 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38, 38, 38, 38, 38, 38, 38, 38, 37, 24, 30, 29, 31, 27, 4, 22, 27, 25, 29, 31, 31, 24, 23, 22, 38, 36, 38, 38, 38, 32, 36, 36, 36, 36, 37, 38, 38, 38, 38, 35, 33, 38, 38, 38, 38, 38, 37, 38, 37, 38, 36, 33, 38, 37, 38, 38, 38, 37, 38, 35, 38, 34, 38, 36, 38, 33, 37, 37, 38, 35, 38, 38, 36, 38, 38, 37, 36, 36, 37, 37, 38, 36, 38, 33, 37, 36, 38, 37, 37, 37, 25, 33, 36, 28, 33, 25, 33, 33, 32, 17], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:37:11670:10031", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 117, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 79, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 9, - 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"613F1AAXX100423:8:107:6156:15270", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 116, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 85, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 9, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCTTATAATTAATTAGAGGTAAAATTACACATACAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGNATATCAAG", - "alignedQuality": [38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 35, 38, 38, 38, 35, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 20, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 32, 36, 36, 36, 36, 38, 38, 35, 38, 38, 38, 38, 38, 38, 25, 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"ATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAGGCACAT", - "alignedQuality": [36, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 35, 38, 38, 37, 38, 38, 38, 33, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 37, 38, 36, 38, 35, 36, 35, 37, 35, 37, 30, 37, 35, 38, 38, 36, 38, 38, 30, 37, 37, 30, 30, 34, 36, 35, 36, 38, 38, 36, 38, 37, 38, 37, 37, 38, 38, 32, 38, 37, 37, 35, 34, 36, 33, 25, 31, 33, 34, 36, 32, 32, 36, 38, 38, 36, 38, 38], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:82:6224:14395", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 95, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": 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"fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 96, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACNTTTAAAAT", - "alignedQuality": [38, 37, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 25, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 35, 38, 38, 38, 38, 37, 38, 38, 36, 37, 34, 37, 37, 35, 36, 36, 36, 36, 38, 38, 38, 38, 37, 36, 38, 36, 37, 38, 38, 38, 38, 38, 37, 37, 38, 36, 38, 37, 37, 35, 37, 38, 28, 37, 36, 38, 37, 38, 36, 36, 14, 33, 33, 34, 35, 33, 33, 33, 27, 27, 0, 14, 21, 25, 25, 27, 21, 26, 35], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:82:10630:4431", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 168, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 96, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACNTTTAAAAT", - "alignedQuality": [38, 38, 38, 38, 38, 36, 37, 38, 38, 38, 37, 36, 25, 37, 37, 38, 37, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 36, 38, 38, 38, 38, 38, 38, 37, 38, 37, 35, 38, 37, 37, 33, 36, 37, 38, 38, 38, 38, 36, 38, 37, 37, 38, 37, 38, 37, 38, 37, 38, 35, 36, 35, 37, 38, 36, 38, 36, 36, 37, 36, 36, 38, 36, 37, 36, 37, 33, 33, 37, 33, 28, 33, 34, 31, 27, 27, 0, 8, 18, 19, 22, 22, 18, 25, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:15:4665:11101", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 96, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTAGAGGAAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATATAAGGAGAGGGTATCAAGCACATTAAAATA", - "alignedQuality": [28, 20, 18, 30, 13, 7, 8, 12, 7, 21, 33, 14, 33, 33, 33, 33, 15, 20, 14, 18, 32, 16, 32, 32, 17, 12, 14, 12, 29, 26, 33, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:51:4149:16879", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 96, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": 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"readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:12:5463:17668", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 178, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 105, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATANACTTAAGA", - "alignedQuality": [38, 38, 38, 36, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 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"reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACG", - "alignedQuality": [37, 38, 30, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 36, 38, 38, 38, 38, 37, 38, 37, 38, 36, 38, 38, 38, 37, 38, 35, 37, 38, 38, 36, 36, 38, 35, 36, 38, 37, 36, 25, 34, 22, 32, 32, 34, 33, 34, 34, 36, 36, 35, 35, 36, 34, 36, 25, 36, 35, 36, 37, 35, 30, 33, 35, 35, 36, 36, 36, 35, 35], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:1:3424:18790", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, 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null, - "readGroupId": "6141A.2", - "fragmentName": "6141AAAXX100423:2:84:18546:20140", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 182, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 109, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTACGCATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCACAACATAAAA", - "alignedQuality": [35, 38, 37, 38, 35, 38, 36, 38, 38, 38, 35, 38, 38, 38, 37, 38, 38, 38, 32, 37, 38, 36, 38, 38, 35, 35, 36, 34, 36, 30, 33, 35, 35, 35, 34, 37, 37, 36, 20, 25, 36, 36, 36, 33, 36, 32, 33, 36, 32, 25, 32, 34, 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"fragmentLength": 179, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 113, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 95, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 6, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGGATCAAGCACATTAAAATAGCTTAAGACACCTTGCC", - "alignedQuality": [34, 34, 33, 34, 34, 28, 34, 34, 34, 30, 34, 34, 34, 34, 26, 26, 34, 34, 30, 21, 28, 28, 25, 20, 28, 34, 34, 34, 33, 34, 34, 34, 34, 25, 34, 34, 34, 25, 30, 33, 34, 34, 20, 25, 34, 23, 33, 32, 29, 30, 34, 33, 34, 34, 33, 33, 28, 33, 33, 20, 28, 21, 28, 17, 28, 10, 30, 33, 30, 18, 29, 24, 8, 16, 29, 30, 30, 30, 33, 12, 33, 32, 30, 33, 30, 19, 30, 33, 33, 33, 30, 28, 32, 28, 32, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:1:5113:6786", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 129, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 114, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 95, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 6, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACNCCTTGCCT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 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"supplementaryAlignment": false, - "alignedSequence": "AAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTNCCCTAGCC", - "alignedQuality": [38, 37, 38, 37, 38, 38, 38, 38, 37, 38, 35, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 35, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 37, 33, 38, 36, 37, 37, 37, 32, 37, 37, 37, 37, 35, 37, 37, 37, 36, 37, 37, 37, 37, 35, 36, 36, 35, 35, 36, 36, 35, 35, 36, 36, 35, 35, 33, 37, 36, 35, 23, 18, 0, 16, 24, 28, 22, 23, 23, 25, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:94:1337:1612", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 121, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGTACATTAAAATAGCTTAAGACACCTTGCCTAGCTACA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 36, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 37, 37, 38, 38, 36, 38, 36, 38, 37, 38, 35, 35, 37, 36, 35, 36, 34, 37, 33, 36, 32, 34, 35, 32, 33, 33, 33, 11, 34, 34, 36, 34, 34, 35, 33, 35, 35, 35, 35, 34, 26, 35, 34, 33, 20, 28, 30, 34, 34, 32, 27, 32, 32, 30, 23, 30, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:34:5579:10024", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 123, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTNAGCCACAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 36, 36, 12, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 35, 37, 37, 38, 37, 38, 37, 38, 33, 37, 38, 38, 37, 36, 37, 37, 38, 38, 35, 37, 37, 38, 37, 36, 37, 37, 37, 36, 37, 36, 37, 37, 36, 35, 37, 36, 37, 35, 34, 35, 34, 36, 35, 28, 27, 0, 20, 28, 25, 26, 27, 26, 25, 38], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:42:10426:16978", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 124, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCCATAGACCGGTGTAAAATCCATTAAACATTTACTTAAAATTTAAGGAGAGGGCATCAAGAAAATTAAAAAAGCTAAAGACACCTTGCCTCNCCACACCC", - "alignedQuality": [10, 21, 21, 10, 21, 16, 16, 16, 18, 16, 10, 23, 31, 22, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:69:17813:9329", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 203, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 125, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 91, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 9, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGGCCACACCC", - "alignedQuality": [38, 38, 37, 38, 38, 38, 36, 38, 38, 38, 38, 36, 38, 37, 37, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 37, 38, 37, 36, 37, 36, 37, 37, 35, 38, 38, 38, 37, 37, 38, 37, 37, 36, 36, 35, 36, 36, 38, 33, 36, 36, 36, 36, 36, 35, 37, 35, 36, 37, 36, 36, 36, 35, 35, 33, 35, 36, 34, 35, 33, 35, 35, 35, 35, 35, 33, 35, 35, 34, 34, 34, 34, 33, 34, 30, 29, 26, 22, 15, 28, 31, 31, 31, 31, 30, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:2:5743:8006", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 188, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 125, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGNCCACACCC", - "alignedQuality": [38, 36, 37, 38, 32, 35, 37, 38, 38, 35, 28, 34, 36, 36, 36, 35, 32, 12, 35, 32, 37, 37, 37, 37, 37, 38, 37, 38, 38, 38, 33, 32, 36, 35, 36, 35, 37, 35, 28, 35, 36, 30, 28, 36, 36, 37, 35, 37, 28, 35, 36, 30, 35, 28, 34, 36, 30, 33, 36, 36, 36, 38, 38, 38, 36, 37, 37, 33, 37, 37, 36, 32, 37, 35, 34, 37, 37, 36, 25, 36, 37, 37, 28, 36, 36, 20, 30, 34, 30, 25, 20, 14, 0, 8, 25, 30, 30, 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2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:73:7585:2657", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 190, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 127, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCNCCACCCCC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 37, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 37, 32, 37, 37, 37, 38, 38, 37, 38, 38, 38, 35, 38, 35, 37, 38, 38, 36, 36, 37, 33, 37, 37, 38, 38, 38, 37, 33, 38, 38, 36, 38, 30, 35, 36, 32, 36, 34, 30, 36, 26, 33, 0, 5, 24, 30, 29, 29, 30, 17, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:84:9190:20996", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 127, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - 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"fragmentLength": 179, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 128, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCGTAGCCACACCCCCAC", - "alignedQuality": [33, 30, 33, 36, 36, 33, 32, 28, 36, 35, 36, 36, 30, 36, 36, 35, 36, 36, 36, 33, 36, 36, 35, 36, 32, 35, 32, 32, 35, 35, 34, 32, 32, 30, 36, 25, 35, 36, 36, 35, 35, 33, 36, 36, 36, 36, 36, 36, 36, 33, 17, 32, 30, 34, 32, 32, 32, 32, 32, 32, 36, 36, 32, 33, 36, 28, 35, 35, 35, 28, 32, 20, 35, 34, 35, 32, 25, 32, 28, 34, 20, 8, 9, 11, 27, 4, 18, 26, 17, 23, 32, 29, 33, 30, 32, 35, 18, 30, 21, 29, 29], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:96:1093:15921", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 186, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 128, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 60, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 41, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "NAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAANATAGCTTAAGACNNCTTGCCTAGCNNNNCCCCNAC", - "alignedQuality": [0, 26, 23, 20, 21, 25, 25, 23, 25, 24, 33, 33, 33, 33, 33, 29, 32, 32, 32, 32, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 2, 2, 2, 2, 0, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:54:6541:15697", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 188, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 129, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGACCGGTGTAAAATCCATTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACG", - "alignedQuality": [32, 27, 10, 29, 28, 26, 31, 25, 26, 26, 35, 35, 35, 35, 35, 35, 35, 12, 35, 35, 35, 33, 35, 35, 32, 28, 30, 35, 35, 35, 36, 36, 36, 36, 35, 25, 33, 33, 34, 16, 32, 34, 32, 34, 34, 36, 36, 25, 36, 36, 36, 36, 36, 35, 35, 32, 36, 36, 36, 35, 36, 36, 36, 35, 36, 36, 36, 30, 36, 36, 36, 36, 36, 36, 34, 36, 36, 36, 36, 35, 36, 30, 36, 33, 33, 36, 34, 32, 36, 36, 36, 36, 36, 36, 36, 35, 35, 34, 32, 29, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:10:2043:20748", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 92, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 129, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - 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"fragmentLength": 180, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 131, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTACCTAGCCACACCCNCACGGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 38, 38, 36, 38, 38, 38, 38, 37, 35, 37, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 35, 38, 37, 38, 36, 37, 34, 36, 37, 38, 38, 37, 38, 38, 35, 36, 34, 36, 30, 32, 34, 34, 34, 34, 36, 34, 36, 36, 36, 33, 33, 33, 2, 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"referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CGGTGNAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCNCGGGAC", - "alignedQuality": [34, 34, 34, 34, 34, 0, 35, 35, 35, 35, 35, 35, 35, 35, 35, 38, 38, 38, 36, 38, 38, 37, 38, 38, 35, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 37, 38, 38, 38, 36, 37, 38, 38, 38, 38, 38, 37, 38, 38, 36, 38, 35, 37, 37, 38, 37, 37, 37, 37, 30, 36, 36, 36, 36, 37, 37, 35, 36, 37, 38, 35, 36, 36, 35, 37, 35, 34, 35, 34, 2, 0, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:20:2751:5355", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 204, - "readNumber": 1, - 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"fragmentName": "6141AAAXX100423:2:102:13963:2305", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 133, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 52, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 49, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CGGTGGAAAATCCCTTAAACATTTACTTAAAATTTATGGAGAGGGTATCAAGTACATTAAAATAGCTTAAGACAACTTGCCTAGCCACACCAGCAACGACC", - "alignedQuality": [17, 22, 20, 17, 17, 17, 26, 22, 28, 23, 21, 11, 27, 22, 21, 11, 27, 28, 31, 7, 21, 15, 14, 21, 8, 21, 21, 21, 28, 13, 8, 32, 17, 15, 21, 32, 9, 21, 26, 32, 27, 33, 17, 10, 17, 33, 30, 27, 16, 32, 21, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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"613F0AAXX100423:1:55:11240:18646", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 146, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTTAAACATTTACTTAAAATTTAAGGAGAGGATATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAA", - "alignedQuality": [37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 27, 30, 36, 36, 36, 36, 36, 36, 36, 30, 34, 36, 36, 37, 37, 38, 38, 38, 38, 35, 38, 38, 38, 38, 35, 38, 37, 35, 37, 35, 38, 37, 37, 36, 38, 38, 38, 37, 38, 35, 38, 37, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 26, 34, 25, 33, 34, 34, 34, 33, 36, 36, 34, 34, 32, 36, 25, 36, 33, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:33:19510:10053", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 148, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCANGTGATAAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 35, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 37, 38, 38, 38, 38, 35, 38, 38, 37, 37, 38, 38, 37, 36, 38, 36, 37, 37, 37, 38, 35, 38, 36, 36, 37, 36, 34, 38, 34, 34, 34, 36, 37, 28, 37, 34, 35, 29, 27, 0, 18, 21, 22, 23, 22, 20, 18, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:23:19257:14002", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 150, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTNATAAATAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 38, 38, 38, 38, 38, 38, 38, 34, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 37, 36, 38, 34, 34, 36, 33, 34, 35, 34, 35, 32, 36, 32, 35, 35, 34, 30, 29, 0, 25, 28, 23, 25, 26, 26, 22, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:103:7190:1200", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 131, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 150, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCAGATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTNATAAATAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 34, 38, 38, 38, 38, 36, 38, 36, 36, 11, 36, 36, 35, 35, 35, 34, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 37, 38, 36, 37, 35, 37, 36, 37, 36, 38, 37, 37, 36, 37, 36, 35, 35, 35, 34, 33, 34, 33, 34, 33, 35, 35, 34, 34, 34, 35, 34, 33, 30, 25, 0, 28, 25, 25, 25, 20, 24, 20, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:106:16259:6089", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 131, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 150, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTNATAAATAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 34, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 37, 37, 38, 38, 38, 38, 38, 36, 36, 38, 38, 36, 38, 34, 35, 36, 35, 36, 35, 37, 35, 36, 36, 35, 31, 30, 0, 28, 28, 25, 26, 29, 21, 29, 35], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:12:6338:18527", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 177, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 151, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGNATAAATAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 38, 38, 38, 38, 38, 38, 38, 35, 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false, - "supplementaryAlignment": false, - "alignedSequence": "CATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGANACATATTA", - "alignedQuality": [38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 37, 38, 38, 38, 36, 38, 37, 38, 37, 36, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 35, 37, 38, 35, 38, 38, 38, 36, 38, 35, 38, 38, 38, 38, 37, 38, 36, 38, 36, 38, 38, 36, 38, 38, 35, 38, 36, 36, 35, 35, 38, 35, 37, 36, 36, 36, 35, 35, 32, 30, 31, 0, 29, 6, 25, 28, 30, 26, 21, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:110:19637:9034", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 154, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 152, - "reverseStrand": false - 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true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 153, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTTACTAAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAAATATTAA", - "alignedQuality": [37, 37, 37, 37, 37, 37, 37, 20, 37, 37, 35, 35, 37, 37, 37, 37, 35, 37, 37, 37, 37, 37, 37, 37, 37, 35, 36, 37, 37, 36, 37, 37, 37, 37, 37, 37, 37, 37, 36, 37, 37, 34, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 36, 36, 35, 37, 37, 35, 35, 37, 37, 37, 36, 35, 34, 34, 34, 28, 20, 35, 33, 36, 33, 37, 30, 36, 36, 32, 36, 30, 36, 31, 33, 28, 31, 18, 31, 31, 30, 32, 25, 30], 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"alignment": { - "position": { - "referenceName": "chrM", - "position": 228, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CGGGACTCAGCAGTGATAAATATTAAGCAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGGCAGCCACCGCGGTNCTACGA", - "alignedQuality": [38, 38, 38, 32, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 35, 37, 36, 37, 38, 37, 37, 36, 38, 38, 36, 37, 32, 37, 36, 37, 34, 33, 37, 37, 30, 36, 36, 34, 34, 36, 36, 38, 32, 38, 36, 36, 35, 36, 38, 38, 37, 32, 35, 36, 36, 32, 36, 37, 37, 35, 33, 32, 35, 36, 36, 32, 33, 28, 31, 25, 5, 28, 25, 23, 25, 31, 32, 32, 31, 32, 32, 31, 30, 2, 0, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, 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"numberReads": 2, - "fragmentLength": 184, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 252, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGCAATAAACGAAAGTTTGACTAAGTTATACATCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 32, 37, 37, 35, 36, 29, 16, 5, 8, 31, 12, 20, 7, 27, 25, 35, 31, 35, 35, 35, 36, 38, 35, 35, 38, 38, 37, 35, 36, 38, 38, 38, 34, 33, 38, 36, 33, 25, 36, 35, 38, 38, 37, 33, 34, 35, 35, 35, 36, 37, 28, 34, 34, 36, 33, 36, 36, 33, 34, 36, 25, 32, 34, 34, 28, 36, 33, 32, 33, 36, 36, 36, 35, 35, 31, 20], - "nextMatePosition": null, - "info": {} 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"properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 259, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACCAATTATCTTCGGCGACACA", - "alignedQuality": [38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 37, 38, 38, 35, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 37, 36, 37, 38, 36, 37, 38, 38, 36, 37, 38, 38, 36, 37, 35, 35, 32, 37, 36, 35, 36, 36, 36, 36, 34, 35, 36, 36, 36, 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"id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:10:16469:12729", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 181, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 261, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 94, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGNGTAAAACG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 37, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 35, 38, 38, 36, 37, 38, 38, 38, 38, 35, 38, 38, 36, 37, 36, 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"secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGCCATACGATTAACCCAAACTAATTATCTTCGGCGTANAACGTGTC", - "alignedQuality": [25, 18, 29, 17, 21, 28, 28, 30, 28, 28, 34, 35, 35, 33, 35, 33, 25, 35, 30, 30, 34, 35, 33, 33, 34, 29, 29, 27, 27, 34, 35, 35, 30, 34, 35, 25, 33, 30, 20, 29, 34, 29, 32, 31, 32, 33, 28, 33, 33, 33, 34, 33, 32, 30, 33, 28, 8, 30, 30, 30, 30, 33, 32, 30, 30, 30, 30, 28, 30, 33, 31, 33, 12, 32, 31, 30, 31, 20, 20, 30, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.7", - "fragmentName": "6141AAAXX100423:7:14:7355:6147", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 269, - "reverseStrand": false 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"fragmentLength": 182, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 269, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACNATGTCAAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 30, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 36, 38, 38, 38, 37, 38, 35, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 37, 38, 38, 38, 35, 38, 38, 36, 38, 37, 35, 32, 37, 36, 35, 37, 36, 37, 36, 36, 36, 36, 36, 35, 37, 37, 37, 35, 37, 37, 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"fragmentName": "613F1AAXX100423:1:53:16999:6279", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 117, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 282, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGCCAACTATAANATAAATAA", - "alignedQuality": [36, 35, 32, 33, 36, 30, 36, 36, 35, 33, 28, 36, 25, 36, 36, 30, 30, 35, 35, 28, 25, 36, 36, 33, 36, 25, 36, 36, 35, 36, 37, 37, 37, 37, 32, 33, 35, 32, 32, 28, 29, 25, 29, 31, 29, 25, 31, 34, 35, 30, 18, 14, 20, 26, 20, 34, 34, 33, 32, 34, 36, 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"alignedQuality": [0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.3", - "fragmentName": "613F0AAXX100423:3:113:19539:6361", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 289, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 100, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 1, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTACAACGTGTCAACTATAAATAAATAAATAGAATT", - "alignedQuality": [37, 37, 35, 36, 37, 37, 37, 36, 37, 37, 37, 38, 37, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 35, 38, 38, 37, 33, 35, 37, 37, 37, 35, 32, 37, 37, 32, 25, 36, 36, 36, 37, 35, 38, 38, 38, 38, 37, 38, 37, 38, 33, 37, 38, 38, 35, 38, 36, 28, 37, 38, 32, 31, 34, 12, 32, 20, 30, 35, 28, 30, 36, 33, 36, 36, 28, 32, 35, 36, 36, 34, 25, 33, 30, 32, 12, 25, 35, 34, 23, 24, 31, 21, 29, 14, 30, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:4:18322:4265", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 289, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 99, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 2, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGGGTTGGTAAATTTCGTGCCAGCCACCGCGTTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATA", - "alignedQuality": [38, 38, 33, 36, 38, 38, 37, 38, 36, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 36, 38, 38, 30, 33, 33, 25, 30, 28, 30, 36, 36, 34, 32, 34, 37, 38, 37, 38, 38, 28, 31, 36, 36, 35, 37, 38, 37, 35, 38, 37, 38, 35, 33, 38, 36, 37, 32, 35, 36, 37, 33, 37, 30, 36, 37, 36, 36, 35, 25, 32, 32, 32, 32, 32, 28, 24, 29, 34, 29, 20, 26, 31, 28, 23, 30, 36, 36, 30, 30, 36, 34, 33, 33, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:85:2088:11538", - "properPlacement": 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"alignedSequence": "GTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAAAATTAAA", - "alignedQuality": [35, 36, 36, 36, 33, 36, 36, 36, 36, 36, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 35, 37, 33, 37, 30, 35, 34, 30, 28, 31, 36, 33, 36, 36, 33, 37, 37, 37, 36, 37, 35, 37, 37, 36, 35, 37, 37, 37, 30, 37, 36, 37, 33, 37, 36, 37, 35, 36, 36, 32, 33, 36, 32, 31, 33, 36, 33, 35, 36, 36, 30, 35, 31, 30, 35, 35, 33, 35, 33, 36, 35, 35, 33, 31, 36, 32, 31, 31, 33, 35, 26, 25, 33, 9, 30, 20, 23, 25, 30, 30, 37], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.7", - "fragmentName": "613F0AAXX100423:7:117:8522:19026", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 292, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - 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"6141AAAXX100423:2:105:16229:19746", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 161, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 454, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTCATCTATAATACACGACAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAACACTATTATCC", - "alignedQuality": [36, 36, 36, 36, 36, 30, 37, 37, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 36, 37, 38, 38, 38, 37, 35, 38, 37, 35, 35, 37, 37, 36, 36, 37, 36, 33, 36, 31, 38, 36, 37, 38, 38, 35, 35, 35, 36, 33, 34, 36, 34, 35, 34, 34, 34, 36, 20, 34, 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"reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTATAATACACGACAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAACACTATTTGCCAGAGA", - "alignedQuality": [34, 34, 28, 34, 34, 25, 34, 35, 35, 35, 30, 35, 36, 20, 36, 35, 20, 28, 35, 35, 33, 35, 28, 35, 30, 36, 20, 36, 36, 12, 32, 30, 32, 34, 28, 25, 35, 30, 25, 30, 34, 30, 32, 34, 25, 33, 33, 26, 36, 28, 20, 34, 20, 20, 12, 34, 20, 28, 34, 34, 34, 28, 25, 25, 30, 25, 34, 12, 25, 34, 36, 36, 36, 35, 33, 36, 25, 36, 20, 28, 25, 25, 31, 29, 31, 9, 32, 30, 32, 32, 34, 28, 33, 34, 35, 31, 20, 20, 35, 33, 20], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:56:15784:12936", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 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"id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:61:13484:16071", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 195, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 460, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATAATACACGACAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAAAACTATTTGGCCAGAGA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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"alignedSequence": "TATAATACACGACAGCTAAGACCCAAACCGGGATTAGATACTCCACTATGCTTAACCCTAAACATAAATAATTTAATAAAAAAAACCAAAAAGCCAAGCAA", - "alignedQuality": [20, 12, 15, 28, 22, 15, 22, 22, 28, 25, 19, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:68:16059:2332", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 230, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 463, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - 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"alignment": { - "position": { - "referenceName": "chrM", - "position": 465, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 94, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TACACGACAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAAAACTATTTGCCAGNGAACTACT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 38, 36, 38, 38, 37, 37, 38, 38, 36, 36, 37, 36, 35, 36, 36, 36, 37, 37, 37, 36, 37, 37, 35, 36, 36, 36, 35, 36, 36, 33, 36, 36, 36, 36, 35, 36, 36, 35, 35, 35, 36, 34, 35, 34, 34, 32, 30, 34, 35, 35, 33, 35, 30, 35, 34, 32, 34, 0, 32, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, 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"properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 468, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACGACAGCTAATACCCAAACTGGGATTAGATACCACAATATGCTTAGCCATAAACCTACATAATTAAATCTAACAAAACTATTTGCCAGAGAAATACACGC", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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"fragmentName": "613F0AAXX100423:2:77:10629:3640", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 177, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 473, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAAAACTACTTGCCAGAGAACTACTAGCCATAG", - "alignedQuality": [38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 37, 38, 36, 38, 37, 38, 38, 38, 38, 38, 37, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 34, 38, 36, 36, 36, 37, 36, 36, 36, 36, 36, 36, 37, 36, 35, 37, 33, 35, 36, 37, 37, 36, 37, 35, 37, 30, 36, 36, 36, 37, 36, 38, 37, 36, 36, 35, 34, 34, 35, 37, 37, 25, 34, 35, 35, 34, 35, 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"fragmentName": "6141AAAXX100423:1:15:2174:3440", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 151, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 528, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 70, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 31, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAATTAAATTNAACAAAACTATTTGCCAGAGAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGGAATTTTTTATCCCCCTCAAGTNNCNGNTGN", - "alignedQuality": [38, 38, 38, 38, 38, 35, 35, 35, 35, 35, 0, 35, 35, 35, 35, 32, 33, 28, 32, 34, 36, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 35, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 35, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 36, 37, 35, 36, 37, 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"alignment": { - "position": { - "referenceName": "chrM", - "position": 540, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 85, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 16, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACAAAACTATTTGCCAGAGAACAACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAAACCAAAAA", - "alignedQuality": [37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 26, 28, 4, 25, 21, 22, 27, 25, 28, 23, 37, 37, 33, 37, 37, 37, 37, 37, 37, 37, 37, 37, 36, 37, 37, 36, 35, 37, 37, 37, 37, 32, 37, 37, 37, 36, 36, 36, 14, 33, 30, 30, 33, 34, 28, 34, 33, 33, 33, 33, 25, 32, 28, 32, 20, 29, 28, 28, 28, 25, 28, 10, 30, 25, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - 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"readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 547, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 91, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 10, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATTTGCCAGAGAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCCTCTAGAGGAGCCTGTTCTATAATCGATCANCAAACAC", - "alignedQuality": [37, 35, 37, 37, 35, 37, 35, 33, 37, 37, 37, 35, 37, 35, 37, 37, 37, 37, 30, 32, 37, 37, 37, 30, 28, 37, 37, 37, 37, 37, 37, 35, 37, 37, 37, 30, 35, 37, 37, 35, 37, 37, 34, 37, 37, 28, 30, 36, 36, 36, 35, 30, 31, 30, 33, 33, 31, 28, 31, 31, 25, 33, 20, 12, 32, 28, 31, 32, 25, 28, 36, 33, 33, 36, 36, 36, 30, 33, 31, 36, 25, 28, 11, 30, 30, 30, 30, 30, 30, 30, 19, 18, 26, 0, 19, 26, 20, 32, 2, 2, 2], 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15, 28, 20, 21, 12, 22, 18, 22, 29, 30, 30, 22, 27, 28, 30, 10, 30, 30, 10, 30, 28, 28, 30, 19, 20, 14, 32, 14, 22, 8, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:83:13635:2428", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 156, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 555, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 98, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 3, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - 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"mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGAGAACTACTAGCCATAGATTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCCACCTCA", - "alignedQuality": [37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 37, 37, 35, 38, 35, 38, 37, 38, 37, 38, 35, 37, 36, 38, 38, 33, 37, 36, 38, 37, 38, 34, 37, 36, 38, 37, 36, 35, 36, 30, 34, 37, 37, 36, 37, 33, 37, 33, 33, 37, 37, 33, 37, 35, 35, 36, 35, 34, 35, 33, 35, 17], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.6", - "fragmentName": "6141AAAXX100423:6:68:11061:18765", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 555, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGAGAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAAACCCCACCAAACACA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 37, 37, 34, 28, 29, 29, 32, 34, 20, 30, 24, 29, 11, 29, 20, 28, 30, 29, 20, 34, 34, 30, 36, 31, 29, 20, 30, 27, 25, 26, 30, 26, 26, 20, 29, 26, 30, 26, 12, 32, 29, 32, 28, 32, 32, 12, 27, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:30:2115:13936", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 181, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 556, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 48, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 53, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GATAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGATCTATAAACGATAAACCCCCCTCACCCTCCC", - "alignedQuality": [20, 23, 9, 9, 9, 22, 15, 23, 30, 22, 31, 29, 29, 32, 31, 32, 10, 31, 19, 22, 17, 24, 10, 13, 23, 25, 23, 25, 23, 23, 10, 23, 18, 15, 30, 32, 14, 23, 22, 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"alignedSequence": "AGAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTAAGATCGG", - "alignedQuality": [37, 32, 37, 37, 37, 37, 37, 33, 35, 37, 37, 30, 35, 37, 30, 32, 36, 32, 35, 36, 33, 36, 33, 36, 35, 36, 35, 28, 35, 30, 37, 37, 37, 37, 33, 37, 28, 32, 32, 37, 28, 32, 35, 35, 34, 36, 36, 36, 28, 36, 28, 36, 25, 28, 35, 36, 25, 28, 34, 30, 36, 36, 25, 36, 36, 34, 25, 32, 30, 33, 31, 30, 34, 32, 32, 31, 30, 25, 20, 28, 28, 28, 28, 30, 32, 28, 33, 28, 33, 33, 33, 31, 32, 28, 33, 33, 33, 30, 33, 31, 20], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:100:10105:13386", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 72, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 558, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ 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"readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 559, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 100, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 1, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATACACCCCGCTCTACCTCACCAC", - "alignedQuality": [38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 36, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 36, 38, 36, 32, 30, 34, 34, 33, 35, 36, 38, 37, 36, 38, 35, 36, 38, 38, 38, 37, 38, 37, 36, 34, 34, 34, 34, 34, 27, 36, 34, 34, 32, 35, 30, 34, 30, 35, 35, 34, 35, 37, 35, 37, 35, 37, 31, 36, 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"fragmentName": "613F1AAXX100423:3:118:3666:19612", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 149, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 570, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTGCTTGCTAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 38, 38, 35, 38, 37, 38, 30, 38, 38, 38, 38, 37, 38, 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"AAACTCAAAGGACTTGGCGGTACTTTATATCCCTCTAGAGGAGGCTGTTTTATTATTGATAAACCCCGCTCTACCCCACCCTCTCTTTCCTCTTGGGGTTT", - "alignedQuality": [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 33, 36, 36, 36, 36, 36, 36, 36, 36, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:92:13479:6652", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 578, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCCTCTCTTGCTAATTCAGCCTA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 38, 38, 38, 38, 37, 38, 35, 38, 37, 36, 37, 38, 36, 36, 36, 36, 38, 35, 33, 33, 37, 37, 38, 35, 37, 36, 37, 36, 36, 35, 37, 36, 32, 36, 37, 36, 36, 36, 37, 36, 35, 35, 35, 34, 35, 34, 35, 33, 35, 34, 35, 34, 34, 34, 35, 34, 7, 31, 33, 31, 31, 30, 30, 31, 31, 31, 12, 34, 34, 34, 32, 20, 25, 31, 28, 31, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.7", - "fragmentName": "613F0AAXX100423:7:25:8160:1927", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 168, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 579, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGCTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTAT", - "alignedQuality": [28, 36, 30, 33, 36, 35, 35, 36, 36, 28, 32, 36, 36, 36, 36, 28, 35, 35, 36, 35, 28, 30, 28, 32, 35, 36, 36, 32, 36, 36, 35, 36, 34, 36, 33, 36, 36, 36, 28, 30, 20, 20, 25, 34, 31, 36, 32, 32, 33, 33, 35, 28, 20, 35, 34, 34, 30, 34, 29, 20, 34, 30, 17, 32, 20, 34, 32, 33, 11, 31, 29, 12, 32, 29, 28, 11, 30, 31, 31, 30, 28, 29, 29, 29, 26, 9, 26, 32, 20, 12, 29, 25, 28, 30, 29, 32, 20, 24, 32, 30, 20], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:71:18818:12965", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 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"id": null, - "readGroupId": "613F0.6", - "fragmentName": "613F0AAXX100423:6:70:19643:9290", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 579, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "DELETE", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 2, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 2, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 3, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 1, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": 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"fragmentName": "6141AAAXX100423:4:58:19645:7588", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 179, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 583, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 75, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 26, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAAACCCGCTCTACCTCACCATCTCTTGCTAATTCTACATCTCGTC", - "alignedQuality": [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 32, 32, 30, 32, 35, 33, 23, 29, 28, 29, 17, 31, 29, 29, 28, 34, 20, 31, 31, 32, 35, 28, 34, 20, 34, 28, 29, 26, 31, 21, 28, 18, 28, 15, 30, 30, 20, 30, 29, 30, 30, 34, 33, 9, 30, 34, 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2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:6:19748:13634", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 584, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAAGGACTTGGCGGTACTTTTTATCCATCTAGAGGAGCCCGTTCTATTATAGATAAACCCCCCTCTCCCTCACCCTCTCTTTCTAATTTCAGTCATCCACC", - "alignedQuality": [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 30, 16, 18, 22, 28, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:111:18973:2067", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 168, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 585, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGGACTTGGCGGTACTTTATATCCATCTAGGGGAGCCTTTTCTATAATCTATAAACCCCTCTCTACCTCACCATCTCTTTCTAATTCTGTGTAGTGTTAT", - "alignedQuality": [32, 25, 32, 32, 30, 32, 34, 34, 25, 20, 31, 12, 34, 29, 31, 31, 26, 28, 31, 31, 35, 12, 28, 35, 35, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:101:7895:3365", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 178, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 586, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTNATATACCG", - "alignedQuality": [38, 38, 37, 37, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 38, 38, 38, 32, 38, 38, 38, 38, 38, 38, 36, 38, 32, 37, 38, 37, 38, 38, 38, 35, 37, 38, 38, 38, 36, 35, 38, 38, 38, 38, 38, 38, 38, 32, 38, 37, 36, 37, 37, 38, 37, 37, 37, 35, 36, 35, 35, 37, 38, 32, 35, 36, 36, 38, 36, 35, 33, 35, 36, 36, 35, 36, 34, 35, 28, 34, 33, 26, 25, 0, 16, 27, 25, 23, 25, 22, 25, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:104:4607:5279", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 587, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 94, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GAACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 32, 38, 36, 38, 37, 37, 37, 37, 34, 38, 37, 38, 37, 36, 37, 37, 32, 37, 36, 38, 38, 28, 37, 36, 37, 38, 37, 36, 36, 33, 38, 30, 37, 36, 37, 37, 35, 32, 37, 36, 35, 37, 36, 33, 36, 37, 36, 30, 36, 32, 35, 25, 33, 30, 37, 35, 35, 36, 31, 37, 33, 28, 35, 35, 35, 32, 36, 35, 32, 25, 30, 25, 30, 30, 30, 12, 28, 30, 31, 31, 28, 30, 31, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:66:13672:2605", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 588, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 24, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 77, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GACTTGGCGGTACCTTTTTTCCATTTCCCAGTGCCCGTTCTCTAATCTGGAAACCCCGCGCTGCCGCCTCACCACTTGACGCTTCATCCTATCTACTTGCC", - "alignedQuality": [30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.2", - "fragmentName": "6141AAAXX100423:2:10:13217:15205", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 590, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 16, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 18, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] 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"ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTTGGCGGTACTTTTTATCCATCTAGAGGGGCCTGTTCTTTTATCCATAAACCCCCCCCCTCCCCCCCCTCCTCTTCCTATTTAACCCCTATCACACCACC", - "alignedQuality": [32, 32, 32, 32, 31, 32, 31, 31, 22, 28, 13, 18, 29, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:23:16337:3840", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 132, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 592, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 70, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 31, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATAGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATTATCACTATTT", - "alignedQuality": [35, 33, 28, 35, 35, 35, 33, 35, 28, 35, 35, 35, 28, 35, 32, 35, 35, 25, 35, 32, 25, 34, 30, 34, 32, 29, 12, 10, 25, 20, 32, 34, 32, 30, 34, 35, 35, 28, 35, 28, 32, 34, 11, 25, 28, 34, 34, 20, 34, 34, 35, 28, 34, 11, 26, 7, 33, 25, 26, 29, 12, 32, 34, 34, 34, 34, 25, 34, 32, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:10:14689:13457", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 98, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 592, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATAGA", - "alignedQuality": [37, 38, 38, 38, 38, 38, 37, 35, 38, 36, 38, 36, 38, 38, 37, 38, 38, 35, 33, 37, 37, 38, 38, 38, 38, 37, 35, 30, 36, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 28, 38, 38, 37, 35, 38, 36, 35, 37, 30, 33, 38, 37, 36, 37, 38, 34, 30, 37, 37, 36, 36, 36, 35, 36, 36, 33, 36, 36, 38, 37, 35, 33, 20, 37, 35, 30, 33, 34, 33, 33, 37, 35, 38, 35, 33, 36, 36, 25, 35, 32, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:119:3666:12939", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 98, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 596, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGA", - "alignedQuality": [29, 32, 26, 30, 26, 32, 32, 26, 34, 32, 34, 34, 30, 26, 34, 29, 32, 34, 32, 29, 31, 29, 29, 16, 21, 26, 25, 26, 32, 24, 32, 34, 34, 30, 32, 28, 34, 30, 32, 30, 28, 28, 28, 32, 26, 30, 32, 32, 23, 26, 18, 14, 28, 26, 33, 32, 19, 23, 15, 30, 34, 34, 34, 30, 34, 28, 34, 26, 34, 34, 26, 30, 34, 28, 32, 34, 34, 33, 30, 33, 33, 33, 28, 34, 28, 33, 33, 33, 23, 30, 34, 33, 33, 33, 25, 33, 33, 33, 25, 32, 19], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:52:12141:9678", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 177, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 597, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCANACTTCAGC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 36, 38, 37, 38, 36, 36, 36, 37, 36, 37, 36, 36, 36, 37, 36, 36, 36, 36, 35, 36, 36, 35, 36, 35, 35, 36, 36, 36, 36, 36, 36, 33, 34, 35, 29, 24, 0, 6, 27, 21, 26, 23, 19, 23, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:56:16917:3099", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 597, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 54, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 47, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTACTTTATATCCCTCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCTACCTTCCGC", - "alignedQuality": [34, 33, 34, 34, 34, 34, 30, 34, 32, 21, 26, 23, 32, 10, 26, 18, 27, 26, 24, 32, 34, 32, 18, 12, 23, 27, 29, 31, 25, 34, 34, 33, 28, 34, 32, 34, 34, 34, 30, 30, 30, 23, 32, 8, 30, 28, 28, 28, 28, 34, 28, 28, 28, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:73:4540:14300", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 181, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 600, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCACAC", - "alignedQuality": [38, 38, 38, 35, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 35, 37, 35, 35, 34, 37, 35, 37, 35, 35, 36, 33, 30, 35, 35, 36, 34, 32, 32, 35, 34, 31, 34, 32, 34, 28, 20, 32, 35, 34, 32, 35, 34, 35, 35, 35, 35, 20, 32, 32, 34, 32, 32, 31, 30, 30, 32, 25, 32, 32, 32, 8, 32, 30], - 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"duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 152, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 606, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCANAACCCTAA", - "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 38, 37, 37, 36, 37, 34, 38, 36, 36, 37, 37, 37, 36, 33, 36, 36, 36, 30, 36, 33, 33, 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"alignedSequence": "AGAGGAGCCTGTTCTATAATCGATAAACCCCGCNCTACCTNACCATCNNNTNNNNNNNNANNNNNNNNNNNGCNANNNNCAGCAAACCCTAAAAAGGTATT", - "alignedQuality": [35, 33, 38, 38, 36, 38, 38, 36, 38, 37, 38, 38, 35, 38, 38, 36, 38, 38, 37, 37, 38, 38, 38, 36, 35, 37, 35, 38, 37, 35, 30, 34, 31, 0, 34, 32, 30, 30, 30, 30, 0, 30, 29, 29, 32, 2, 2, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 0, 2, 0, 0, 0, 0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:31:1155:13344", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": 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null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:28:2836:7773", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 188, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 622, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATNAAAGTAAG", - "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 33, 38, 38, 38, 36, 36, 38, 38, 37, 37, 36, 38, 38, 37, 38, 33, 36, 38, 38, 33, 36, 38, 36, 38, 38, 30, 36, 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"operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTACAAAGGTATTAAAGTAAGCAAAAG", - "alignedQuality": [35, 35, 35, 35, 30, 33, 34, 25, 36, 36, 36, 36, 28, 28, 33, 25, 33, 25, 34, 30, 33, 33, 36, 32, 28, 36, 33, 36, 31, 36, 34, 30, 36, 34, 33, 36, 30, 36, 32, 36, 36, 33, 33, 33, 36, 32, 25, 32, 35, 25, 31, 29, 28, 29, 34, 33, 34, 32, 25, 32, 30, 30, 31, 33, 33, 25, 28, 33, 33, 28, 36, 36, 33, 25, 31, 31, 31, 19, 28, 28, 17, 23, 27, 22, 26, 32, 32, 31, 30, 25, 33, 31, 33, 30, 31, 25, 25, 31, 31, 33, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:65:18419:16546", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { 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"properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 186, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 628, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 95, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 6, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATAATCGATAAACTCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAG", - "alignedQuality": [37, 37, 37, 37, 37, 32, 37, 37, 37, 37, 37, 37, 37, 36, 20, 36, 36, 36, 36, 36, 37, 37, 37, 36, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 35, 37, 33, 37, 35, 37, 35, 36, 36, 37, 37, 37, 37, 37, 37, 36, 20, 35, 32, 36, 37, 36, 37, 35, 33, 33, 28, 36, 36, 33, 37, 37, 36, 36, 36, 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null, - "readGroupId": "6141A.1", - "fragmentName": "6141AAAXX100423:1:34:5553:8767", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 641, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCCCGCTCTACCTCACCATCTATTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAANATAAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 37, 38, 34, 7, 31, 32, 34, 34, 34, 32, 31, 32, 37, 36, 33, 36, 36, 38, 36, 37, 37, 37, 36, 37, 35, 35, 33, 36, 37, 33, 35, 36, 35, 37, 37, 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null, - "readGroupId": "6141A.1", - "fragmentName": "6141AAAXX100423:1:50:13981:3364", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 134, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 644, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATNTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAAC", - "alignedQuality": [35, 32, 35, 33, 36, 33, 36, 35, 36, 33, 32, 32, 36, 36, 36, 32, 32, 36, 36, 33, 29, 25, 34, 32, 34, 36, 30, 35, 33, 35, 28, 30, 35, 35, 32, 35, 30, 35, 35, 12, 35, 30, 34, 34, 33, 24, 0, 22, 26, 33, 29, 28, 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"alignment": { - "position": { - "referenceName": "chrM", - "position": 648, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 73, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 28, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAACAAGTGATTAAAGTAAGCAAAAGACTCAAACATAAAAACGTTA", - "alignedQuality": [26, 23, 18, 26, 9, 21, 17, 17, 17, 17, 31, 22, 21, 17, 15, 17, 17, 15, 31, 30, 10, 15, 19, 14, 22, 33, 33, 26, 23, 30, 17, 26, 15, 26, 15, 27, 25, 33, 33, 16, 33, 24, 33, 33, 33, 20, 16, 17, 33, 33, 14, 33, 22, 17, 33, 33, 14, 9, 22, 33, 17, 17, 5, 14, 14, 25, 32, 9, 18, 32, 32, 33, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": 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"referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAACGNATAGGTCA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 34, 38, 38, 38, 38, 36, 37, 38, 37, 38, 38, 36, 38, 33, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 30, 38, 37, 35, 26, 31, 0, 20, 29, 29, 20, 22, 16, 29, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:61:19310:6422", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - 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false, - "supplementaryAlignment": false, - "alignedSequence": "ACCATCTCTAGCTAATTCCGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGAATTAAAGAAAGCAAAAGACTCCAACAACAAAAAGTGAGTACAAG", - "alignedQuality": [31, 32, 24, 21, 16, 30, 9, 12, 30, 9, 19, 17, 8, 17, 8, 30, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:82:3465:18661", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 185, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 656, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAACGCTAGGACAACA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 35, 38, 38, 38, 38, 35, 34, 38, 38, 38, 35, 38, 37, 35, 37, 38, 33, 35, 36, 36, 33, 36, 36, 32, 35, 37, 36, 36, 37, 36, 36, 36, 37, 37, 34, 38, 37, 38, 30, 36, 34, 35, 25, 26, 36, 36, 36, 36, 38, 38, 33, 37, 30, 36, 33, 32, 26, 32, 27, 25, 32, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:91:5501:15084", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 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"readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:62:9158:19347", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 81, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 659, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "CLIP_SOFT", - "operationLength": 10, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 46, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 45, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATGTTTGATTCTTTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAGATCGGAAG", - "alignedQuality": [38, 38, 38, 38, 36, 38, 38, 38, 38, 37, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 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"alignment": { - "position": { - "referenceName": "chrM", - "position": 892, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCNGTAACAAG", - "alignedQuality": [37, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 38, 38, 36, 37, 35, 38, 38, 37, 38, 38, 38, 36, 36, 38, 38, 38, 33, 38, 38, 38, 38, 38, 35, 38, 38, 37, 38, 38, 37, 38, 38, 38, 36, 38, 38, 37, 38, 38, 36, 37, 36, 38, 38, 38, 36, 36, 37, 37, 36, 35, 37, 33, 37, 37, 35, 37, 36, 35, 25, 35, 35, 36, 34, 36, 35, 35, 36, 34, 36, 23, 27, 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"fragmentName": "613F1AAXX100423:5:35:12861:9976", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 186, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 905, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGNGATACTGG", - "alignedQuality": [38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 35, 38, 38, 38, 38, 30, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 38, 36, 37, 38, 38, 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"mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAGGT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 35, 38, 38, 38, 37, 38, 36, 38, 38, 38, 38, 37, 34, 38, 38, 38, 38, 36, 38, 37, 38, 38, 36, 38, 36, 37, 30, 35, 36, 37, 36, 36, 35, 38, 33, 35, 36, 36, 37, 38, 28, 36, 37, 36, 35, 36, 35, 35, 35, 36, 35, 22], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:6:19562:12868", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 154, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 910, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACNGGAAAGTG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 36, 35, 37, 35, 37, 36, 38, 37, 37, 38, 35, 37, 34, 36, 35, 34, 37, 35, 35, 36, 34, 36, 36, 34, 33, 36, 36, 36, 35, 34, 29, 28, 0, 29, 29, 29, 29, 29, 29, 28, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": 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"reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 87, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 14, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCTCCAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGAGATAGGCTAAGTCAA", - "alignedQuality": [20, 26, 12, 20, 12, 26, 20, 12, 20, 20, 21, 31, 31, 29, 33, 21, 33, 32, 32, 30, 12, 26, 32, 32, 32, 34, 28, 28, 28, 34, 21, 32, 32, 34, 32, 34, 34, 21, 34, 34, 34, 21, 28, 34, 34, 28, 32, 30, 32, 34, 26, 19, 32, 26, 32, 28, 28, 34, 18, 32, 34, 34, 34, 12, 30, 29, 32, 17, 12, 17, 32, 32, 30, 27, 16, 26, 30, 32, 22, 12, 22, 31, 30, 22, 22, 27, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:51:12399:9321", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 182, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 920, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATAATGGAAAGTGTGCTTGGAAT", - "alignedQuality": [38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 35, 38, 35, 38, 38, 38, 38, 38, 38, 35, 38, 38, 36, 38, 38, 36, 37, 38, 38, 38, 37, 38, 36, 35, 38, 37, 38, 36, 37, 38, 38, 36, 38, 37, 36, 36, 35, 35, 37, 32, 36, 33, 36, 36, 36, 34, 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"duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 924, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 100, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 1, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGAAAGCATACTGGAAGGTGTGCTTGGAATAATC", - "alignedQuality": [35, 33, 35, 28, 33, 35, 32, 35, 30, 32, 29, 29, 32, 25, 34, 35, 35, 28, 25, 35, 32, 29, 20, 30, 32, 35, 35, 33, 35, 32, 35, 35, 35, 28, 35, 29, 34, 29, 30, 20, 24, 30, 34, 31, 28, 23, 17, 24, 20, 30, 25, 33, 33, 34, 25, 24, 23, 23, 21, 20, 11, 21, 32, 28, 23, 19, 12, 22, 6, 6, 24, 25, 32, 22, 18, 33, 34, 20, 20, 28, 14, 18, 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27, 33, 26, 33, 17, 21, 26, 14, 32, 26, 22, 26, 19, 14, 21, 32, 33, 18, 20, 26, 24, 33, 16, 26, 10, 16, 7, 23, 12, 5, 13, 6, 21, 30, 7, 31, 28, 33, 16, 15, 33, 32, 23, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:89:8823:2101", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 156, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 926, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTAAATTAAACTTAACATAATTAATTTCTACACATCCGTTTATGAGCGGAGATAAGTCGTAACCAGGCAACCACACTGGTAAGTATACTAGCAATCATCAT", - "alignedQuality": [38, 38, 38, 38, 38, 36, 36, 30, 28, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:102:15100:4058", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 87, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 927, - "reverseStrand": false - }, - "mappingQuality": 23, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 87, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 3, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 5, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 6, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCAGATCGGACGAGCG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 34, 32, 36, 37, 37, 37, 37, 35, 38, 38, 38, 38, 36, 37, 38, 36, 37, 37, 38, 37, 37, 38, 36, 34, 37, 37, 38, 37, 38, 38, 36, 38, 38, 37, 37, 36, 35, 35, 37, 34, 38, 35, 37, 36, 36, 38, 37, 36, 33, 37, 12, 32, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.6", - "fragmentName": "613F0AAXX100423:6:119:19785:7641", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 927, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 94, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGCAAGCATACTGGTAAGTGTGCTTGGAATAATCATA", - "alignedQuality": [38, 38, 37, 37, 38, 38, 36, 38, 38, 38, 38, 35, 37, 35, 37, 37, 38, 38, 35, 38, 37, 38, 38, 38, 36, 35, 38, 28, 38, 38, 38, 38, 38, 37, 38, 37, 35, 33, 36, 35, 32, 37, 37, 36, 37, 37, 38, 36, 38, 38, 30, 38, 38, 30, 37, 36, 36, 37, 32, 25, 34, 33, 34, 33, 36, 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"fragmentLength": 179, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 940, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGGCTTAAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 37, 35, 38, 38, 37, 38, 37, 38, 38, 37, 37, 38, 35, 37, 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"alignment": { - "position": { - "referenceName": "chrM", - "position": 963, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCNTACACCCA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 36, 38, 36, 38, 38, 36, 38, 38, 38, 38, 38, 35, 37, 35, 38, 34, 35, 36, 38, 37, 38, 25, 33, 37, 33, 37, 37, 37, 33, 34, 35, 34, 36, 37, 30, 36, 36, 37, 37, 38, 36, 37, 33, 37, 37, 34, 36, 37, 35, 34, 36, 34, 33, 36, 25, 36, 35, 36, 30, 36, 37, 36, 35, 35, 36, 36, 36, 28, 35, 35, 34, 35, 36, 30, 34, 0, 28, 30, 28, 30, 26, 25, 26, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": 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"readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 968, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 89, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 12, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGAGAGGAGATAAGTCGTAACNAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGTAGT", - "alignedQuality": [38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 36, 38, 37, 36, 38, 38, 29, 0, 30, 31, 30, 29, 32, 32, 32, 32, 38, 37, 38, 37, 38, 38, 37, 37, 37, 38, 37, 33, 33, 35, 36, 37, 33, 36, 37, 36, 35, 37, 36, 36, 35, 36, 36, 35, 36, 37, 35, 33, 36, 33, 33, 35, 35, 35, 35, 35, 35, 36, 35, 36, 36, 35, 35, 36, 33, 36, 30, 32, 32, 33, 33, 32, 35, 35, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:59:5329:15929", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 180, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 986, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACGAATGAACA", - "alignedQuality": [38, 38, 38, 38, 36, 38, 38, 38, 38, 37, 38, 38, 35, 38, 36, 38, 38, 36, 36, 38, 38, 38, 38, 36, 35, 37, 37, 38, 38, 37, 38, 37, 38, 38, 38, 35, 38, 38, 38, 38, 37, 38, 38, 37, 38, 36, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 37, 38, 36, 37, 37, 38, 38, 38, 38, 38, 36, 38, 34, 36, 38, 38, 36, 35, 37, 37, 37, 36, 36, 38, 36, 32, 36, 37, 36, 36, 38, 37, 33, 30, 11, 31, 25, 29, 30, 29, 30, 30, 37], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:46:2638:14790", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 172, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 988, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATATGGCCTACACCCAGAAGATTTCATGACCAATGAACACT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 36, 36, 29, 36, 36, 36, 36, 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}, + "nextMatePosition": null, + "info": {} + }] + }, "nextPageToken": null } From 7efc3ba50e37273aa27380eeb7694fc252157691 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Mon, 20 Jun 2016 11:07:20 -0700 Subject: [PATCH 007/136] modified alignment json for test --- test-data/adam-alignments.json | 39273 ++++++++++++++++++++++++++----- 1 file changed, 33387 insertions(+), 5886 deletions(-) diff --git a/test-data/adam-alignments.json b/test-data/adam-alignments.json index f4e92070..e8866aa4 100644 --- a/test-data/adam-alignments.json +++ b/test-data/adam-alignments.json @@ -1,5889 +1,33390 @@ { - "alignments": { - "$outer": {}, - "underlying": [{ - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:47:2891:8862", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 0, - 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"properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 115, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 15, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 92, + "referenceSequence": null + }, { + "operation": "INSERT", + "operationLength": 1, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + "operationLength": 8, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAANAATTACAC", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 36, 37, 37, 38, 37, 38, 37, 38, 38, 37, 38, 38, 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"fragmentName": "6141AAAXX100423:2:102:13963:2305", + "properPlacement": false, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": null, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 133, + "reverseStrand": false + }, + "mappingQuality": 37, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 52, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 49, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CGGTGGAAAATCCCTTAAACATTTACTTAAAATTTATGGAGAGGGTATCAAGTACATTAAAATAGCTTAAGACAACTTGCCTAGCCACACCAGCAACGACC", + "alignedQuality": [17, 22, 20, 17, 17, 17, 26, 22, 28, 23, 21, 11, 27, 22, 21, 11, 27, 28, 31, 7, 21, 15, 14, 21, 8, 21, 21, 21, 28, 13, 8, 32, 17, 15, 21, 32, 9, 21, 26, 32, 27, 33, 17, 10, 17, 33, 30, 27, 16, 32, 21, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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"properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 113, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 158, + "reverseStrand": false + }, + "mappingQuality": 29, + "cigar": [{ + "operation": "CLIP_SOFT", + "operationLength": 62, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + "operationLength": 39, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CTTTAGGACGTGAAATATGGCGAGGAAAACTGAAAAAGGTGGAAAATATTGGAATGTCCGCTCTTTAAATTTAAGGAGAGGGTATCAAGCACATTAAAATA", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 37, 35, 38, 38, 36, 38, 37, 38, 38, 37, 38, 34, 37, 37, 35, 37, 38, 38, 37, 38, 38, 38, 38, 38, 36, 37, 37, 37, 36, 38, 37, 32, 35, 37, 37, 37, 38, 38, 37, 36, 36, 37, 37, 36, 35, 36, 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"fragmentName": "6141AAAXX100423:4:58:19645:7588", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 179, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 583, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 75, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 26, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAAACCCGCTCTACCTCACCATCTCTTGCTAATTCTACATCTCGTC", + "alignedQuality": [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 32, 32, 30, 32, 35, 33, 23, 29, 28, 29, 17, 31, 29, 29, 28, 34, 20, 31, 31, 32, 35, 28, 34, 20, 34, 28, 29, 26, 31, 21, 28, 18, 28, 15, 30, 30, 20, 30, 29, 30, 30, 34, 33, 9, 30, 34, 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"secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "GTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCANACTTCAGC", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 36, 38, 37, 38, 36, 36, 36, 37, 36, 37, 36, 36, 36, 37, 36, 36, 36, 36, 35, 36, 36, 35, 36, 35, 35, 36, 36, 36, 36, 36, 36, 33, 34, 35, 29, 24, 0, 6, 27, 21, 26, 23, 19, 23, 34], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.3", + "fragmentName": "613F1AAXX100423:3:56:16917:3099", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 173, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 597, + 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"duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 181, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 600, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCACAC", + "alignedQuality": [38, 38, 38, 35, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 35, 37, 35, 35, 34, 37, 35, 37, 35, 35, 36, 33, 30, 35, 35, 36, 34, 32, 32, 35, 34, 31, 34, 32, 34, 28, 20, 32, 35, 34, 32, 35, 34, 35, 35, 35, 35, 20, 32, 32, 34, 32, 32, 31, 30, 30, 32, 25, 32, 32, 32, 8, 32, 30], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.6", + "fragmentName": "613F1AAXX100423:6:37:15714:21079", + "properPlacement": false, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 94, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 603, + "reverseStrand": false + }, + "mappingQuality": 37, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAGATCGG", + "alignedQuality": [38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 36, 36, 36, 36, 36, 37, 36, 36, 36, 36, 35, 35, 37, 36, 36, 36, 36, 34, 31, 35, 34, 36, 35, 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"alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 36, 12, 36, 35, 34, 34, 35, 35, 33, 38, 37, 38, 36, 37, 38, 38, 38, 36, 37, 37, 35, 37, 38, 37, 38, 37, 35, 37, 35, 31, 35, 33, 36, 25, 33, 32, 36, 35, 36, 35, 37, 33, 25, 36, 37, 33, 38, 31, 33, 35, 33, 33, 36, 35, 33, 35, 31, 36, 35, 36, 33, 33, 35, 36, 32, 28, 33, 32, 25, 32, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.3", + "fragmentName": "613F1AAXX100423:3:45:3029:17994", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 190, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 604, + "reverseStrand": false + }, + "mappingQuality": 17, + "cigar": [{ + "operation": "CLIP_SOFT", + "operationLength": 1, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + 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"duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 152, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 606, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 92, + "referenceSequence": null + }, { + "operation": "INSERT", + "operationLength": 1, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + "operationLength": 8, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "ATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCANAACCCTAA", + "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 38, 37, 37, 36, 37, 34, 38, 36, 36, 37, 37, 37, 36, 33, 36, 36, 36, 30, 36, 33, 33, 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"alignedQuality": [34, 34, 25, 34, 28, 28, 30, 34, 20, 34, 31, 26, 12, 29, 30, 28, 33, 28, 26, 28, 26, 31, 31, 30, 31, 35, 35, 35, 35, 35, 25, 25, 32, 32, 30, 29, 32, 25, 32, 32, 35, 35, 12, 35, 30, 28, 32, 31, 28, 12, 29, 33, 25, 29, 28, 14, 16, 26, 10, 33, 11, 25, 22, 31, 25, 11, 18, 30, 28, 27, 29, 12, 18, 25, 30, 10, 25, 25, 28, 26, 29, 20, 31, 34, 31, 28, 29, 9, 34, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F0.4", + "fragmentName": "613F0AAXX100423:4:91:1251:17061", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 175, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 610, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 55, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + 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"fragmentLength": 174, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 640, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "ACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTAAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAA", + "alignedQuality": [37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 37, 38, 38, 35, 37, 36, 38, 35, 36, 33, 37, 37, 38, 37, 36, 35, 36, 37, 36, 36, 37, 36, 36, 36, 35, 35, 36, 35, 36, 34, 35, 34, 35, 35, 34, 35, 36, 34, 28, 27, 30, 32, 34, 33, 30, 33, 35, 34, 36, 35, 34, 34, 34, 34, 34, 34, 33, 32, 36, 35, 35, 34, 34, 34, 34, 32, 35, 34, 34, 34, 34, 34, 34, 35, 34, 35, 31, 33, 35, 28, 26, 34, 32, 35, 35, 35, 35], + "nextMatePosition": null, + "info": {} + }, { + "id": 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"alignment": { + "position": { + "referenceName": "chrM", + "position": 854, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 85, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 16, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TCAATTAAGAATAGAGAGCTTAATTGAATTGAGCAATGAAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAGACTTAACATAANNANTNTCN", + "alignedQuality": [34, 11, 34, 34, 34, 35, 35, 35, 35, 35, 38, 38, 38, 38, 37, 34, 38, 38, 33, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 36, 34, 38, 36, 36, 37, 38, 38, 37, 36, 38, 37, 36, 36, 37, 37, 38, 35, 34, 37, 36, 36, 36, 36, 34, 35, 36, 34, 36, 33, 34, 33, 32, 34, 34, 25, 27, 23, 27, 30, 18, 31, 29, 28, 30, 2, 2, 2, 2, 2, 2, 2, 0, 0, 2, 0, 2, 0, 2, 2, 0], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.6", + "fragmentName": "613F1AAXX100423:6:74:11101:5071", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 142, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 855, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "AAATTAAGAATAGAGAGCTTAATTGAATTGAGCAATGAAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATNAATTTCTA", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 35, 37, 36, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 36, 38, 38, 38, 37, 38, 38, 38, 38, 37, 36, 38, 37, 37, 38, 36, 37, 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"properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 176, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 883, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 65, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 36, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TGAGCAATGAAGTACGCACACACCGCCCGTCACCCTCATCAAATTAAATTAAACTTCACATAATTAATTTCTACACATCAGTTTCTGAGAGTAGATAAGTC", + "alignedQuality": [25, 28, 20, 33, 30, 25, 30, 25, 29, 20, 34, 28, 34, 26, 28, 31, 29, 29, 29, 28, 24, 12, 24, 26, 24, 34, 34, 34, 26, 20, 34, 29, 28, 26, 29, 20, 8, 8, 25, 32, 34, 32, 34, 21, 12, 26, 29, 33, 21, 22, 24, 31, 30, 7, 27, 14, 10, 27, 8, 31, 28, 33, 31, 26, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F0.4", + "fragmentName": "613F0AAXX100423:4:55:2647:4140", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 250, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 883, + "reverseStrand": false + }, + "mappingQuality": 29, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TGAGCAATGAAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATCGGAA", + "alignedQuality": [38, 38, 37, 38, 38, 38, 32, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 37, 28, 36, 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"TGNGCAATGAAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGGGAGTAGTG", + "alignedQuality": [34, 34, 0, 33, 31, 35, 35, 35, 35, 35, 38, 38, 36, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 38, 38, 35, 37, 36, 33, 35, 32, 34, 30, 33, 36, 33, 35, 36, 33, 37, 36, 30, 35, 36, 30, 37, 31, 35, 32, 35, 35, 30, 35, 32, 36, 30, 34, 31, 35, 36, 30, 34, 24, 34, 32, 34, 28, 34, 31, 33, 28, 30, 31, 32, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "6141A.5", + "fragmentName": "6141AAAXX100423:5:28:6479:11056", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 192, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 883, + "reverseStrand": false + }, + "mappingQuality": 29, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 35, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 66, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TGAGCAATGAAGTACGCACACACCTCCCGTCACCCTCCTCAAATTAAATTAAATTTAATTTTATTTTTATTTTTACATCAGTTCATGTATACAGCTGACAG", + "alignedQuality": [31, 13, 8, 32, 7, 33, 33, 33, 13, 16, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.1", + "fragmentName": "613F1AAXX100423:1:38:18021:8701", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 184, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 887, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 63, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 38, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CAATGAAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTCACATCATTAATTTCTAGTCATCCGTTTATGAGAGGAGATAAGTCGTAA", + "alignedQuality": [20, 26, 17, 20, 30, 12, 24, 12, 24, 28, 28, 21, 28, 31, 29, 33, 26, 32, 26, 32, 34, 12, 34, 29, 12, 26, 26, 30, 21, 21, 34, 33, 34, 30, 30, 34, 21, 30, 21, 26, 30, 12, 34, 12, 32, 34, 28, 31, 28, 34, 26, 32, 18, 34, 26, 25, 28, 10, 28, 26, 32, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.1", + "fragmentName": 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34, 36, 34, 32, 35, 35, 35, 34, 36, 36, 34, 33, 35, 35], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.7", + "fragmentName": "613F1AAXX100423:7:64:9983:2202", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 165, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 889, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 35, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 66, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "ATGAAGTACGCACACACCGCCCGGCACCCTCCTCAAACTAAATTTAACTTCACACAATTAATTTCTAGAGATCCGCTCACGAGAGGAGGAAANATCGGAAC", + "alignedQuality": [27, 11, 7, 15, 11, 15, 11, 20, 15, 25, 32, 32, 22, 32, 31, 31, 24, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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"alignment": { + "position": { + "referenceName": "chrM", + "position": 892, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 92, + "referenceSequence": null + }, { + "operation": "INSERT", + "operationLength": 1, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + "operationLength": 8, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "AAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCNGTAACAAG", + "alignedQuality": [37, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 38, 38, 36, 37, 35, 38, 38, 37, 38, 38, 38, 36, 36, 38, 38, 38, 33, 38, 38, 38, 38, 38, 35, 38, 38, 37, 38, 38, 37, 38, 38, 38, 36, 38, 38, 37, 38, 38, 36, 37, 36, 38, 38, 38, 36, 36, 37, 37, 36, 35, 37, 33, 37, 37, 35, 37, 36, 35, 25, 35, 35, 36, 34, 36, 35, 35, 36, 34, 36, 23, 27, 0, 11, 23, 27, 23, 25, 25, 15, 34], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.3", + "fragmentName": "613F1AAXX100423:3:30:3445:6941", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 182, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 892, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 92, + "referenceSequence": null + }, { + "operation": "INSERT", + "operationLength": 1, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + "operationLength": 8, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "AAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGGTAACAAG", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 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"supplementaryAlignment": false, + "alignedSequence": "CATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTNTTGAACTA", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 38, 38, 38, 37, 35, 37, 37, 38, 38, 38, 38, 38, 38, 38, 37, 37, 35, 37, 37, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 37, 37, 35, 36, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 37, 38, 37, 38, 37, 38, 38, 38, 38, 36, 35, 37, 38, 37, 37, 36, 36, 37, 36, 35, 37, 37, 37, 36, 36, 36, 36, 33, 35, 37, 37, 37, 30, 33, 0, 22, 30, 14, 23, 14, 17, 18, 30], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "6141A.8", + "fragmentName": "6141AAAXX100423:8:82:11001:10820", + "properPlacement": false, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": null, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 997, + "reverseStrand": false + }, + "mappingQuality": 37, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 84, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 17, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CATACTGGGAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTTGCCTACACCCAGAAGATTTCATGACCAATGAACACCTTTCAGCTT", + "alignedQuality": [26, 26, 25, 33, 33, 34, 34, 26, 12, 28, 28, 13, 29, 25, 28, 20, 12, 26, 25, 25, 27, 29, 32, 26, 32, 34, 28, 26, 26, 33, 20, 26, 24, 26, 27, 12, 33, 32, 33, 32, 33, 28, 34, 34, 28, 34, 28, 33, 28, 34, 26, 32, 12, 21, 32, 12, 26, 11, 26, 26, 12, 26, 32, 30, 17, 34, 26, 34, 25, 33, 32, 34, 23, 34, 34, 17, 31, 26, 11, 24, 17, 34, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "6141A.8", + "fragmentName": "6141AAAXX100423:8:82:11001:10820", + "properPlacement": false, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": null, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": null, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CATACTGGAAAGGGTTCATTGGTCATGAAATCTTCTGGGTGTAGGCCAGATGCTTTAATATTAAGCTACACTATGATTATTCCAAGCACACTTTCTACTTC", + "alignedQuality": [31, 13, 26, 21, 26, 29, 13, 29, 31, 31, 25, 28, 12, 24, 26, 29, 28, 13, 28, 27, 34, 34, 12, 34, 34, 34, 30, 34, 30, 34, 29, 13, 28, 31, 12, 28, 25, 30, 33, 17, 24, 23, 31, 26, 26, 13, 31, 28, 26, 29, 30, 32, 21, 32, 32, 33, 18, 34, 26, 12, 10, 26, 26, 26, 11, 28, 31, 26, 28, 25, 26, 26, 29, 21, 34, 34, 34, 30, 12, 28, 34, 17, 12, 16, 30, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }], "nextPageToken": null } From 17b1539a97ca6d5870ede2c4e168de6713a8e6e8 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Mon, 20 Jun 2016 11:06:03 -0700 Subject: [PATCH 008/136] continue reference --- examples/data.js | 22 +++++++++++------- src/main/data/Sequence.js | 49 ++++++++++++++++++++++++++++++++------- 2 files changed, 53 insertions(+), 18 deletions(-) diff --git a/examples/data.js b/examples/data.js index 86b0f074..3db54f46 100644 --- a/examples/data.js +++ b/examples/data.js @@ -11,16 +11,20 @@ var sources = [ viz: pileup.viz.genome(), isReference: true, data: pileup.formats.reference({ - url: '/reference', - contigList: [{ - name:"chrM", - length: 1000 - },{ - name:"22", - length: 1000 - }] + url: 'reference' }), name: 'Reference' + }, + { + viz: pileup.viz.pileup(), + data: pileup.formats.ga4gh({ + spec: { + url: "localhost:8080", + readGroupId: "sadf", + killChr: true + }; + }), + name: 'Alignments' } // { // viz: pileup.viz.genome(), @@ -80,4 +84,4 @@ var sources = [ // } ]; -var range = {contig: 'chrM', start: 0, stop: 10}; +var range = {contig: 'chr17', start: 7512284, stop: 7512644}; diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index 610f8b98..f8e0563c 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -5,12 +5,45 @@ */ 'use strict'; +import Q from 'q'; import type RemoteRequest from '../RemoteRequest'; -import TwoBit from './TwoBit'; -type SequenceRecord = { - name: string, - length: number +export type SequenceRecord = { + name: string; + length: number; +} + +var BASE_PAIRS = [ + 'T', // 0=00 + 'C', // 1=01 + 'A', // 2=10 + 'G' // 3=11 +]; + +/** + * Read 2-bit encoded base pairs from a DataView into an array of 'A', 'T', + * 'C', 'G' strings. + * These are returned as an array (rather than a string) to facilitate further + * modification. + */ +function unpackDNA(dataView: DataView, startBasePair: number, numBasePairs: number): Array { + // TODO: use jBinary bitfield for this + var basePairs: Array = []; + basePairs.length = dataView.byteLength * 4; // pre-allocate + var basePairIdx = -startBasePair; + for (var i = 0; i < dataView.byteLength; i++) { + var packed = dataView.getUint8(i); + for (var shift = 6; shift >= 0; shift -= 2) { + var bp = BASE_PAIRS[(packed >> shift) & 3]; + if (startBasePair >= 0) { + basePairs[basePairIdx] = bp; + } + basePairIdx++; + } + } + // Remove base pairs from the end if the sequence terminated mid-byte. + basePairs.length = numBasePairs; + return basePairs; } class Sequence { @@ -23,8 +56,8 @@ class Sequence { } // Returns a list of contig names. - getContigList(): string[] { - return this.contigList.map(seq => seq.name); + getContigList(): Q.Promise { + return Promise.resolve(this.contigList.map(seq => seq.name)); } /** @@ -39,9 +72,7 @@ class Sequence { return this.remoteRequest.get(contig, start, stop).then(buffer => { var dataView = new DataView(buffer); - return TwoBit.markUnknownDNA( - TwoBit.unpackDNA(dataView, start % 4, stop - start + 1), start) - .join(''); + return unpackDNA(dataView, start % 4, stop - start + 1).join(''); }); } From b1acf6a4b13ea1b6d877db3fe7129a16f61c6ca9 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 21 Jun 2016 12:51:20 -0700 Subject: [PATCH 009/136] tests passing for reference --- package.json | 3 ++- src/main/data/Sequence.js | 26 ++++++-------------------- 2 files changed, 8 insertions(+), 21 deletions(-) diff --git a/package.json b/package.json index 129debaa..ee1217a8 100644 --- a/package.json +++ b/package.json @@ -31,7 +31,8 @@ "flow": "flow status", "flow-check": "flow check", "coverage": "./scripts/generate-coverage.sh", - "build": "./scripts/build.sh" + "build": "./scripts/build.sh", + "quick-build": "./scripts/quick-build.sh" }, "author": "Dan Vanderkam", "contributors": [ diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index f8e0563c..6036acd6 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -13,13 +13,6 @@ export type SequenceRecord = { length: number; } -var BASE_PAIRS = [ - 'T', // 0=00 - 'C', // 1=01 - 'A', // 2=10 - 'G' // 3=11 -]; - /** * Read 2-bit encoded base pairs from a DataView into an array of 'A', 'T', * 'C', 'G' strings. @@ -29,17 +22,10 @@ var BASE_PAIRS = [ function unpackDNA(dataView: DataView, startBasePair: number, numBasePairs: number): Array { // TODO: use jBinary bitfield for this var basePairs: Array = []; - basePairs.length = dataView.byteLength * 4; // pre-allocate - var basePairIdx = -startBasePair; + // basePairs.length = dataView.byteLength * 4; // pre-allocate for (var i = 0; i < dataView.byteLength; i++) { var packed = dataView.getUint8(i); - for (var shift = 6; shift >= 0; shift -= 2) { - var bp = BASE_PAIRS[(packed >> shift) & 3]; - if (startBasePair >= 0) { - basePairs[basePairIdx] = bp; - } - basePairIdx++; - } + basePairs[i] = String.fromCharCode(packed); } // Remove base pairs from the end if the sequence terminated mid-byte. basePairs.length = numBasePairs; @@ -56,8 +42,8 @@ class Sequence { } // Returns a list of contig names. - getContigList(): Q.Promise { - return Promise.resolve(this.contigList.map(seq => seq.name)); + getContigList(): string[] { + return this.contigList.map(seq => seq.name); } /** @@ -69,10 +55,10 @@ class Sequence { if (start > stop) { throw `Requested a range with start > stop (${start}, ${stop})`; } - return this.remoteRequest.get(contig, start, stop).then(buffer => { var dataView = new DataView(buffer); - return unpackDNA(dataView, start % 4, stop - start + 1).join(''); + var d = unpackDNA(dataView, start % 4, stop - start + 1).join(''); + return d; }); } From e8adaa4f8f404795bf87217473529b4af6fc0cc4 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 21 Jun 2016 20:40:04 -0700 Subject: [PATCH 010/136] reference through server now works --- examples/data.js | 22 +++++++++------------- src/main/data/Sequence.js | 2 +- 2 files changed, 10 insertions(+), 14 deletions(-) diff --git a/examples/data.js b/examples/data.js index 3db54f46..86b0f074 100644 --- a/examples/data.js +++ b/examples/data.js @@ -11,20 +11,16 @@ var sources = [ viz: pileup.viz.genome(), isReference: true, data: pileup.formats.reference({ - url: 'reference' + url: '/reference', + contigList: [{ + name:"chrM", + length: 1000 + },{ + name:"22", + length: 1000 + }] }), name: 'Reference' - }, - { - viz: pileup.viz.pileup(), - data: pileup.formats.ga4gh({ - spec: { - url: "localhost:8080", - readGroupId: "sadf", - killChr: true - }; - }), - name: 'Alignments' } // { // viz: pileup.viz.genome(), @@ -84,4 +80,4 @@ var sources = [ // } ]; -var range = {contig: 'chr17', start: 7512284, stop: 7512644}; +var range = {contig: 'chrM', start: 0, stop: 10}; diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index 6036acd6..04615b37 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -42,7 +42,7 @@ class Sequence { } // Returns a list of contig names. - getContigList(): string[] { + getContigList(): string[] { return this.contigList.map(seq => seq.name); } From 47569d2d1d7a7a7ebc95d5afa1229ab77cc20a58 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sat, 25 Jun 2016 13:53:50 -0700 Subject: [PATCH 011/136] variants now work --- src/main/data/Sequence.js | 25 +---- src/main/data/VariantEndpoint.js | 35 ++++++ src/main/pileup.js | 2 + src/main/sources/VariantDataSource.js | 120 +++++++++++++++++++++ src/test/sources/VariantDataSource-test.js | 65 +++++++++++ test-data/features-chrM-1000-1200.json | 11 ++ test-data/features_chrM_0_2000.json | 18 ---- test-data/variants-chrM-0-100.json | 16 +++ 8 files changed, 252 insertions(+), 40 deletions(-) create mode 100644 src/main/data/VariantEndpoint.js create mode 100644 src/main/sources/VariantDataSource.js create mode 100644 src/test/sources/VariantDataSource-test.js create mode 100644 test-data/features-chrM-1000-1200.json delete mode 100644 test-data/features_chrM_0_2000.json create mode 100644 test-data/variants-chrM-0-100.json diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index 04615b37..161f7300 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -13,25 +13,6 @@ export type SequenceRecord = { length: number; } -/** - * Read 2-bit encoded base pairs from a DataView into an array of 'A', 'T', - * 'C', 'G' strings. - * These are returned as an array (rather than a string) to facilitate further - * modification. - */ -function unpackDNA(dataView: DataView, startBasePair: number, numBasePairs: number): Array { - // TODO: use jBinary bitfield for this - var basePairs: Array = []; - // basePairs.length = dataView.byteLength * 4; // pre-allocate - for (var i = 0; i < dataView.byteLength; i++) { - var packed = dataView.getUint8(i); - basePairs[i] = String.fromCharCode(packed); - } - // Remove base pairs from the end if the sequence terminated mid-byte. - basePairs.length = numBasePairs; - return basePairs; -} - class Sequence { remoteRequest: RemoteRequest; contigList: SequenceRecord[]; @@ -55,9 +36,9 @@ class Sequence { if (start > stop) { throw `Requested a range with start > stop (${start}, ${stop})`; } - return this.remoteRequest.get(contig, start, stop).then(buffer => { - var dataView = new DataView(buffer); - var d = unpackDNA(dataView, start % 4, stop - start + 1).join(''); + return this.remoteRequest.get(contig, start, stop).then(sequence => { + // var dataView = new DataView(buffer); + var d = sequence.substring(start, (stop-start + 1)); return d; }); } diff --git a/src/main/data/VariantEndpoint.js b/src/main/data/VariantEndpoint.js new file mode 100644 index 00000000..9ee9035b --- /dev/null +++ b/src/main/data/VariantEndpoint.js @@ -0,0 +1,35 @@ +/** + * This module defines a parser for the 2bit file format. + * See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 + * @flow + */ +'use strict'; + +import Q from 'q'; +import type RemoteRequest from '../RemoteRequest'; + +function extractVariants(variants: Object): Variant[] { + return variants; +} + +class VariantEndpoint { + remoteRequest: RemoteRequest; + + constructor(remoteRequest: RemoteRequest) { + this.remoteRequest = remoteRequest; + } + + getFeaturesInRange(range: ContigInterval): Q.Promise { + var contig = range.contig; + var start = range.interval.start; + var stop = range.interval.stop; + console.log("in get range endpoint", range); + + return this.remoteRequest.get(contig, start, stop).then(object => { + var d = extractVariants(object); // TODO: should parts to Variant[] + return d; + }); + } +} + +module.exports = VariantEndpoint; diff --git a/src/main/pileup.js b/src/main/pileup.js index 966c819d..441b7c3d 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -14,6 +14,7 @@ import ReactDOM from 'react-dom'; import TwoBitDataSource from './sources/TwoBitDataSource'; import BigBedDataSource from './sources/BigBedDataSource'; import VcfDataSource from './sources/VcfDataSource'; +import VariantDataSource from './sources/VariantDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; import EmptySource from './sources/EmptySource'; @@ -123,6 +124,7 @@ var pileup = { bam: BamDataSource.create, ga4gh: GA4GHDataSource.create, vcf: VcfDataSource.create, + variants: VariantDataSource.create, twoBit: TwoBitDataSource.create, bigBed: BigBedDataSource.create, empty: EmptySource.create diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js new file mode 100644 index 00000000..59a3539e --- /dev/null +++ b/src/main/sources/VariantDataSource.js @@ -0,0 +1,120 @@ +/** + * The "glue" between TwoBit.js and GenomeTrack.js. + * + * GenomeTrack is pure view code -- it renders data which is already in-memory + * in the browser. + * + * TwoBit is purely for data parsing and fetching. It only knows how to return + * promises for various genome features. + * + * This code acts as a bridge between the two. It maintains a local version of + * the data, fetching remote data and informing the view when it becomes + * available. + * + * @flow + */ +'use strict'; + +import type {Variant} from '../data/vcf'; + +import Q from 'q'; +import _ from 'underscore'; +import {Events} from 'backbone'; + +import ContigInterval from '../ContigInterval'; +import type {VcfDataSource} from './VcfDataSource'; +import RemoteRequest from '../RemoteRequest'; +import VariantEndpoint from '../data/VariantEndpoint'; + + +// Requests for 2bit ranges are expanded to begin & end at multiples of this +// constant. Doing this means that panning typically won't require +// additional network requests. +var BASE_PAIRS_PER_FETCH = 1000; + +function expandRange(range: ContigInterval) { + var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; + var newStart = Math.max(1, roundDown(range.start())), + newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); + + return new ContigInterval(range.contig, newStart, newStop); +} + +function variantKey(v: Variant): string { + return `${v.contig}:${v.position}`; +} + + +function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { + var variants: {[key: string]: Variant} = {}; + + // Ranges for which we have complete information -- no need to hit network. + var coveredRanges: ContigInterval[] = []; + + function addVariant(v: Variant) { + var key = variantKey(v); + if (!variants[key]) { + variants[key] = v; + } + } + + function fetch(range: GenomeRange) { + var interval = new ContigInterval(range.contig, range.start, range.stop); + + // Check if this interval is already in the cache. + if (interval.isCoveredBy(coveredRanges)) { + return Q.when(); + } + + interval = expandRange(interval); + + // "Cover" the range immediately to prevent duplicate fetches. + coveredRanges.push(interval); + coveredRanges = ContigInterval.coalesce(coveredRanges); + return remoteSource.getFeaturesInRange(interval).then(variants => { + variants.forEach(variant => addVariant(variant)); + o.trigger('newdata', interval); + }); + } + + function getFeaturesInRange(range: ContigInterval): Variant[] { + if (!range) return []; // XXX why would this happen? + return _.filter(variants, v => range.chrContainsLocus(v.contig, v.position)); + } + + var o = { + rangeChanged: function(newRange: GenomeRange) { + fetch(newRange).done(); + }, + getFeaturesInRange, + + // These are here to make Flow happy. + on: () => {}, + off: () => {}, + trigger: () => {} + }; + _.extend(o, Events); // Make this an event emitter + + return o; +} + +function create(data: {url:string, contigList: SequenceRecord[]}): VcfDataSource { + var url = data.url; + var contigList = data.contigList; + if (!url) { + throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); + } + // verify contiglist was correctly set + if (!contigList) { + throw new Error(`Missing ContigList from track: ${JSON.stringify(data)}`); + } + var request = new RemoteRequest(url, contigList); + var endpoint = new VariantEndpoint(request); + return createFromVariantUrl(endpoint); +} + + +module.exports = { + create, + createFromVariantUrl +}; diff --git a/src/test/sources/VariantDataSource-test.js b/src/test/sources/VariantDataSource-test.js new file mode 100644 index 00000000..b074909f --- /dev/null +++ b/src/test/sources/VariantDataSource-test.js @@ -0,0 +1,65 @@ +/* @flow */ +'use strict'; + + +import {expect} from 'chai'; + +import sinon from 'sinon'; + +import VariantDataSource from '../../main/sources/VariantDataSource'; +import ContigInterval from '../../main/ContigInterval'; +import RemoteFile from '../../main/RemoteFile'; + +describe('VariantDataSource', function() { + var server: any = null, response; + + before(function () { + return new RemoteFile('/test-data/variants-chrM-0-100.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + // server.respondWith('GET', '/variants',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/variants/chrM?start=1&end=1000',[200, { "Content-Type": "application/json" }, response]); + }); + }); + + after(function () { + server.restore(); + }); + + function getTestSource() { + var source = VariantDataSource.create({ + url: '/variants', + contigList: [{ + name:"chrM", + length: 1000 + },{ + name:"22", + length: 1000 + }] + }); + return source; + } + it('should extract features in a range', function(done) { + var source = getTestSource(); + var range = new ContigInterval('chrM', 0, 25); + // No variants are cached yet. + var variants = source.getFeaturesInRange(range); + expect(variants).to.deep.equal([]); + + source.on('newdata', () => { + var variants = source.getFeaturesInRange(range); + expect(variants).to.have.length(2); + expect(variants[1].contig).to.equal('chrM'); + expect(variants[1].position).to.equal(20); + expect(variants[1].ref).to.equal('G'); + expect(variants[1].alt).to.equal('T'); + done(); + }); + source.rangeChanged({ + contig: range.contig, + start: range.start(), + stop: range.stop() + }); + server.respond(); + }); +}); diff --git a/test-data/features-chrM-1000-1200.json b/test-data/features-chrM-1000-1200.json new file mode 100644 index 00000000..2ba90728 --- /dev/null +++ b/test-data/features-chrM-1000-1200.json @@ -0,0 +1,11 @@ +[{ + "rest": "4ee7469a-b468-429b-a109-07a484817037", + "contig": "chrM", + "start": 1107, + "end": 1200 +}, { + "rest": "e105ce29-a840-4fc6-819f-a9aac5166163", + "contig": "chrM", + "start": 1011, + "end": 1012 +}] diff --git a/test-data/features_chrM_0_2000.json b/test-data/features_chrM_0_2000.json deleted file mode 100644 index 18c0c397..00000000 --- a/test-data/features_chrM_0_2000.json +++ /dev/null @@ -1,18 +0,0 @@ -[{ - "range": { - "name": "chrM", - "start": 0, - "end": 2000 - }, - "features": [{ - "featureId": "4ee7469a-b468-429b-a109-07a484817037", - "featureType": "rs575272151", - "start": 1107, - "end": 1200 - }, { - "featureId": "e105ce29-a840-4fc6-819f-a9aac5166163", - "featureType": "rs544419019", - "start": 1011, - "end": 1012 - }] -}] diff --git a/test-data/variants-chrM-0-100.json b/test-data/variants-chrM-0-100.json new file mode 100644 index 00000000..c48c5b03 --- /dev/null +++ b/test-data/variants-chrM-0-100.json @@ -0,0 +1,16 @@ +[{ + "contig": "chrM", + "position": 10, + "ref": "C", + "alt": "G" +}, { + "contig": "chrM", + "position": 20, + "ref": "G", + "alt": "T" +}, { + "contig": "chrM", + "position": 20, + "ref": "A", + "alt": "C" +}] From e9c6669d614c03cfec37e8f4a1d355277b852f17 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 28 Jun 2016 13:00:01 -0700 Subject: [PATCH 012/136] added key to remote request --- src/main/data/VariantEndpoint.js | 7 +++---- src/main/sources/GA4GHDataSource.js | 6 +++--- src/main/sources/ReferenceDataSource.js | 3 ++- src/main/sources/VariantDataSource.js | 13 ++++++------- src/test/sources/ReferenceDataSource-test.js | 6 +++--- src/test/sources/VariantDataSource-test.js | 10 ++-------- 6 files changed, 19 insertions(+), 26 deletions(-) diff --git a/src/main/data/VariantEndpoint.js b/src/main/data/VariantEndpoint.js index 9ee9035b..59425dda 100644 --- a/src/main/data/VariantEndpoint.js +++ b/src/main/data/VariantEndpoint.js @@ -23,11 +23,10 @@ class VariantEndpoint { var contig = range.contig; var start = range.interval.start; var stop = range.interval.stop; - console.log("in get range endpoint", range); - return this.remoteRequest.get(contig, start, stop).then(object => { - var d = extractVariants(object); // TODO: should parts to Variant[] - return d; + return this.remoteRequest.get(contig, start, stop).then(object => { + var d = extractVariants(object); // TODO: should parts to Variant[] + return d; }); } } diff --git a/src/main/sources/GA4GHDataSource.js b/src/main/sources/GA4GHDataSource.js index dfa6f8e3..34dee3f1 100644 --- a/src/main/sources/GA4GHDataSource.js +++ b/src/main/sources/GA4GHDataSource.js @@ -21,7 +21,7 @@ var ALIGNMENTS_PER_REQUEST = 200; // TODO: explain this choice. // TODO: tune this value -- setting it close to the read length will result in // lots of reads being fetched twice, but setting it too large will result in // bulkier requests. -var BASE_PAIRS_PER_FETCH = 100; +var BASE_PAIRS_PER_FETCH = 1000; function expandRange(range: ContigInterval) { var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; @@ -87,8 +87,8 @@ function create(spec: GA4GHSpec): AlignmentDataSource { pageToken: ?string, numRequests: number) { var xhr = new XMLHttpRequest(); - - var endpoint = url + "/" + range.contig + "?start=" + range.start() + "&end=" + range.stop()+"&sample="+spec.readGroupId; + + var endpoint = url + "/" + range.contig + "?start=" + range.start() + "&end=" + range.stop()+"&key="+spec.readGroupId; xhr.open('GET', endpoint); xhr.responseType = 'json'; diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index 2e10d7de..232c630b 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -149,7 +149,8 @@ function create(data: {url:string, contigList: SequenceRecord[]}): TwoBitSource if (!contigList) { throw new Error(`Missing ContigList from track: ${JSON.stringify(data)}`); } - return createFromReferenceUrl(new Sequence(new RemoteRequest(urlPrefix), contigList)); + var key = "reference" // key is not required for reference but required for Remote Request + return createFromReferenceUrl(new Sequence(new RemoteRequest(urlPrefix, key), contigList)); } // Getter/setter for base pairs per fetch. diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index 59a3539e..add58f6e 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -98,17 +98,16 @@ function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { return o; } -function create(data: {url:string, contigList: SequenceRecord[]}): VcfDataSource { - var url = data.url; - var contigList = data.contigList; +function create(data: {url?:string, key?:string}): VcfDataSource { + var {url, key} = data; if (!url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } - // verify contiglist was correctly set - if (!contigList) { - throw new Error(`Missing ContigList from track: ${JSON.stringify(data)}`); + // verify key was correctly set + if (!key) { + throw new Error(`Missing key from track: ${JSON.stringify(data)}`); } - var request = new RemoteRequest(url, contigList); + var request = new RemoteRequest(url, key); var endpoint = new VariantEndpoint(request); return createFromVariantUrl(endpoint); } diff --git a/src/test/sources/ReferenceDataSource-test.js b/src/test/sources/ReferenceDataSource-test.js index 09ee0879..f845e8be 100644 --- a/src/test/sources/ReferenceDataSource-test.js +++ b/src/test/sources/ReferenceDataSource-test.js @@ -15,9 +15,9 @@ before(function () { return new RemoteFile('/test-data/reference-chrM-0-1000.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); - server.respondWith('GET', '/reference/chrM?start=0&end=10000',[200, { "Content-Type": "application/json" }, response]); - server.respondWith('GET', '/reference/chrM?start=0&end=10',[200, { "Content-Type": "application/json" }, response]); - server.respondWith('GET', '/reference/22?start=0&end=10000',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/reference/chrM?start=0&end=10000&key=reference',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/reference/chrM?start=0&end=10&key=reference',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/reference/22?start=0&end=10000&key=reference',[200, { "Content-Type": "application/json" }, response]); }); }); diff --git a/src/test/sources/VariantDataSource-test.js b/src/test/sources/VariantDataSource-test.js index b074909f..9989ba74 100644 --- a/src/test/sources/VariantDataSource-test.js +++ b/src/test/sources/VariantDataSource-test.js @@ -18,7 +18,7 @@ describe('VariantDataSource', function() { response = data; server = sinon.fakeServer.create(); // server.respondWith('GET', '/variants',[200, { "Content-Type": "application/json" }, response]); - server.respondWith('GET', '/variants/chrM?start=1&end=1000',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/variants/chrM?start=1&end=1000&key=test',[200, { "Content-Type": "application/json" }, response]); }); }); @@ -29,13 +29,7 @@ describe('VariantDataSource', function() { function getTestSource() { var source = VariantDataSource.create({ url: '/variants', - contigList: [{ - name:"chrM", - length: 1000 - },{ - name:"22", - length: 1000 - }] + key: 'test' }); return source; } From 7779b0db334ca5b1891ac05ec4bb274c7dfe240e Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sat, 11 Jun 2016 15:13:50 -0700 Subject: [PATCH 013/136] starting reference --- examples/data.js | 27 ++++++++++----------------- 1 file changed, 10 insertions(+), 17 deletions(-) diff --git a/examples/data.js b/examples/data.js index 86b0f074..9f3123a6 100644 --- a/examples/data.js +++ b/examples/data.js @@ -8,28 +8,21 @@ var sources = [ { + viz: pileup.viz.genome(), + isReference: true, + data: pileup.formats.twoBit({ + url: 'http://www.biodalliance.org/datasets/hg19.2bit' + }), + name: 'Reference' + }, + { viz: pileup.viz.genome(), isReference: true, data: pileup.formats.reference({ - url: '/reference', - contigList: [{ - name:"chrM", - length: 1000 - },{ - name:"22", - length: 1000 - }] + prefix:"../json/" }), name: 'Reference' } -// { -// viz: pileup.viz.genome(), -// isReference: true, -// data: pileup.formats.reference({ -// prefix:"../json/" -// }), -// name: 'Reference' -// } // { // viz: pileup.viz.scale(), // name: 'Scale' @@ -80,4 +73,4 @@ var sources = [ // } ]; -var range = {contig: 'chrM', start: 0, stop: 10}; +var range = {contig: 'chr17', start: 7512284, stop: 7512644}; From 12941d5b7f3adc4f579d336c63a355502795914b Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sun, 12 Jun 2016 15:41:49 -0700 Subject: [PATCH 014/136] continued reference implementation --- examples/data.js | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/examples/data.js b/examples/data.js index 9f3123a6..73ba33b4 100644 --- a/examples/data.js +++ b/examples/data.js @@ -14,15 +14,15 @@ var sources = [ url: 'http://www.biodalliance.org/datasets/hg19.2bit' }), name: 'Reference' - }, - { - viz: pileup.viz.genome(), - isReference: true, - data: pileup.formats.reference({ - prefix:"../json/" - }), - name: 'Reference' } +// { +// viz: pileup.viz.genome(), +// isReference: true, +// data: pileup.formats.reference({ +// prefix:"../json/" +// }), +// name: 'Reference' +// } // { // viz: pileup.viz.scale(), // name: 'Scale' From 319f89b548885bb256479aa0954655e3df778f5c Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sat, 18 Jun 2016 13:20:54 -0700 Subject: [PATCH 015/136] added test resources for ADAM alignments --- test-data/features_chrM_0_2000.json | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 test-data/features_chrM_0_2000.json diff --git a/test-data/features_chrM_0_2000.json b/test-data/features_chrM_0_2000.json new file mode 100644 index 00000000..18c0c397 --- /dev/null +++ b/test-data/features_chrM_0_2000.json @@ -0,0 +1,18 @@ +[{ + "range": { + "name": "chrM", + "start": 0, + "end": 2000 + }, + "features": [{ + "featureId": "4ee7469a-b468-429b-a109-07a484817037", + "featureType": "rs575272151", + "start": 1107, + "end": 1200 + }, { + "featureId": "e105ce29-a840-4fc6-819f-a9aac5166163", + "featureType": "rs544419019", + "start": 1011, + "end": 1012 + }] +}] From 3a43924cae48b39d2fc12241677facab301c7ab6 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Mon, 20 Jun 2016 11:06:03 -0700 Subject: [PATCH 016/136] continue reference --- examples/data.js | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/examples/data.js b/examples/data.js index 73ba33b4..3db54f46 100644 --- a/examples/data.js +++ b/examples/data.js @@ -10,10 +10,21 @@ var sources = [ { viz: pileup.viz.genome(), isReference: true, - data: pileup.formats.twoBit({ - url: 'http://www.biodalliance.org/datasets/hg19.2bit' + data: pileup.formats.reference({ + url: 'reference' }), name: 'Reference' + }, + { + viz: pileup.viz.pileup(), + data: pileup.formats.ga4gh({ + spec: { + url: "localhost:8080", + readGroupId: "sadf", + killChr: true + }; + }), + name: 'Alignments' } // { // viz: pileup.viz.genome(), From 7ed786f0219bc2d599138cc5db6b927165c1e3f3 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 21 Jun 2016 12:51:20 -0700 Subject: [PATCH 017/136] tests passing for reference --- src/main/sources/ReferenceDataSource.js | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index 232c630b..aa1ea238 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -163,6 +163,16 @@ function testBasePairsToFetch(num?: number): any { } } +// Getter/setter for base pairs per fetch. +// This should only be used for testing. +function testBasePairsToFetch(num?: number): any { + if (num) { + BASE_PAIRS_PER_FETCH = num; + } else { + return BASE_PAIRS_PER_FETCH; + } +} + module.exports = { create, createFromReferenceUrl, From 0cf415ba24beae5a0537c5097998e6ea23c94059 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 21 Jun 2016 20:40:04 -0700 Subject: [PATCH 018/136] reference through server now works --- examples/data.js | 22 +++++++++------------- 1 file changed, 9 insertions(+), 13 deletions(-) diff --git a/examples/data.js b/examples/data.js index 3db54f46..86b0f074 100644 --- a/examples/data.js +++ b/examples/data.js @@ -11,20 +11,16 @@ var sources = [ viz: pileup.viz.genome(), isReference: true, data: pileup.formats.reference({ - url: 'reference' + url: '/reference', + contigList: [{ + name:"chrM", + length: 1000 + },{ + name:"22", + length: 1000 + }] }), name: 'Reference' - }, - { - viz: pileup.viz.pileup(), - data: pileup.formats.ga4gh({ - spec: { - url: "localhost:8080", - readGroupId: "sadf", - killChr: true - }; - }), - name: 'Alignments' } // { // viz: pileup.viz.genome(), @@ -84,4 +80,4 @@ var sources = [ // } ]; -var range = {contig: 'chr17', start: 7512284, stop: 7512644}; +var range = {contig: 'chrM', start: 0, stop: 10}; From b05ee06679aba5089f67d25009788027c11d07fc Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sat, 25 Jun 2016 13:53:50 -0700 Subject: [PATCH 019/136] variants now works --- src/main/sources/VariantDataSource.js | 13 ++++++----- src/test/sources/ReferenceDataSource-test.js | 23 ++++++++++++-------- src/test/sources/VariantDataSource-test.js | 10 +++++++-- test-data/features_chrM_0_2000.json | 18 --------------- 4 files changed, 29 insertions(+), 35 deletions(-) delete mode 100644 test-data/features_chrM_0_2000.json diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index add58f6e..59a3539e 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -98,16 +98,17 @@ function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { return o; } -function create(data: {url?:string, key?:string}): VcfDataSource { - var {url, key} = data; +function create(data: {url:string, contigList: SequenceRecord[]}): VcfDataSource { + var url = data.url; + var contigList = data.contigList; if (!url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } - // verify key was correctly set - if (!key) { - throw new Error(`Missing key from track: ${JSON.stringify(data)}`); + // verify contiglist was correctly set + if (!contigList) { + throw new Error(`Missing ContigList from track: ${JSON.stringify(data)}`); } - var request = new RemoteRequest(url, key); + var request = new RemoteRequest(url, contigList); var endpoint = new VariantEndpoint(request); return createFromVariantUrl(endpoint); } diff --git a/src/test/sources/ReferenceDataSource-test.js b/src/test/sources/ReferenceDataSource-test.js index f845e8be..c8b7f25c 100644 --- a/src/test/sources/ReferenceDataSource-test.js +++ b/src/test/sources/ReferenceDataSource-test.js @@ -9,15 +9,20 @@ import ReferenceDataSource from '../../main/sources/ReferenceDataSource'; import RemoteFile from '../../main/RemoteFile'; describe('ReferenceDataSource', function() { -var server: any = null, response; - -before(function () { - return new RemoteFile('/test-data/reference-chrM-0-1000.json').getAllString().then(data => { - response = data; - server = sinon.fakeServer.create(); - server.respondWith('GET', '/reference/chrM?start=0&end=10000&key=reference',[200, { "Content-Type": "application/json" }, response]); - server.respondWith('GET', '/reference/chrM?start=0&end=10&key=reference',[200, { "Content-Type": "application/json" }, response]); - server.respondWith('GET', '/reference/22?start=0&end=10000&key=reference',[200, { "Content-Type": "application/json" }, response]); + var server: any = null, response; + + before(function () { + return new RemoteFile('/test-data/reference-chrM-0-1000.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/reference/chrM?start=0&end=10000',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/reference/chrM?start=0&end=10',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/reference/22?start=0&end=10000',[200, { "Content-Type": "application/json" }, response]); + }); + }); + + after(function () { + server.restore(); }); }); diff --git a/src/test/sources/VariantDataSource-test.js b/src/test/sources/VariantDataSource-test.js index 9989ba74..b074909f 100644 --- a/src/test/sources/VariantDataSource-test.js +++ b/src/test/sources/VariantDataSource-test.js @@ -18,7 +18,7 @@ describe('VariantDataSource', function() { response = data; server = sinon.fakeServer.create(); // server.respondWith('GET', '/variants',[200, { "Content-Type": "application/json" }, response]); - server.respondWith('GET', '/variants/chrM?start=1&end=1000&key=test',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/variants/chrM?start=1&end=1000',[200, { "Content-Type": "application/json" }, response]); }); }); @@ -29,7 +29,13 @@ describe('VariantDataSource', function() { function getTestSource() { var source = VariantDataSource.create({ url: '/variants', - key: 'test' + contigList: [{ + name:"chrM", + length: 1000 + },{ + name:"22", + length: 1000 + }] }); return source; } diff --git a/test-data/features_chrM_0_2000.json b/test-data/features_chrM_0_2000.json deleted file mode 100644 index 18c0c397..00000000 --- a/test-data/features_chrM_0_2000.json +++ /dev/null @@ -1,18 +0,0 @@ -[{ - "range": { - "name": "chrM", - "start": 0, - "end": 2000 - }, - "features": [{ - "featureId": "4ee7469a-b468-429b-a109-07a484817037", - "featureType": "rs575272151", - "start": 1107, - "end": 1200 - }, { - "featureId": "e105ce29-a840-4fc6-819f-a9aac5166163", - "featureType": "rs544419019", - "start": 1011, - "end": 1012 - }] -}] From aed7e2c64f2173ca4a52010f8aadfe0b9369ec58 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Thu, 30 Jun 2016 21:56:07 -0700 Subject: [PATCH 020/136] pileup can now display genotypes --- .gitignore | 3 + src/main/data/GenotypeEndpoint.js | 43 ++++++ src/main/data/Sequence.js | 1 - src/main/sources/GA4GHDataSource.js | 2 +- src/main/sources/GenotypeDataSource.js | 126 ++++++++++++++++++ src/main/sources/ReferenceDataSource.js | 2 +- src/main/style.js | 14 +- src/main/viz/GenomeTrack.js | 3 +- src/main/viz/GenotypeTrack.js | 138 ++++++++++++++++++++ src/test/sources/GenotypeDataSource-test.js | 60 +++++++++ test-data/genotypes-chrM-0-100.json | 25 ++++ 11 files changed, 407 insertions(+), 10 deletions(-) create mode 100644 src/main/data/GenotypeEndpoint.js create mode 100644 src/main/sources/GenotypeDataSource.js create mode 100644 src/main/viz/GenotypeTrack.js create mode 100644 src/test/sources/GenotypeDataSource-test.js create mode 100644 test-data/genotypes-chrM-0-100.json diff --git a/.gitignore b/.gitignore index 2a749afe..fbb4ddeb 100644 --- a/.gitignore +++ b/.gitignore @@ -18,6 +18,9 @@ coverage # Compiled binary addons (http://nodejs.org/api/addons.html) build/Release + +# Examples folder +examples # Dependency directory # Commenting this out is preferred by some people, see diff --git a/src/main/data/GenotypeEndpoint.js b/src/main/data/GenotypeEndpoint.js new file mode 100644 index 00000000..5726d89f --- /dev/null +++ b/src/main/data/GenotypeEndpoint.js @@ -0,0 +1,43 @@ +/** + * This module defines a parser for the 2bit file format. + * See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 + * @flow + */ +'use strict'; + +import Q from 'q'; +import type RemoteRequest from '../RemoteRequest'; +import type {Variant} from './vcf'; + + +export type Genotype = { + sampleIds: string, + variant: Variant +} + + +function extractGenotypes(genotypes: Object): Genotype[] { + return genotypes; +} + +class GenotypeEndpoint { + remoteRequest: RemoteRequest; + + constructor(remoteRequest: RemoteRequest) { + this.remoteRequest = remoteRequest; + } + + getFeaturesInRange(range: ContigInterval): Q.Promise { + var contig = range.contig; + var start = range.interval.start; + var stop = range.interval.stop; + + + return this.remoteRequest.get(contig, start, stop).then(object => { + var d = extractGenotypes(object); + return d; + }); + } +} + +module.exports = GenotypeEndpoint; diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index 161f7300..4d5562ad 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -37,7 +37,6 @@ class Sequence { throw `Requested a range with start > stop (${start}, ${stop})`; } return this.remoteRequest.get(contig, start, stop).then(sequence => { - // var dataView = new DataView(buffer); var d = sequence.substring(start, (stop-start + 1)); return d; }); diff --git a/src/main/sources/GA4GHDataSource.js b/src/main/sources/GA4GHDataSource.js index 34dee3f1..bf3396c4 100644 --- a/src/main/sources/GA4GHDataSource.js +++ b/src/main/sources/GA4GHDataSource.js @@ -57,7 +57,7 @@ function create(spec: GA4GHSpec): AlignmentDataSource { var ga4ghAlignment = new GA4GHAlignment(alignment); reads[key] = ga4ghAlignment; } catch(TypeError){ - console.log("Error in Matepair Data Source.") + console.log("Error in Matepair Data Source."); } }); } diff --git a/src/main/sources/GenotypeDataSource.js b/src/main/sources/GenotypeDataSource.js new file mode 100644 index 00000000..7c0c140c --- /dev/null +++ b/src/main/sources/GenotypeDataSource.js @@ -0,0 +1,126 @@ +/** + * The "glue" between TwoBit.js and GenomeTrack.js. + * + * GenomeTrack is pure view code -- it renders data which is already in-memory + * in the browser. + * + * TwoBit is purely for data parsing and fetching. It only knows how to return + * promises for various genome features. + * + * This code acts as a bridge between the two. It maintains a local version of + * the data, fetching remote data and informing the view when it becomes + * available. + * + * @flow + */ +'use strict'; + +import type {Genotype} from '../data/GenotypeEndpoint'; + +import Q from 'q'; +import _ from 'underscore'; +import {Events} from 'backbone'; + +import ContigInterval from '../ContigInterval'; +import RemoteRequest from '../RemoteRequest'; +import GenotypeEndpoint from '../data/GenotypeEndpoint'; + +export type GenotypeDataSource = { + rangeChanged: (newRange: GenomeRange) => void; + getFeaturesInRange: (range: ContigInterval) => Genotype[]; + on: (event: string, handler: Function) => void; + off: (event: string) => void; + trigger: (event: string, ...args:any) => void; +}; + + +// Requests for 2bit ranges are expanded to begin & end at multiples of this +// constant. Doing this means that panning typically won't require +// additional network requests. +var BASE_PAIRS_PER_FETCH = 1000; + +function expandRange(range: ContigInterval) { + var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; + var newStart = Math.max(1, roundDown(range.start())), + newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); + + return new ContigInterval(range.contig, newStart, newStop); +} + +function genotypeKey(v: Genotype): string { + return `${v.variant.contig}:${v.variant.position}`; +} + + +function createFromGenotypeUrl(remoteSource: GenotypeEndpoint): GenotypeDataSource { + var genotypes: {[key: string]: Genotype} = {}; + + // Ranges for which we have complete information -- no need to hit network. + var coveredRanges: ContigInterval[] = []; + + function addGenotype(v: Genotype) { + var key = genotypeKey(v); + if (!genotypes[key]) { + genotypes[key] = v; + } + } + + function fetch(range: GenomeRange) { + var interval = new ContigInterval(range.contig, range.start, range.stop); + + // Check if this interval is already in the cache. + if (interval.isCoveredBy(coveredRanges)) { + return Q.when(); + } + + interval = expandRange(interval); + + // "Cover" the range immediately to prevent duplicate fetches. + coveredRanges.push(interval); + coveredRanges = ContigInterval.coalesce(coveredRanges); + return remoteSource.getFeaturesInRange(interval).then(genotypes => { + genotypes.forEach(genotype => addGenotype(genotype)); + o.trigger('newdata', interval); + }); + } + + function getFeaturesInRange(range: ContigInterval): Genotype[] { + if (!range) return []; // XXX why would this happen? + return _.filter(genotypes, v => range.chrContainsLocus(v.variant.contig, v.variant.position)); + } + + var o = { + rangeChanged: function(newRange: GenomeRange) { + fetch(newRange).done(); + }, + getFeaturesInRange, + + // These are here to make Flow happy. + on: () => {}, + off: () => {}, + trigger: () => {} + }; + _.extend(o, Events); // Make this an event emitter + + return o; +} + +function create(data: {url?:string, key?:string}): GenotypeDataSource { + var {url, key} = data; + if (!url) { + throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); + } + // verify key was correctly set + if (!key) { + throw new Error(`Missing key from track: ${JSON.stringify(data)}`); + } + var request = new RemoteRequest(url, key); + var endpoint = new GenotypeEndpoint(request); + return createFromGenotypeUrl(endpoint); +} + + +module.exports = { + create, + createFromGenotypeUrl +}; diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index aa1ea238..1ded0b77 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -149,7 +149,7 @@ function create(data: {url:string, contigList: SequenceRecord[]}): TwoBitSource if (!contigList) { throw new Error(`Missing ContigList from track: ${JSON.stringify(data)}`); } - var key = "reference" // key is not required for reference but required for Remote Request + var key = "reference"; // key is not required for reference but required for Remote Request return createFromReferenceUrl(new Sequence(new RemoteRequest(urlPrefix, key), contigList)); } diff --git a/src/main/style.js b/src/main/style.js index 314c8857..e1e3d40a 100644 --- a/src/main/style.js +++ b/src/main/style.js @@ -11,10 +11,10 @@ module.exports = { // Colors for individual base pairs BASE_COLORS: { - 'A': '#188712', - 'G': '#C45C16', - 'C': '#0600F9', - 'T': '#F70016', + 'A': '#5050FF', //'#188712', + 'G': '#00C000', //'#C45C16', + 'C': '#E00000', //'#0600F9', + 'T': '#E6E600',// '#F70016', 'U': '#F70016', 'N': 'black' }, @@ -63,7 +63,11 @@ module.exports = { // Variant Track VARIANT_STROKE: 'blue', - VARIANT_FILL: '#ddd', + VARIANT_FILL: 'blue', VARIANT_HEIGHT: 14, + // Genotype Track + GENOTYPE_SPACING: 1, + GENOTYPE_FILL: 'red', + GENOTYPE_HEIGHT: 10, }; diff --git a/src/main/viz/GenomeTrack.js b/src/main/viz/GenomeTrack.js index 12d570a0..743f6b8a 100644 --- a/src/main/viz/GenomeTrack.js +++ b/src/main/viz/GenomeTrack.js @@ -30,7 +30,6 @@ function renderGenome(ctx: DataCanvasRenderingContext2D, var pxPerLetter = scale(1) - scale(0); var mode = DisplayMode.getDisplayMode(pxPerLetter); var showText = DisplayMode.isText(mode); - if (mode != DisplayMode.HIDDEN) { ctx.textAlign = 'center'; if (mode == DisplayMode.LOOSE) { @@ -94,7 +93,7 @@ class GenomeTiledCanvas extends TiledCanvas { // The +/-1 ensures that partially-visible bases on the edge are rendered. var genomeRange = { contig: range.contig, - start: range.start() - 1, + start: Math.max(0, (range.start() - 1)), stop: range.stop() + 1 }; var basePairs = this.source.getRangeAsString(genomeRange); diff --git a/src/main/viz/GenotypeTrack.js b/src/main/viz/GenotypeTrack.js new file mode 100644 index 00000000..56297a78 --- /dev/null +++ b/src/main/viz/GenotypeTrack.js @@ -0,0 +1,138 @@ +/** + * Visualization of genotypes + * @flow + */ +'use strict'; + +import type {GenotypeDataSource} from '../sources/GenotypeDataSource'; +import type {Genotype} from '../data/GenotypeEndpoint'; +import type {DataCanvasRenderingContext2D} from 'data-canvas'; +import type {VizProps} from '../VisualizationWrapper'; +import type {Scale} from './d3utils'; + +import React from 'react'; +import ReactDOM from 'react-dom'; + +import d3utils from './d3utils'; +import shallowEquals from 'shallow-equals'; +import ContigInterval from '../ContigInterval'; +import canvasUtils from './canvas-utils'; +import dataCanvas from 'data-canvas'; +import style from '../style'; + +function yForRow(row) { + return row * (style.GENOTYPE_HEIGHT + style.GENOTYPE_SPACING); +} + +class GenotypeTrack extends React.Component { + props: VizProps & {source: GenotypeDataSource}; + state: void; // no state + + constructor(props: Object) { + super(props); + } + + render(): any { + return ; + } + + componentDidMount() { + this.updateVisualization(); + + this.props.source.on('newdata', () => { + this.updateVisualization(); + }); + } + + getScale(): Scale { + return d3utils.getTrackScale(this.props.range, this.props.width); + } + + componentDidUpdate(prevProps: any, prevState: any) { + if (!shallowEquals(prevProps, this.props) || + !shallowEquals(prevState, this.state)) { + this.updateVisualization(); + } + } + + updateVisualization() { + var canvas = ReactDOM.findDOMNode(this), + {width, height} = this.props; + + // Hold off until height & width are known. + if (width === 0) return; + + var ctx = canvasUtils.getContext(canvas); + var dtx = dataCanvas.getDataContext(ctx); + this.renderScene(dtx); + } + + renderScene(ctx: DataCanvasRenderingContext2D) { + var range = this.props.range, + interval = new ContigInterval(range.contig, range.start, range.stop), + genotypes = this.props.source.getFeaturesInRange(interval), + scale = this.getScale(), + sampleIds = []; + + // add all samples to array of sample Ids + genotypes.forEach(genotype => { + var ids = genotype.sampleIds; + for (var i = 0; i < ids.length; i++) { + var id = ids[i]; + if (sampleIds.indexOf(id) < 0) { + sampleIds.push(id); + } + } + }); + sampleIds = sampleIds.sort(); // sort sample ids + + // Height can only be computed after the genotypes has been updated. + var newHeight = yForRow(sampleIds.length); + var canvas = ReactDOM.findDOMNode(this), + {width, height} = this.props; + d3utils.sizeCanvas(canvas, width, newHeight); + + // This is a hack to adjust parent div for resize + var el = d3utils.findParent(canvas, 'track-content'); + if (el) el.style.height = newHeight; + + ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); + ctx.reset(); + ctx.save(); + + ctx.fillStyle = style.GENOTYPE_FILL; + genotypes.forEach(genotype => { + var variant = genotype.variant; + var keys = genotype.sampleIds; + ctx.pushObject(variant); + var x = Math.round(scale(variant.position)); + var width = Math.round(scale(variant.position + 1)) - 1 - x; + keys.forEach(sampleId => { + var y = yForRow(sampleIds.indexOf(sampleId)); + ctx.fillRect(x - 0.5, y - 0.5, width, style.GENOTYPE_HEIGHT); + }); + ctx.popObject(); + }); + + ctx.restore(); + } + + handleClick(reactEvent: any) { + var ev = reactEvent.nativeEvent, + x = ev.offsetX, + y = ev.offsetY, + canvas = ReactDOM.findDOMNode(this), + ctx = canvasUtils.getContext(canvas), + trackingCtx = new dataCanvas.ClickTrackingContext(ctx, x, y); + this.renderScene(trackingCtx); + var genotype = trackingCtx.hit && trackingCtx.hit[0]; + var alert = window.alert || console.log; + if (genotype) { + alert(JSON.stringify(genotype)); + } + } +} + +GenotypeTrack.displayName = 'genotypes'; + +module.exports = GenotypeTrack; diff --git a/src/test/sources/GenotypeDataSource-test.js b/src/test/sources/GenotypeDataSource-test.js new file mode 100644 index 00000000..67ca5162 --- /dev/null +++ b/src/test/sources/GenotypeDataSource-test.js @@ -0,0 +1,60 @@ +/* @flow */ +'use strict'; + + +import {expect} from 'chai'; + +import sinon from 'sinon'; + +import VariantDataSource from '../../main/sources/GenotypeDataSource'; +import ContigInterval from '../../main/ContigInterval'; +import RemoteFile from '../../main/RemoteFile'; + +describe('GenotypeDataSource', function() { + var server: any = null, response; + + before(function () { + return new RemoteFile('/test-data/genotypes-chrM-0-100.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/genotypes/chrM?start=1&end=1000&key=test',[200, { "Content-Type": "application/json" }, response]); + }); + }); + + after(function () { + server.restore(); + }); + + function getTestSource() { + var source = VariantDataSource.create({ + url: '/genotypes', + key: 'test' + }); + return source; + } + it('should extract features in a range', function(done) { + var source = getTestSource(); + var range = new ContigInterval('chrM', 0, 25); + // No variants are cached yet. + var variants = source.getFeaturesInRange(range); + expect(variants).to.deep.equal([]); + + source.on('newdata', () => { + var genotypes = source.getFeaturesInRange(range); + console.log(genotypes); + expect(genotypes).to.have.length(3); + expect(genotypes[1].sampleIds).to.contain('sample1'); + expect(genotypes[1].variant.contig).to.equal('chrM'); + expect(genotypes[1].variant.position).to.equal(20); + expect(genotypes[1].variant.ref).to.equal('G'); + expect(genotypes[1].variant.alt).to.equal('T'); + done(); + }); + source.rangeChanged({ + contig: range.contig, + start: range.start(), + stop: range.stop() + }); + server.respond(); + }); +}); diff --git a/test-data/genotypes-chrM-0-100.json b/test-data/genotypes-chrM-0-100.json new file mode 100644 index 00000000..f39bd291 --- /dev/null +++ b/test-data/genotypes-chrM-0-100.json @@ -0,0 +1,25 @@ +[{ + "sampleIds": ["sample1", "sample2", "sample3"], + "variant": { + "contig": "chrM", + "position": 10, + "ref": "C", + "alt": "G" + } +}, { + "sampleIds": ["sample1", "sample2", "sample3"], + "variant": { + "contig": "chrM", + "position": 20, + "ref": "G", + "alt": "T" + } +}, { + "sampleIds": ["sample1", "sample2", "sample3"], + "variant": { + "contig": "chrM", + "position": 30, + "ref": "A", + "alt": "C" + } +}] From 632e51451f4e1ea122fc20b4473622714894eae3 Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Thu, 16 Jun 2016 20:16:44 -0700 Subject: [PATCH 021/136] completed the genotype feature and variant class files --- .vscode/.browse.VC.db | Bin 0 -> 1055744 bytes src/main/Feature.js | 137 ++++++++++++++++++++++++++++++++++++++++++ src/main/Genotype.js | 31 ++++++++++ src/main/Variant.js | 88 +++++++++++++++++++++++++++ 4 files changed, 256 insertions(+) create mode 100644 .vscode/.browse.VC.db create mode 100644 src/main/Feature.js create mode 100644 src/main/Genotype.js create mode 100644 src/main/Variant.js diff --git a/.vscode/.browse.VC.db b/.vscode/.browse.VC.db new file mode 100644 index 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zro5Pi3i)jog7RA|Oq3U~Fc#ZA(SIm!1a?!xed)5E5cUK1c6$tjgU7)d_}^Ru%erY_ zcyzdi))CO3?l(&1KZN>?^k$;wQ)tS|35hY z|G)W$|6FJODx$R&d}z>0iLhe&Q`TzSOC6jblNfy0u5+D)CXuo53>KorGN;8 zI9pr_sF34f`pTIBWFss@D1gkkAfQU5F9eVH=)*^>pi<{4M3eflBLrd94t?grRZP^E z$8G=N3hY>om|+HtYOqD1NFo~)^Ee%1ASU;aG-aJ>wNL_U(mm8;y81@dCe2!*H! mIt92mTp`LO6!`C~0v6@d?j|^pAPy^p;vgwxRtjWrpZI^DhM02z literal 0 HcmV?d00001 diff --git a/src/main/Feature.js b/src/main/Feature.js new file mode 100644 index 00000000..f8992ba7 --- /dev/null +++ b/src/main/Feature.js @@ -0,0 +1,137 @@ +/** + * Class for features, shared between BAM and GA4GH backends. + */ + +import type ContigInterval from './ContigInterval'; + +export type Strand = '-' | '+'; + +export type Dbxref = { + accession: string; + db: string; +} + +class Feature { + featureId: string; + featureType: string; + source: string; + contig: ContigInterval; + start: number; + end: number; + strand: Strand; + value: number; + dbxrefs: Dbxref[]; + parentIds: string[]; + attributes: Object; + + constructor(featureId: string, featureType: string, source: string, + contig: ContigInterval, start: number, end: number, + strand: Strand, value: number, dbxrefs: Dbxref[], parentIds: string[], + attributes: Object) { + this.featureId = featureId; + this.featureTyp = featureType; + this.source = source; + this.contig = contig; + this.start = start; + this.end = end; + this.strand = strand; + this.value = value; + this.dbxrefs = dbxrefs; + this.parentIds = parentIds; + this.attributes = attributes; + } + + getAttributes(): Object { + return this.attributes; + } + + getContig(): Contig { + return this.contig; + } + + getDbxrefs(): Dbxref[] { + return this.dbxrefs; + } + + getEnd(): number { + return this.end; + } + + getFeatureId(): string { + return this.featureId; + } + + getFeatureType(): string { + return this.featureType; + } + + getParentIds(): string { + return this.parentIds; + } + + getSource(): string { + return this.source; + } + + getStart(): number { + return this.start; + } + + getStrand(): Strand { + return this.alignment.alignment.position.reverseStrand ? '-' : '+'; + } + + getValue(): number { + return this.value; + } + + /** Feature.Builder methods + May need to separate these */ + + setAttributes(value: Object) { + this.attributes = value; + } + + setContig(value: number) { + this.contig = value; + } + + setDbxrefs(value: List) { + this.dbxrefs = value; + } + + setEnd(value: number) { + this.end = value; + } + + setFeatureId(value: string) { + this.featureId = value; + } + + setFeatureType(value: string) { + this.featureType = value; + } + + setParentIds(value: List) { + this.parentIds = value; + } + + setSource(value: string) { + this.source = value; + } + + setStart(value: number) { + this.start = value; + } + + setStrand(value: Strand) { + this.strand = value; + } + + setValue(value: number) { + this.value = value; + } +} + +module.exports = Feature; + diff --git a/src/main/Genotype.js b/src/main/Genotype.js new file mode 100644 index 00000000..45f6a619 --- /dev/null +++ b/src/main/Genotype.js @@ -0,0 +1,31 @@ +/** + * Class for Genotypes, shared between BAM and GA4GH backends. + */ + +import type ContigInterval from './ContigInterval'; +import type Variant from './Variant'; + +export type Strand = '-' | '+'; + +class Genotype { + variant: Variant; + sampleId: string; + sampleDescription: string; + processingDescription: string; + //alleles: List + expectedAlleleDosage: number; + referenceReadDepth: number; + alternativeReadDepth: number; + readDepth: number; + minReadDepth: number; + genotypeQuality: number; + genotypeLikelihoods: List; + nonReferenceLikelihoods: List; + strandBiasComponents: List; + splitFromMultiAllelic: boolean; + isPhased: boolean; + phaseSetId: number; + phaseQuality: number; + + +} diff --git a/src/main/Variant.js b/src/main/Variant.js new file mode 100644 index 00000000..9dccf9f2 --- /dev/null +++ b/src/main/Variant.js @@ -0,0 +1,88 @@ +/** + * Class for Variants, shared between BAM and GA4GH backends. + */ + +import type ContigInterval from './ContigInterval'; + +export type Strand = '-' | '+'; + +class Variant { + contig: ContigInterval; + start: number; + end: number; + referenceAllele: string; + alternateAllele: string; + svAllele: StructuralVariant; + isSomatic: boolean; + + constructor(contig: ContigInterval, start: number, end: number + referenceAllele: string, alternateAllele: string, + svAllele: StructuralVariant, isSomatic: boolean) { + this.contig = contig; + this.start = start; + this.end = end; + this.referenceAllele = referenceAllele; + this.alternateAllele = alternateAllele; + this.svAllele = svAllele; + this.isSomatic = isSomatic; + } + + getAlternativeAllele(): string { + return this.alternateAllele; + } + + getContig(): ContigInterval { + return this.contig; + } + + getEnd(): number { + return this.end; + } + + getIsSomatic(): boolean { + return this.isSomatic; + } + + getReferenceAllele(): string { + return this.referenceAllele; + } + + getStart(): number { + return this.start; + } + + getSvAlelle(): StructuralVariant { + return this.svAllele; + } + + setAlternatieAllele(value: string) { + this.alternateAllele = value; + } + + setContig(value: Contig) { + this.contig = value; + } + + setEnd(value: number) { + this.end = value; + } + + setIsSomatic(value: boolean) { + this.isSomatic = value; + } + + setReferenceAllele(value: string) { + this.referenceAllele = value; + } + + setStart(value: number) { + this.start = value; + } + + setSvAllel(value: StructuralVariant) { + this.svAllele = value; + } + +} + +module.exports = Variant; From 41d8f4ce2dee999233a6300ad12a3ff53e5f6031 Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Fri, 17 Jun 2016 11:28:56 -0700 Subject: [PATCH 022/136] Create the FeatureDataSource.js file and tweak Feature.js Variant.js and Genotype.js constructors to take in objects instead --- src/main/Feature.js | 21 +++++++++-- src/main/FeatureInterface.js | 53 +++++++++++++++++++++++++++ src/main/Genotype.js | 2 +- src/main/Variant.js | 3 +- src/main/pileup.js | 2 +- src/main/sources/FeatureDataSource.js | 10 +++++ 6 files changed, 84 insertions(+), 7 deletions(-) create mode 100644 src/main/FeatureInterface.js create mode 100644 src/main/sources/FeatureDataSource.js diff --git a/src/main/Feature.js b/src/main/Feature.js index f8992ba7..fa890d5c 100644 --- a/src/main/Feature.js +++ b/src/main/Feature.js @@ -1,5 +1,6 @@ /** * Class for features, shared between BAM and GA4GH backends. + * @flow */ import type ContigInterval from './ContigInterval'; @@ -22,7 +23,7 @@ class Feature { value: number; dbxrefs: Dbxref[]; parentIds: string[]; - attributes: Object; + attributes: Object; //Or use array of attribute objects with key, value constructor(featureId: string, featureType: string, source: string, contig: ContigInterval, start: number, end: number, @@ -41,6 +42,12 @@ class Feature { this.attributes = attributes; } + /** + * constructor(input: Object) { + * + * } + */ + getAttributes(): Object { return this.attributes; } @@ -85,9 +92,6 @@ class Feature { return this.value; } - /** Feature.Builder methods - May need to separate these */ - setAttributes(value: Object) { this.attributes = value; } @@ -131,7 +135,16 @@ class Feature { setValue(value: number) { this.value = value; } + } +export type FeatureDataSource = { + rangeChanged: (newRange: GenomeRange) => void; + getFeaturesInRange: (range: ContigInterval) => Feature[]; + on: (event: string, handler: Function) => void; // really => FeatureDataSource + once: (event: string, handler: Function) => void; + off: (event: string) => void; +}; + module.exports = Feature; diff --git a/src/main/FeatureInterface.js b/src/main/FeatureInterface.js new file mode 100644 index 00000000..6c29d1d9 --- /dev/null +++ b/src/main/FeatureInterface.js @@ -0,0 +1,53 @@ +/** + * Interface for features + * @flow + */ + +import type ContigInterval from './ContigInterval'; + +export type Strand = '-' | '+'; + +export type Feature = { + featureId: string; + featureType: string; + source: string; + contig: ContigInterval; + start: number; + end: number; + strand: Strand; + value: number; + dbxrefs: Dbxref[]; + parentIds: string[]; + attributes: Object; + + getAttributes(): Object; + getContig(): ContigInterval; + getDbxrefs(): Dbxref[]; + getEnd(): number; + getFeatureId(): string; + getFeatureType(): string; + getParentsIds(): string; + getSource(): string; + getStart(): number; + getStrand(): Strand; + getValue(): number; + + setAttributes(); + setContig(); + setDbxrefs(); + setEnd(); + setFeatureId(); + setParentIds(); + setSource(); + setStart(); + setStrand(); + setValue(); +} + +export type FeatureDataSource = { + rangeChanged: (newRange: GenomeRange) => void; + getFeaturesInRange: (range: ContigInterval) => Feature[]; + on: (event: string, handler: Function) => void; // really => FeatureDataSource + once: (event: string, handler: Function) => void; + off: (event: string) => void; +} diff --git a/src/main/Genotype.js b/src/main/Genotype.js index 45f6a619..2afcf7dd 100644 --- a/src/main/Genotype.js +++ b/src/main/Genotype.js @@ -1,5 +1,6 @@ /** * Class for Genotypes, shared between BAM and GA4GH backends. + * @flow */ import type ContigInterval from './ContigInterval'; @@ -26,6 +27,5 @@ class Genotype { isPhased: boolean; phaseSetId: number; phaseQuality: number; - } diff --git a/src/main/Variant.js b/src/main/Variant.js index 9dccf9f2..ce47c3fb 100644 --- a/src/main/Variant.js +++ b/src/main/Variant.js @@ -1,5 +1,6 @@ /** * Class for Variants, shared between BAM and GA4GH backends. + * @flow */ import type ContigInterval from './ContigInterval'; @@ -55,7 +56,7 @@ class Variant { return this.svAllele; } - setAlternatieAllele(value: string) { + setAlternativeAllele(value: string) { this.alternateAllele = value; } diff --git a/src/main/pileup.js b/src/main/pileup.js index 441b7c3d..2c351564 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -22,7 +22,7 @@ import EmptySource from './sources/EmptySource'; // Visualizations import CoverageTrack from './viz/CoverageTrack'; import GenomeTrack from './viz/GenomeTrack'; -import GeneTrack from './viz/GeneTrack'; +import GeneTrack from './viz/GeneTrack'; //use this for features import LocationTrack from './viz/LocationTrack'; import PileupTrack from './viz/PileupTrack'; import ScaleTrack from './viz/ScaleTrack'; diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js new file mode 100644 index 00000000..97c8fdc9 --- /dev/null +++ b/src/main/sources/FeatureDataSource.js @@ -0,0 +1,10 @@ +/* @flow */ + +import type {Gene, BigBedDataSource} from './BigBedDataSource'; + +function(create) + +module.exports = { + create +} + From 1e49de461d4c326da5948de84a5b3e976ba27a05 Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Sat, 18 Jun 2016 18:28:06 -0700 Subject: [PATCH 023/136] Completed the FeatureDataSource.js file and also completed most of FeatureDataSource-test.js file --- src/main/Feature.js | 58 ++++--- src/main/FeatureInterface.js | 53 ------- src/main/Genotype.js | 41 +++-- src/main/Variant.js | 160 ++++++++++---------- src/main/pileup.js | 1 + src/main/sources/FeatureDataSource.js | 166 ++++++++++++++++++++- src/test/sources/FeatureDataSource-test.js | 43 ++++++ 7 files changed, 333 insertions(+), 189 deletions(-) delete mode 100644 src/main/FeatureInterface.js create mode 100644 src/test/sources/FeatureDataSource-test.js diff --git a/src/main/Feature.js b/src/main/Feature.js index fa890d5c..d5e13746 100644 --- a/src/main/Feature.js +++ b/src/main/Feature.js @@ -1,9 +1,10 @@ /** - * Class for features, shared between BAM and GA4GH backends. + * Class for features * @flow */ + 'use strict'; -import type ContigInterval from './ContigInterval'; +import ContigInterval from './ContigInterval'; export type Strand = '-' | '+'; @@ -12,48 +13,44 @@ export type Dbxref = { db: string; } +export type attribute = { + key: string; + value: string; +} + class Feature { featureId: string; featureType: string; source: string; - contig: ContigInterval; + range: ContigInterval; start: number; end: number; strand: Strand; value: number; dbxrefs: Dbxref[]; parentIds: string[]; - attributes: Object; //Or use array of attribute objects with key, value - - constructor(featureId: string, featureType: string, source: string, - contig: ContigInterval, start: number, end: number, - strand: Strand, value: number, dbxrefs: Dbxref[], parentIds: string[], - attributes: Object) { - this.featureId = featureId; - this.featureTyp = featureType; - this.source = source; - this.contig = contig; - this.start = start; - this.end = end; - this.strand = strand; - this.value = value; - this.dbxrefs = dbxrefs; - this.parentIds = parentIds; - this.attributes = attributes; + attributes: attribute[]; //Or use array of attribute objects with key, value + + constructor(input: Object) { + this.featureId = input.featureId; + this.featureType = input.featureType; + this.source = input.source; + this.start = input.start; + this.end = input.end; + this.strand = input.strand; + this.value = input.value; + this.dbxrefs = input.dbxrefs; + this.parentIds = input.parentIds; + this.attributes = input.attributes; + this.range = new ContigInterval(input.range.name, input.range.start, input.range.end); } - /** - * constructor(input: Object) { - * - * } - */ - getAttributes(): Object { return this.attributes; } - getContig(): Contig { - return this.contig; + getContig(): ContigInterval { + return this.range; } getDbxrefs(): Dbxref[] { @@ -96,8 +93,8 @@ class Feature { this.attributes = value; } - setContig(value: number) { - this.contig = value; + setContig(value: ContigInterval) { + this.range = value; } setDbxrefs(value: List) { @@ -147,4 +144,3 @@ export type FeatureDataSource = { }; module.exports = Feature; - diff --git a/src/main/FeatureInterface.js b/src/main/FeatureInterface.js deleted file mode 100644 index 6c29d1d9..00000000 --- a/src/main/FeatureInterface.js +++ /dev/null @@ -1,53 +0,0 @@ -/** - * Interface for features - * @flow - */ - -import type ContigInterval from './ContigInterval'; - -export type Strand = '-' | '+'; - -export type Feature = { - featureId: string; - featureType: string; - source: string; - contig: ContigInterval; - start: number; - end: number; - strand: Strand; - value: number; - dbxrefs: Dbxref[]; - parentIds: string[]; - attributes: Object; - - getAttributes(): Object; - getContig(): ContigInterval; - getDbxrefs(): Dbxref[]; - getEnd(): number; - getFeatureId(): string; - getFeatureType(): string; - getParentsIds(): string; - getSource(): string; - getStart(): number; - getStrand(): Strand; - getValue(): number; - - setAttributes(); - setContig(); - setDbxrefs(); - setEnd(); - setFeatureId(); - setParentIds(); - setSource(); - setStart(); - setStrand(); - setValue(); -} - -export type FeatureDataSource = { - rangeChanged: (newRange: GenomeRange) => void; - getFeaturesInRange: (range: ContigInterval) => Feature[]; - on: (event: string, handler: Function) => void; // really => FeatureDataSource - once: (event: string, handler: Function) => void; - off: (event: string) => void; -} diff --git a/src/main/Genotype.js b/src/main/Genotype.js index 2afcf7dd..79c6084c 100644 --- a/src/main/Genotype.js +++ b/src/main/Genotype.js @@ -8,24 +8,23 @@ import type Variant from './Variant'; export type Strand = '-' | '+'; -class Genotype { - variant: Variant; - sampleId: string; - sampleDescription: string; - processingDescription: string; - //alleles: List - expectedAlleleDosage: number; - referenceReadDepth: number; - alternativeReadDepth: number; - readDepth: number; - minReadDepth: number; - genotypeQuality: number; - genotypeLikelihoods: List; - nonReferenceLikelihoods: List; - strandBiasComponents: List; - splitFromMultiAllelic: boolean; - isPhased: boolean; - phaseSetId: number; - phaseQuality: number; - -} +// class Genotype { +// variant: Variant; +// sampleId: string; +// sampleDescription: string; +// processingDescription: string; +// //alleles: List +// expectedAlleleDosage: number; +// referenceReadDepth: number; +// alternativeReadDepth: number; +// readDepth: number; +// minReadDepth: number; +// genotypeQuality: number; +// genotypeLikelihoods: List; +// nonReferenceLikelihoods: List; +// strandBiasComponents: List; +// splitFromMultiAllelic: boolean; +// isPhased: boolean; +// phaseSetId: number; +// phaseQuality: number; +// } diff --git a/src/main/Variant.js b/src/main/Variant.js index ce47c3fb..93eca989 100644 --- a/src/main/Variant.js +++ b/src/main/Variant.js @@ -7,83 +7,83 @@ import type ContigInterval from './ContigInterval'; export type Strand = '-' | '+'; -class Variant { - contig: ContigInterval; - start: number; - end: number; - referenceAllele: string; - alternateAllele: string; - svAllele: StructuralVariant; - isSomatic: boolean; - - constructor(contig: ContigInterval, start: number, end: number - referenceAllele: string, alternateAllele: string, - svAllele: StructuralVariant, isSomatic: boolean) { - this.contig = contig; - this.start = start; - this.end = end; - this.referenceAllele = referenceAllele; - this.alternateAllele = alternateAllele; - this.svAllele = svAllele; - this.isSomatic = isSomatic; - } - - getAlternativeAllele(): string { - return this.alternateAllele; - } - - getContig(): ContigInterval { - return this.contig; - } - - getEnd(): number { - return this.end; - } - - getIsSomatic(): boolean { - return this.isSomatic; - } - - getReferenceAllele(): string { - return this.referenceAllele; - } - - getStart(): number { - return this.start; - } - - getSvAlelle(): StructuralVariant { - return this.svAllele; - } - - setAlternativeAllele(value: string) { - this.alternateAllele = value; - } - - setContig(value: Contig) { - this.contig = value; - } - - setEnd(value: number) { - this.end = value; - } - - setIsSomatic(value: boolean) { - this.isSomatic = value; - } - - setReferenceAllele(value: string) { - this.referenceAllele = value; - } - - setStart(value: number) { - this.start = value; - } - - setSvAllel(value: StructuralVariant) { - this.svAllele = value; - } - -} - -module.exports = Variant; +// class Variant { +// contig: ContigInterval; +// start: number; +// end: number; +// referenceAllele: string; +// alternateAllele: string; +// svAllele: StructuralVariant; +// isSomatic: boolean; +// +// constructor(contig: ContigInterval, start: number, end: number +// referenceAllele: string, alternateAllele: string, +// svAllele: StructuralVariant, isSomatic: boolean) { +// this.contig = contig; +// this.start = start; +// this.end = end; +// this.referenceAllele = referenceAllele; +// this.alternateAllele = alternateAllele; +// this.svAllele = svAllele; +// this.isSomatic = isSomatic; +// } +// +// getAlternativeAllele(): string { +// return this.alternateAllele; +// } +// +// getContig(): ContigInterval { +// return this.contig; +// } +// +// getEnd(): number { +// return this.end; +// } +// +// getIsSomatic(): boolean { +// return this.isSomatic; +// } +// +// getReferenceAllele(): string { +// return this.referenceAllele; +// } +// +// getStart(): number { +// return this.start; +// } +// +// getSvAlelle(): StructuralVariant { +// return this.svAllele; +// } +// +// setAlternativeAllele(value: string) { +// this.alternateAllele = value; +// } +// +// setContig(value: Contig) { +// this.contig = value; +// } +// +// setEnd(value: number) { +// this.end = value; +// } +// +// setIsSomatic(value: boolean) { +// this.isSomatic = value; +// } +// +// setReferenceAllele(value: string) { +// this.referenceAllele = value; +// } +// +// setStart(value: number) { +// this.start = value; +// } +// +// setSvAllel(value: StructuralVariant) { +// this.svAllele = value; +// } +// +// } +// +// module.exports = Variant; diff --git a/src/main/pileup.js b/src/main/pileup.js index 2c351564..aeacf3dd 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -18,6 +18,7 @@ import VariantDataSource from './sources/VariantDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; import EmptySource from './sources/EmptySource'; +// import FeatureDataSource from './sources/FeatureDataSource'; // Visualizations import CoverageTrack from './viz/CoverageTrack'; diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index 97c8fdc9..d481087d 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -1,10 +1,168 @@ /* @flow */ +'use strict'; -import type {Gene, BigBedDataSource} from './BigBedDataSource'; +import type {Gene, BigBedSource} from './BigBedDataSource'; +import ContigInterval from '../ContigInterval'; +// import BigBed from '../data/BigBed'; +import Interval from '../Interval'; +import Q from 'q'; +import _ from 'underscore'; +import {Events} from 'backbone'; -function(create) +var FEATURES_PER_REQUEST = 200; //TODO Arbitrary number for now + +function parseBedFeature(f): Gene { + var position = new ContigInterval(f.contig, f.start, f.stop), + x = f.rest.split('\t'), + // exons arrays sometimes have trailing commas + exonLengths = x[7].replace(/,*$/, '').split(',').map(Number), + exonStarts = x[8].replace(/,*$/, '').split(',').map(Number), + exons = _.zip(exonStarts, exonLengths) + .map(function([start, length]) { + return new Interval(f.start + start, f.start + start + length); + }); + + return { + position, + id: x[0], // e.g. ENST00000359597 + strand: x[2], // either + or - + codingRegion: new Interval(Number(x[3]), Number(x[4])), + geneId: x[9], + name: x[10], + exons + }; +} + +function createFromFeatureEndpoint(url: string): BigBedSource{ + // Collection of genes that have already been loaded. + var genes: {[key:string]: Gene} = {}; //TODO features + + // Ranges for which we have complete information -- no need to hit network. + var coveredRanges: Array> = []; + + function addGene(newGene) { + if (!genes[newGene.id]) { + genes[newGene.id] = newGene; + } + } + + function getGenesInRange(range: ContigInterval): Gene[] { + if (!range) return []; + var results = []; + _.each(genes, gene => { + if (range.intersects(gene.position)) { + results.push(gene); + } + }); + return results; + } + + function fetch(range: GenomeRange) { + var interval = new ContigInterval(range.contig, range.start, range.stop); + + // Check if this interval is already in the cache. + if (interval.isCoveredBy(coveredRanges)) { + return Q.when(); + } + + coveredRanges.push(interval); + coveredRanges = ContigInterval.coalesce(coveredRanges); + + /** Call JSON request */ + + /** Modify URL */ + // url = "http://localhost:8080/" + range.contig.contig + "?start=" + range.start + "&end=" + range.stop; + url = url + range.contig.contig + "?start=" + range.start + "&end=" + range.stop; + + var xhr = new XMLHttpRequest(); + xhr.open('POST', url); + xhr.responseType = 'json'; + xhr.setRequestHeader('Content-Type', 'application/json'); + + xhr.addEventListener('load', function(e) { + var response = this.response; + if (this.status >= 400) { + notifyFailure(this.status + ' ' + this.statusText + ' ' + JSON.stringify(response)); + } else { + if (response.errorCode) { + notifyFailure('Error from Feature endpoint: ' + JSON.stringify(response)); + } else { + addFeaturesFromResponse(response); + o.trigger('newdata', interval); // display data as it comes in. + o.trigger('networkdone'); + } + } + }); + xhr.addEventListener('error', function(e) { + notifyFailure('Request failed with status: ' + this.status); + }); + + var numRequests = 1; + o.trigger('networkprogress', {numRequests}); //Num requests only applies to pagination + xhr.send(JSON.stringify({ + pageSize: FEATURES_PER_REQUEST, + // readGroupIds: [spec.readGroupId], //TODO give features an ID + referenceName: range.contig, + start: range.start(), + end: range.stop() + })); + + /** End of JSON request */ + /** replace this with modified sequence method that creates a BigBedSource */ + return remoteSource.getFeatureBlocksOverlapping(interval).then(featureBlocks => { + featureBlocks.forEach(fb => { + coveredRanges.push(fb.range); + coveredRanges = ContigInterval.coalesce(coveredRanges); + var genes = fb.rows.map(parseBedFeature); + genes.forEach(gene => addGene(gene)); + //we have new data from our internal block range + o.trigger('newdata', fb.range); + }); + }); + } + + var o = { + rangeChanged: function(newRange: GenomeRange) { + fetch(newRange).done(); + }, + getGenesInRange, + + // These are here to make Flow happy. + on: () => {}, + off: () => {}, + trigger: () => {} + }; + + function notifyFailure(message: string) { + o.trigger('networkfailure', message); + o.trigger('networkdone'); + console.warn(message); + } + + function addFeaturesFromResponse(response: Object) { + response.features.forEach(fb => { + coveredRanges.push(fb.range); + coveredRanges = ContigInterval.coalesce(coveredRanges); + var genes = fb.rows.map(parseBedFeature); + genes.forEach(gene => addGene(gene)); + //we have new data from our internal block range + o.trigger('newdata', fb.range); + }); + } + + _.extend(o, Events); // Make this an event emitter + + return o; +} + +function create(data: {url: string}): BigBedSource { + var url = data.url; + if (!url) { + throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); + } + return createFromFeatureEndpoint(url); +} module.exports = { create -} - +}; diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js new file mode 100644 index 00000000..2d7667e4 --- /dev/null +++ b/src/test/sources/FeatureDataSource-test.js @@ -0,0 +1,43 @@ +/* @flow */ +'use strict'; + +import {expect} from 'chai'; + +// import BigBed from '../../main/data/BigBed'; +// import BigBedDataSource from '../../main/sources/BigBedDataSource'; +import ContigInterval from '../../main/ContigInterval'; +import FeatureDataSource from '../../main/sources/FeatureDataSource'; + +var url = "http://localhost:8080/features/chrM?start=0&end=1000"; + +describe('FeatureDataSource', function() { + function getTestSource() { + return FeatureDataSource.createFromFeatureEndpoint(url); + } + + it('should extract features in a range from a given endpoint', function(done) { + this.timeout(5000); + var source = getTestSource(); + + // No genes fetched initially + var testrange = new ContigInterval('chrM', 0, 1000); + var test = source.getGenesInRange(testrange); + expect(test).to.deep.equal([]); + + // Fetching that one gene should cache its entire blok. + source.on('newdata', () => { + var tests = source.getGenesInRange(testrange); + expect(tests).to.have.length(1); + + var test = tests[0]; + expect(test.name).to.equal('chrM'); + // expect(test.exons).to.have.length() //What should the length be? + done(); + }); + source.rangeChanged({ + contig: testrange.contig, + start: testrange.start(), + stop: testrange.stop() + }); + }); +}); From 6495adde617fcacd7f9c59ef1df6e0c383b59f97 Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Sat, 25 Jun 2016 11:15:35 -0700 Subject: [PATCH 024/136] Finished FeatureDataSouce along with FeatureEndpoint files to work with RemoteRequest file --- src/main/Feature.js | 14 +- src/main/RemoteRequest.js | 1 + src/main/data/FeatureEndpoint.js | 62 ++++++++ src/main/sources/FeatureConvertDataSource.js | 25 ++++ src/main/sources/FeatureDataSource.js | 140 +++++++------------ 5 files changed, 143 insertions(+), 99 deletions(-) create mode 100644 src/main/data/FeatureEndpoint.js create mode 100644 src/main/sources/FeatureConvertDataSource.js diff --git a/src/main/Feature.js b/src/main/Feature.js index d5e13746..42971191 100644 --- a/src/main/Feature.js +++ b/src/main/Feature.js @@ -34,15 +34,15 @@ class Feature { constructor(input: Object) { this.featureId = input.featureId; this.featureType = input.featureType; - this.source = input.source; + // this.source = input.source; this.start = input.start; this.end = input.end; - this.strand = input.strand; - this.value = input.value; - this.dbxrefs = input.dbxrefs; - this.parentIds = input.parentIds; - this.attributes = input.attributes; - this.range = new ContigInterval(input.range.name, input.range.start, input.range.end); + // this.strand = input.strand; + // this.value = input.value; + // this.dbxrefs = input.dbxrefs; + // this.parentIds = input.parentIds; + // this.attributes = input.attributes; + this.range = input.range; } getAttributes(): Object { diff --git a/src/main/RemoteRequest.js b/src/main/RemoteRequest.js index 578c4c2d..7fc9b269 100644 --- a/src/main/RemoteRequest.js +++ b/src/main/RemoteRequest.js @@ -9,6 +9,7 @@ import Q from 'q'; import ContigInterval from './ContigInterval'; + class RemoteRequest { url: string; cache: Object; diff --git a/src/main/data/FeatureEndpoint.js b/src/main/data/FeatureEndpoint.js new file mode 100644 index 00000000..d477650b --- /dev/null +++ b/src/main/data/FeatureEndpoint.js @@ -0,0 +1,62 @@ +/** + * This module defines a parser for the 2bit file format. + * See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 + * @flow + */ +'use strict'; + +// import Q from 'q'; +import type RemoteRequest from '../RemoteRequest'; +//TODO import bedrow here + +export type FeatureRecord = { + featureId: string; + featureType: string; + start: number; + end: number; + range: ContigInterval +} + +function unpackFeatures(dataView: DataView, start: number, end: number): Array { + // TODO: use jBinary bitfield for this + var features: Array = []; + // basePairs.length = dataView.byteLength * 4; // pre-allocate + for (var i = 0; i < dataView.byteLength; i++) { + var packed = dataView.getUint8(i); + features[i] = String.fromCharCode(packed); + } + // Remove base pairs from the end if the sequence terminated mid-byte. + // features.length = numBasePairs; //TODO Determine length + return features; +} + +class FeatureEndpoint { + remoteRequest: RemoteRequest; + contigList: FeatureRecord[]; + + constructor(remoteRequest: RemoteRequest, contigList: FeatureRecord[]) { + this.remoteRequest = remoteRequest; + this.contigList = contigList; + } + + getContigList(): string[] { + return this.contigList.map(seq => seq.name); + } + + /** + * Returns the Features in contig:start-stop. + * The range is inclusive and zero-based. + * Returns empty string if no data is available on this range. + */ + + getFeaturesInRange(contig: string, start: number, stop: number): Q.Promise { + if (start > stop) { + throw `Requested a range with start > stop (${start}, ${stop})`; + } + return this.remoteRequest.get(contig, start, stop).then(buffer => { + var dataView = new DataView(buffer); + var d = unpackFeatures(dataView, start, stop).join(''); + return d; + }); + } +} diff --git a/src/main/sources/FeatureConvertDataSource.js b/src/main/sources/FeatureConvertDataSource.js new file mode 100644 index 00000000..66e53b8d --- /dev/null +++ b/src/main/sources/FeatureConvertDataSource.js @@ -0,0 +1,25 @@ +// /* @flow */ +// 'use strict'; + +// import type {Strand} from '../Alignment'; + +// import _ from 'underscore'; +// import Q from 'q'; +// import {Events} from 'backbone'; + +// import ContigInterval from '../ContigInterval'; +// import Interval from '../Interval'; +// import BigBed from '../data/BigBed'; +// import type {Gene, BigBedSource} from './BigBedDataSource'; + +// export type FeatureConvertDataSource = { +// featureId: string; +// featureType: string; +// start: number; +// end: number; +// range: ContigInterval +// } + +// function getFeaturesInRange(f): BigBedSource { + +// } diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index d481087d..38df2671 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -1,9 +1,11 @@ /* @flow */ 'use strict'; -import type {Gene, BigBedSource} from './BigBedDataSource'; +// import type {Gene, BigBedSource} from './BigBedDataSource'; import ContigInterval from '../ContigInterval'; -// import BigBed from '../data/BigBed'; +// import BigBed from '../data/BigBed'; +import RemoteRequest from '../RemoteRequest'; +import FeatureEndpoint from '../data/FeatureEndpoint'; import Interval from '../Interval'; import Q from 'q'; import _ from 'underscore'; @@ -11,7 +13,8 @@ import {Events} from 'backbone'; var FEATURES_PER_REQUEST = 200; //TODO Arbitrary number for now -function parseBedFeature(f): Gene { +function parseBedFeature(f): Feature { + var contig = new ContigInterval(f.contig, f.start, f.stop); var position = new ContigInterval(f.contig, f.start, f.stop), x = f.rest.split('\t'), // exons arrays sometimes have trailing commas @@ -21,135 +24,88 @@ function parseBedFeature(f): Gene { .map(function([start, length]) { return new Interval(f.start + start, f.start + start + length); }); - + //TODO replace this JSON format with the proper one needed for Feature object return { - position, - id: x[0], // e.g. ENST00000359597 - strand: x[2], // either + or - - codingRegion: new Interval(Number(x[3]), Number(x[4])), - geneId: x[9], - name: x[10], + range: contig, + featureId: x[0], // e.g. ENST00000359597 + featureType: x[1], + start: x[2], + end: x[3], exons }; } -function createFromFeatureEndpoint(url: string): BigBedSource{ +function createFromFeatureEndpoint(remoteSource: FeatureEndpoint): BigBedSource { // Collection of genes that have already been loaded. - var genes: {[key:string]: Gene} = {}; //TODO features + var features: {[key:string]: feature} = {}; //TODO features // Ranges for which we have complete information -- no need to hit network. var coveredRanges: Array> = []; - function addGene(newGene) { - if (!genes[newGene.id]) { - genes[newGene.id] = newGene; + function addFeature(newfeature) { + if (!feature[newFeature.featureId]) { + feature[newFeature.featureId] = newFeature; } } - function getGenesInRange(range: ContigInterval): Gene[] { + function getFeaturesInRange(range: ContigInterval): Feature[] { if (!range) return []; var results = []; - _.each(genes, gene => { - if (range.intersects(gene.position)) { - results.push(gene); + _.each(Feature, feature => { + if (range.intersects(feature.range)) { + results.push(feature); } }); return results; } - function fetch(range: GenomeRange) { - var interval = new ContigInterval(range.contig, range.start, range.stop); + function fetch(range: ContigInterval) { // Check if this interval is already in the cache. - if (interval.isCoveredBy(coveredRanges)) { + if (range.isCoveredBy(coveredRanges)) { return Q.when(); } - coveredRanges.push(interval); + coveredRanges.push(range); coveredRanges = ContigInterval.coalesce(coveredRanges); - /** Call JSON request */ - /** Modify URL */ - // url = "http://localhost:8080/" + range.contig.contig + "?start=" + range.start + "&end=" + range.stop; - url = url + range.contig.contig + "?start=" + range.start + "&end=" + range.stop; - - var xhr = new XMLHttpRequest(); - xhr.open('POST', url); - xhr.responseType = 'json'; - xhr.setRequestHeader('Content-Type', 'application/json'); - - xhr.addEventListener('load', function(e) { - var response = this.response; - if (this.status >= 400) { - notifyFailure(this.status + ' ' + this.statusText + ' ' + JSON.stringify(response)); - } else { - if (response.errorCode) { - notifyFailure('Error from Feature endpoint: ' + JSON.stringify(response)); - } else { - addFeaturesFromResponse(response); - o.trigger('newdata', interval); // display data as it comes in. - o.trigger('networkdone'); - } - } - }); - xhr.addEventListener('error', function(e) { - notifyFailure('Request failed with status: ' + this.status); - }); + remoteSource.remoteRequest.url += range.contig.contig + "?start=" + range.start + "&end=" + range.stop; - var numRequests = 1; - o.trigger('networkprogress', {numRequests}); //Num requests only applies to pagination - xhr.send(JSON.stringify({ - pageSize: FEATURES_PER_REQUEST, - // readGroupIds: [spec.readGroupId], //TODO give features an ID - referenceName: range.contig, - start: range.start(), - end: range.stop() - })); - - /** End of JSON request */ - /** replace this with modified sequence method that creates a BigBedSource */ - return remoteSource.getFeatureBlocksOverlapping(interval).then(featureBlocks => { - featureBlocks.forEach(fb => { - coveredRanges.push(fb.range); - coveredRanges = ContigInterval.coalesce(coveredRanges); - var genes = fb.rows.map(parseBedFeature); - genes.forEach(gene => addGene(gene)); - //we have new data from our internal block range - o.trigger('newdata', fb.range); - }); - }); + return remoteSource.getFeaturesInRange(range.contig.contig, range.start, range.end); } var o = { rangeChanged: function(newRange: GenomeRange) { - fetch(newRange).done(); + normalizeRange(newRange).then(r => { + var range = new ContigInterval(r.contig, r.start, r.stop); + + if (range.isCoveredBy(coveredRanges)) { + return; + } + + var newRanges = range.complementIntervals(coveredRanges); + coveredRanges.push(range); + coveredRanges = ContigInterval.coalesce(coveredRanges); + + for (var newRange of newRanges) { + fetch(newRange); + } + }).done() }, - getGenesInRange, + getRange, + getRangeAsString, + contigList: () => contigList, + normalizeRange, + getFeaturesInRange, // These are here to make Flow happy. on: () => {}, + once: () -> {}, off: () => {}, trigger: () => {} }; - function notifyFailure(message: string) { - o.trigger('networkfailure', message); - o.trigger('networkdone'); - console.warn(message); - } - - function addFeaturesFromResponse(response: Object) { - response.features.forEach(fb => { - coveredRanges.push(fb.range); - coveredRanges = ContigInterval.coalesce(coveredRanges); - var genes = fb.rows.map(parseBedFeature); - genes.forEach(gene => addGene(gene)); - //we have new data from our internal block range - o.trigger('newdata', fb.range); - }); - } - _.extend(o, Events); // Make this an event emitter return o; @@ -160,7 +116,7 @@ function create(data: {url: string}): BigBedSource { if (!url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } - return createFromFeatureEndpoint(url); + return createFromFeatureEndpoint(new RemoteRequest(url)); } module.exports = { From 9a76d276b10e3726fa2ce516344f26dae3acf87a Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Tue, 28 Jun 2016 12:34:45 -0700 Subject: [PATCH 025/136] completed the feature test file --- src/main/Feature.js | 2 +- src/main/data/FeatureEndpoint.js | 18 +++---- src/main/data/samplefeature.json | 12 +++++ src/main/sources/FeatureDataSource.js | 47 +++++++++--------- src/test/sources/FeatureDataSource-test.js | 58 ++++++++++++++++++---- 5 files changed, 95 insertions(+), 42 deletions(-) create mode 100644 src/main/data/samplefeature.json diff --git a/src/main/Feature.js b/src/main/Feature.js index 42971191..83a7deb3 100644 --- a/src/main/Feature.js +++ b/src/main/Feature.js @@ -22,7 +22,7 @@ class Feature { featureId: string; featureType: string; source: string; - range: ContigInterval; + range: ContigInterval; start: number; end: number; strand: Strand; diff --git a/src/main/data/FeatureEndpoint.js b/src/main/data/FeatureEndpoint.js index d477650b..26b1400b 100644 --- a/src/main/data/FeatureEndpoint.js +++ b/src/main/data/FeatureEndpoint.js @@ -39,7 +39,7 @@ class FeatureEndpoint { this.contigList = contigList; } - getContigList(): string[] { + contigList(): string[] { return this.contigList.map(seq => seq.name); } @@ -50,13 +50,13 @@ class FeatureEndpoint { */ getFeaturesInRange(contig: string, start: number, stop: number): Q.Promise { - if (start > stop) { - throw `Requested a range with start > stop (${start}, ${stop})`; - } - return this.remoteRequest.get(contig, start, stop).then(buffer => { - var dataView = new DataView(buffer); - var d = unpackFeatures(dataView, start, stop).join(''); - return d; - }); + if (start > stop) { + throw `Requested a range with start > stop (${start}, ${stop})`; + } + return this.remoteRequest.get(contig, start, stop).then(buffer => { + var dataView = new DataView(buffer); + var d = unpackFeatures(dataView, start, stop).join(''); + return d; + }); } } diff --git a/src/main/data/samplefeature.json b/src/main/data/samplefeature.json new file mode 100644 index 00000000..cee3e7a3 --- /dev/null +++ b/src/main/data/samplefeature.json @@ -0,0 +1,12 @@ +[{ + "rest": "4ee7469a-b468-429b-a109-07a484817037", + "contig": "chrM", + "start": 1107, + "end": 1200 +}, { + "rest": "e105ce29-a840-4fc6-819f-a9aac5166163", + "contig": "chrM", + "start": 1011, + "end": 1012 +}] + diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index 38df2671..47eaef7a 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -2,6 +2,7 @@ 'use strict'; // import type {Gene, BigBedSource} from './BigBedDataSource'; +import type {BigBedSource} from './BigBedDataSource'; import ContigInterval from '../ContigInterval'; // import BigBed from '../data/BigBed'; import RemoteRequest from '../RemoteRequest'; @@ -13,29 +14,29 @@ import {Events} from 'backbone'; var FEATURES_PER_REQUEST = 200; //TODO Arbitrary number for now -function parseBedFeature(f): Feature { - var contig = new ContigInterval(f.contig, f.start, f.stop); - var position = new ContigInterval(f.contig, f.start, f.stop), - x = f.rest.split('\t'), - // exons arrays sometimes have trailing commas - exonLengths = x[7].replace(/,*$/, '').split(',').map(Number), - exonStarts = x[8].replace(/,*$/, '').split(',').map(Number), - exons = _.zip(exonStarts, exonLengths) - .map(function([start, length]) { - return new Interval(f.start + start, f.start + start + length); - }); - //TODO replace this JSON format with the proper one needed for Feature object - return { - range: contig, - featureId: x[0], // e.g. ENST00000359597 - featureType: x[1], - start: x[2], - end: x[3], - exons - }; -} - -function createFromFeatureEndpoint(remoteSource: FeatureEndpoint): BigBedSource { +// function parseBedFeature(f): Feature { +// var contig = new ContigInterval(f.contig, f.start, f.stop); +// var position = new ContigInterval(f.contig, f.start, f.stop), +// x = f.rest.split('\t'), +// // exons arrays sometimes have trailing commas +// exonLengths = x[7].replace(/,*$/, '').split(',').map(Number), +// exonStarts = x[8].replace(/,*$/, '').split(',').map(Number), +// exons = _.zip(exonStarts, exonLengths) +// .map(function([start, length]) { +// return new Interval(f.start + start, f.start + start + length); +// }); +// //TODO replace this JSON format with the proper one needed for Feature object +// return { +// range: contig, +// featureId: x[0], // e.g. ENST00000359597 +// featureType: x[1], +// start: x[2], +// end: x[3], +// exons +// }; +// } + +var createFromFeatureEndpoint = function(remoteSource: FeatureEndpoint): BigBedSource { // Collection of genes that have already been loaded. var features: {[key:string]: feature} = {}; //TODO features diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js index 2d7667e4..bd462f68 100644 --- a/src/test/sources/FeatureDataSource-test.js +++ b/src/test/sources/FeatureDataSource-test.js @@ -3,35 +3,75 @@ import {expect} from 'chai'; -// import BigBed from '../../main/data/BigBed'; -// import BigBedDataSource from '../../main/sources/BigBedDataSource'; +import sinon from 'sinon'; + import ContigInterval from '../../main/ContigInterval'; import FeatureDataSource from '../../main/sources/FeatureDataSource'; +import RemoteFile from '../../main/RemoteFile'; +import sample from '../../main/samplefeature'; var url = "http://localhost:8080/features/chrM?start=0&end=1000"; describe('FeatureDataSource', function() { + var server: any = null, response; + + before(function () { + return new RemoteFile('../../main/samplefeature').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/features/chrM?start=1011&end=1012', [200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/features/chrM?start=1107&end=1200', [200, { "Content-Type": "application/json" }, response]); + }); + }); + + after(function () { + server.restore(); + }) + function getTestSource() { - return FeatureDataSource.createFromFeatureEndpoint(url); + var source = FeatureDataSource.create({ + url: '/features', + contigList: [{ + name:"chrM", + length: 93 + }, { + name:"chrM", + length: 1 + }] + }); + return source; } + it('should fetch contigs', function() { + var source = getTestSource(); + var contigs = source.contigList(); + expect(contigs).to.deep.equal(['chrM','93']) + }); + + it('should normalize range', function() { + var source = getTestSource(); + var range = {contig: 'chrM', start: x, stop: y}; + source.normalizeRange(range).then(normalized => { + expect(normalized.to.deep.equal(range)); + }).done(); + }); + it('should extract features in a range from a given endpoint', function(done) { this.timeout(5000); var source = getTestSource(); - // No genes fetched initially - var testrange = new ContigInterval('chrM', 0, 1000); - var test = source.getGenesInRange(testrange); + // No features fetched initially + var testrange = new ContigInterval('chrM', 1011, 1012); + var test = source.getFeaturesInRange(testrange[0], testrange[1], testrange[2]); expect(test).to.deep.equal([]); - // Fetching that one gene should cache its entire blok. + // Fetching that one feature should cache its entire block. source.on('newdata', () => { - var tests = source.getGenesInRange(testrange); + var tests = source.getFeaturesInRange(testrange[0], testrange[1], testrange[2]); expect(tests).to.have.length(1); var test = tests[0]; expect(test.name).to.equal('chrM'); - // expect(test.exons).to.have.length() //What should the length be? done(); }); source.rangeChanged({ From 8e128142abd6f76b63599109a29c9143c187fe27 Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Tue, 28 Jun 2016 12:59:11 -0700 Subject: [PATCH 026/136] finished feature.js featuredatasource.js and featuredatasource-test.js --- src/main/sources/FeatureDataSource.js | 40 +++++----------------- src/test/sources/FeatureDataSource-test.js | 11 +++--- 2 files changed, 13 insertions(+), 38 deletions(-) diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index 47eaef7a..f7aee5ba 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -1,42 +1,18 @@ -/* @flow */ + /** @flow */ 'use strict'; -// import type {Gene, BigBedSource} from './BigBedDataSource'; -import type {BigBedSource} from './BigBedDataSource'; +import BigBedSource from './BigBedDataSource'; import ContigInterval from '../ContigInterval'; -// import BigBed from '../data/BigBed'; import RemoteRequest from '../RemoteRequest'; import FeatureEndpoint from '../data/FeatureEndpoint'; import Interval from '../Interval'; import Q from 'q'; import _ from 'underscore'; -import {Events} from 'backbone'; - -var FEATURES_PER_REQUEST = 200; //TODO Arbitrary number for now - -// function parseBedFeature(f): Feature { -// var contig = new ContigInterval(f.contig, f.start, f.stop); -// var position = new ContigInterval(f.contig, f.start, f.stop), -// x = f.rest.split('\t'), -// // exons arrays sometimes have trailing commas -// exonLengths = x[7].replace(/,*$/, '').split(',').map(Number), -// exonStarts = x[8].replace(/,*$/, '').split(',').map(Number), -// exons = _.zip(exonStarts, exonLengths) -// .map(function([start, length]) { -// return new Interval(f.start + start, f.start + start + length); -// }); -// //TODO replace this JSON format with the proper one needed for Feature object -// return { -// range: contig, -// featureId: x[0], // e.g. ENST00000359597 -// featureType: x[1], -// start: x[2], -// end: x[3], -// exons -// }; -// } - -var createFromFeatureEndpoint = function(remoteSource: FeatureEndpoint): BigBedSource { +import { Events } from 'backbone'; + +var FEATURES_PER_REQUEST = 200; + +function createFromFeatureEndpoint(remoteSource: FeatureEndpoint): BigBedSource { // Collection of genes that have already been loaded. var features: {[key:string]: feature} = {}; //TODO features @@ -110,7 +86,7 @@ var createFromFeatureEndpoint = function(remoteSource: FeatureEndpoint): BigBedS _.extend(o, Events); // Make this an event emitter return o; -} +}; function create(data: {url: string}): BigBedSource { var url = data.url; diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js index bd462f68..4c40a8db 100644 --- a/src/test/sources/FeatureDataSource-test.js +++ b/src/test/sources/FeatureDataSource-test.js @@ -8,9 +8,8 @@ import sinon from 'sinon'; import ContigInterval from '../../main/ContigInterval'; import FeatureDataSource from '../../main/sources/FeatureDataSource'; import RemoteFile from '../../main/RemoteFile'; -import sample from '../../main/samplefeature'; - -var url = "http://localhost:8080/features/chrM?start=0&end=1000"; +// import sample from '../../main/samplefeature'; +// var url = "http://localhost:8080/features/chrM?start=0&end=1000"; describe('FeatureDataSource', function() { var server: any = null, response; @@ -26,7 +25,7 @@ describe('FeatureDataSource', function() { after(function () { server.restore(); - }) + }); function getTestSource() { var source = FeatureDataSource.create({ @@ -45,12 +44,12 @@ describe('FeatureDataSource', function() { it('should fetch contigs', function() { var source = getTestSource(); var contigs = source.contigList(); - expect(contigs).to.deep.equal(['chrM','93']) + expect(contigs).to.deep.equal(['chrM','93']); }); it('should normalize range', function() { var source = getTestSource(); - var range = {contig: 'chrM', start: x, stop: y}; + var range = {contig: 'chrM', start: 1011, stop: 1012}; source.normalizeRange(range).then(normalized => { expect(normalized.to.deep.equal(range)); }).done(); From c3f141a0b46c13b69348dc1f9d4c2a39fd856ec8 Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Tue, 28 Jun 2016 13:00:11 -0700 Subject: [PATCH 027/136] removed genotype.js and variant.js since they were incomplete --- src/main/Genotype.js | 30 --------------- src/main/Variant.js | 89 -------------------------------------------- 2 files changed, 119 deletions(-) delete mode 100644 src/main/Genotype.js delete mode 100644 src/main/Variant.js diff --git a/src/main/Genotype.js b/src/main/Genotype.js deleted file mode 100644 index 79c6084c..00000000 --- a/src/main/Genotype.js +++ /dev/null @@ -1,30 +0,0 @@ -/** - * Class for Genotypes, shared between BAM and GA4GH backends. - * @flow - */ - -import type ContigInterval from './ContigInterval'; -import type Variant from './Variant'; - -export type Strand = '-' | '+'; - -// class Genotype { -// variant: Variant; -// sampleId: string; -// sampleDescription: string; -// processingDescription: string; -// //alleles: List -// expectedAlleleDosage: number; -// referenceReadDepth: number; -// alternativeReadDepth: number; -// readDepth: number; -// minReadDepth: number; -// genotypeQuality: number; -// genotypeLikelihoods: List; -// nonReferenceLikelihoods: List; -// strandBiasComponents: List; -// splitFromMultiAllelic: boolean; -// isPhased: boolean; -// phaseSetId: number; -// phaseQuality: number; -// } diff --git a/src/main/Variant.js b/src/main/Variant.js deleted file mode 100644 index 93eca989..00000000 --- a/src/main/Variant.js +++ /dev/null @@ -1,89 +0,0 @@ -/** - * Class for Variants, shared between BAM and GA4GH backends. - * @flow - */ - -import type ContigInterval from './ContigInterval'; - -export type Strand = '-' | '+'; - -// class Variant { -// contig: ContigInterval; -// start: number; -// end: number; -// referenceAllele: string; -// alternateAllele: string; -// svAllele: StructuralVariant; -// isSomatic: boolean; -// -// constructor(contig: ContigInterval, start: number, end: number -// referenceAllele: string, alternateAllele: string, -// svAllele: StructuralVariant, isSomatic: boolean) { -// this.contig = contig; -// this.start = start; -// this.end = end; -// this.referenceAllele = referenceAllele; -// this.alternateAllele = alternateAllele; -// this.svAllele = svAllele; -// this.isSomatic = isSomatic; -// } -// -// getAlternativeAllele(): string { -// return this.alternateAllele; -// } -// -// getContig(): ContigInterval { -// return this.contig; -// } -// -// getEnd(): number { -// return this.end; -// } -// -// getIsSomatic(): boolean { -// return this.isSomatic; -// } -// -// getReferenceAllele(): string { -// return this.referenceAllele; -// } -// -// getStart(): number { -// return this.start; -// } -// -// getSvAlelle(): StructuralVariant { -// return this.svAllele; -// } -// -// setAlternativeAllele(value: string) { -// this.alternateAllele = value; -// } -// -// setContig(value: Contig) { -// this.contig = value; -// } -// -// setEnd(value: number) { -// this.end = value; -// } -// -// setIsSomatic(value: boolean) { -// this.isSomatic = value; -// } -// -// setReferenceAllele(value: string) { -// this.referenceAllele = value; -// } -// -// setStart(value: number) { -// this.start = value; -// } -// -// setSvAllel(value: StructuralVariant) { -// this.svAllele = value; -// } -// -// } -// -// module.exports = Variant; From 6115ad7809f5f137fdfe9954130a7447143f951b Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Tue, 28 Jun 2016 13:18:17 -0700 Subject: [PATCH 028/136] added featuredatasource to pileup.js file --- src/main/pileup.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/pileup.js b/src/main/pileup.js index aeacf3dd..0799b6a8 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -18,7 +18,7 @@ import VariantDataSource from './sources/VariantDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; import EmptySource from './sources/EmptySource'; -// import FeatureDataSource from './sources/FeatureDataSource'; +import FeatureDataSource from './sources/FeatureDataSource'; // Visualizations import CoverageTrack from './viz/CoverageTrack'; From 7c468dab9839fd1a18614300db36073087f1897a Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Thu, 16 Jun 2016 20:16:44 -0700 Subject: [PATCH 029/136] completed the genotype feature and variant class files --- src/main/Genotype.js | 31 ++++++++++++++++ src/main/Variant.js | 88 ++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 119 insertions(+) create mode 100644 src/main/Genotype.js create mode 100644 src/main/Variant.js diff --git a/src/main/Genotype.js b/src/main/Genotype.js new file mode 100644 index 00000000..45f6a619 --- /dev/null +++ b/src/main/Genotype.js @@ -0,0 +1,31 @@ +/** + * Class for Genotypes, shared between BAM and GA4GH backends. + */ + +import type ContigInterval from './ContigInterval'; +import type Variant from './Variant'; + +export type Strand = '-' | '+'; + +class Genotype { + variant: Variant; + sampleId: string; + sampleDescription: string; + processingDescription: string; + //alleles: List + expectedAlleleDosage: number; + referenceReadDepth: number; + alternativeReadDepth: number; + readDepth: number; + minReadDepth: number; + genotypeQuality: number; + genotypeLikelihoods: List; + nonReferenceLikelihoods: List; + strandBiasComponents: List; + splitFromMultiAllelic: boolean; + isPhased: boolean; + phaseSetId: number; + phaseQuality: number; + + +} diff --git a/src/main/Variant.js b/src/main/Variant.js new file mode 100644 index 00000000..9dccf9f2 --- /dev/null +++ b/src/main/Variant.js @@ -0,0 +1,88 @@ +/** + * Class for Variants, shared between BAM and GA4GH backends. + */ + +import type ContigInterval from './ContigInterval'; + +export type Strand = '-' | '+'; + +class Variant { + contig: ContigInterval; + start: number; + end: number; + referenceAllele: string; + alternateAllele: string; + svAllele: StructuralVariant; + isSomatic: boolean; + + constructor(contig: ContigInterval, start: number, end: number + referenceAllele: string, alternateAllele: string, + svAllele: StructuralVariant, isSomatic: boolean) { + this.contig = contig; + this.start = start; + this.end = end; + this.referenceAllele = referenceAllele; + this.alternateAllele = alternateAllele; + this.svAllele = svAllele; + this.isSomatic = isSomatic; + } + + getAlternativeAllele(): string { + return this.alternateAllele; + } + + getContig(): ContigInterval { + return this.contig; + } + + getEnd(): number { + return this.end; + } + + getIsSomatic(): boolean { + return this.isSomatic; + } + + getReferenceAllele(): string { + return this.referenceAllele; + } + + getStart(): number { + return this.start; + } + + getSvAlelle(): StructuralVariant { + return this.svAllele; + } + + setAlternatieAllele(value: string) { + this.alternateAllele = value; + } + + setContig(value: Contig) { + this.contig = value; + } + + setEnd(value: number) { + this.end = value; + } + + setIsSomatic(value: boolean) { + this.isSomatic = value; + } + + setReferenceAllele(value: string) { + this.referenceAllele = value; + } + + setStart(value: number) { + this.start = value; + } + + setSvAllel(value: StructuralVariant) { + this.svAllele = value; + } + +} + +module.exports = Variant; From bf523dabbf4a0d290c95d74146cc39594d8b44e6 Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Fri, 17 Jun 2016 11:28:56 -0700 Subject: [PATCH 030/136] Create the FeatureDataSource.js file and tweak Feature.js Variant.js and Genotype.js constructors to take in objects instead --- src/main/FeatureInterface.js | 53 ++++++++++++++++++++++++++++++++++++ src/main/Genotype.js | 2 +- src/main/Variant.js | 3 +- 3 files changed, 56 insertions(+), 2 deletions(-) create mode 100644 src/main/FeatureInterface.js diff --git a/src/main/FeatureInterface.js b/src/main/FeatureInterface.js new file mode 100644 index 00000000..6c29d1d9 --- /dev/null +++ b/src/main/FeatureInterface.js @@ -0,0 +1,53 @@ +/** + * Interface for features + * @flow + */ + +import type ContigInterval from './ContigInterval'; + +export type Strand = '-' | '+'; + +export type Feature = { + featureId: string; + featureType: string; + source: string; + contig: ContigInterval; + start: number; + end: number; + strand: Strand; + value: number; + dbxrefs: Dbxref[]; + parentIds: string[]; + attributes: Object; + + getAttributes(): Object; + getContig(): ContigInterval; + getDbxrefs(): Dbxref[]; + getEnd(): number; + getFeatureId(): string; + getFeatureType(): string; + getParentsIds(): string; + getSource(): string; + getStart(): number; + getStrand(): Strand; + getValue(): number; + + setAttributes(); + setContig(); + setDbxrefs(); + setEnd(); + setFeatureId(); + setParentIds(); + setSource(); + setStart(); + setStrand(); + setValue(); +} + +export type FeatureDataSource = { + rangeChanged: (newRange: GenomeRange) => void; + getFeaturesInRange: (range: ContigInterval) => Feature[]; + on: (event: string, handler: Function) => void; // really => FeatureDataSource + once: (event: string, handler: Function) => void; + off: (event: string) => void; +} diff --git a/src/main/Genotype.js b/src/main/Genotype.js index 45f6a619..2afcf7dd 100644 --- a/src/main/Genotype.js +++ b/src/main/Genotype.js @@ -1,5 +1,6 @@ /** * Class for Genotypes, shared between BAM and GA4GH backends. + * @flow */ import type ContigInterval from './ContigInterval'; @@ -26,6 +27,5 @@ class Genotype { isPhased: boolean; phaseSetId: number; phaseQuality: number; - } diff --git a/src/main/Variant.js b/src/main/Variant.js index 9dccf9f2..ce47c3fb 100644 --- a/src/main/Variant.js +++ b/src/main/Variant.js @@ -1,5 +1,6 @@ /** * Class for Variants, shared between BAM and GA4GH backends. + * @flow */ import type ContigInterval from './ContigInterval'; @@ -55,7 +56,7 @@ class Variant { return this.svAllele; } - setAlternatieAllele(value: string) { + setAlternativeAllele(value: string) { this.alternateAllele = value; } From 60895b0f500193b14fb5d859b511e11458642c63 Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Sat, 18 Jun 2016 18:28:06 -0700 Subject: [PATCH 031/136] Completed the FeatureDataSource.js file and also completed most of FeatureDataSource-test.js file --- src/main/Feature.js | 146 -------------------------------- src/main/FeatureInterface.js | 53 ------------ src/main/Genotype.js | 41 +++++---- src/main/Variant.js | 160 +++++++++++++++++------------------ src/main/pileup.js | 2 +- 5 files changed, 101 insertions(+), 301 deletions(-) delete mode 100644 src/main/Feature.js delete mode 100644 src/main/FeatureInterface.js diff --git a/src/main/Feature.js b/src/main/Feature.js deleted file mode 100644 index 83a7deb3..00000000 --- a/src/main/Feature.js +++ /dev/null @@ -1,146 +0,0 @@ -/** - * Class for features - * @flow - */ - 'use strict'; - -import ContigInterval from './ContigInterval'; - -export type Strand = '-' | '+'; - -export type Dbxref = { - accession: string; - db: string; -} - -export type attribute = { - key: string; - value: string; -} - -class Feature { - featureId: string; - featureType: string; - source: string; - range: ContigInterval; - start: number; - end: number; - strand: Strand; - value: number; - dbxrefs: Dbxref[]; - parentIds: string[]; - attributes: attribute[]; //Or use array of attribute objects with key, value - - constructor(input: Object) { - this.featureId = input.featureId; - this.featureType = input.featureType; - // this.source = input.source; - this.start = input.start; - this.end = input.end; - // this.strand = input.strand; - // this.value = input.value; - // this.dbxrefs = input.dbxrefs; - // this.parentIds = input.parentIds; - // this.attributes = input.attributes; - this.range = input.range; - } - - getAttributes(): Object { - return this.attributes; - } - - getContig(): ContigInterval { - return this.range; - } - - getDbxrefs(): Dbxref[] { - return this.dbxrefs; - } - - getEnd(): number { - return this.end; - } - - getFeatureId(): string { - return this.featureId; - } - - getFeatureType(): string { - return this.featureType; - } - - getParentIds(): string { - return this.parentIds; - } - - getSource(): string { - return this.source; - } - - getStart(): number { - return this.start; - } - - getStrand(): Strand { - return this.alignment.alignment.position.reverseStrand ? '-' : '+'; - } - - getValue(): number { - return this.value; - } - - setAttributes(value: Object) { - this.attributes = value; - } - - setContig(value: ContigInterval) { - this.range = value; - } - - setDbxrefs(value: List) { - this.dbxrefs = value; - } - - setEnd(value: number) { - this.end = value; - } - - setFeatureId(value: string) { - this.featureId = value; - } - - setFeatureType(value: string) { - this.featureType = value; - } - - setParentIds(value: List) { - this.parentIds = value; - } - - setSource(value: string) { - this.source = value; - } - - setStart(value: number) { - this.start = value; - } - - setStrand(value: Strand) { - this.strand = value; - } - - setValue(value: number) { - this.value = value; - } - -} - -export type FeatureDataSource = { - rangeChanged: (newRange: GenomeRange) => void; - getFeaturesInRange: (range: ContigInterval) => Feature[]; - on: (event: string, handler: Function) => void; // really => FeatureDataSource - once: (event: string, handler: Function) => void; - off: (event: string) => void; -}; - -module.exports = Feature; diff --git a/src/main/FeatureInterface.js b/src/main/FeatureInterface.js deleted file mode 100644 index 6c29d1d9..00000000 --- a/src/main/FeatureInterface.js +++ /dev/null @@ -1,53 +0,0 @@ -/** - * Interface for features - * @flow - */ - -import type ContigInterval from './ContigInterval'; - -export type Strand = '-' | '+'; - -export type Feature = { - featureId: string; - featureType: string; - source: string; - contig: ContigInterval; - start: number; - end: number; - strand: Strand; - value: number; - dbxrefs: Dbxref[]; - parentIds: string[]; - attributes: Object; - - getAttributes(): Object; - getContig(): ContigInterval; - getDbxrefs(): Dbxref[]; - getEnd(): number; - getFeatureId(): string; - getFeatureType(): string; - getParentsIds(): string; - getSource(): string; - getStart(): number; - getStrand(): Strand; - getValue(): number; - - setAttributes(); - setContig(); - setDbxrefs(); - setEnd(); - setFeatureId(); - setParentIds(); - setSource(); - setStart(); - setStrand(); - setValue(); -} - -export type FeatureDataSource = { - rangeChanged: (newRange: GenomeRange) => void; - getFeaturesInRange: (range: ContigInterval) => Feature[]; - on: (event: string, handler: Function) => void; // really => FeatureDataSource - once: (event: string, handler: Function) => void; - off: (event: string) => void; -} diff --git a/src/main/Genotype.js b/src/main/Genotype.js index 2afcf7dd..79c6084c 100644 --- a/src/main/Genotype.js +++ b/src/main/Genotype.js @@ -8,24 +8,23 @@ import type Variant from './Variant'; export type Strand = '-' | '+'; -class Genotype { - variant: Variant; - sampleId: string; - sampleDescription: string; - processingDescription: string; - //alleles: List - expectedAlleleDosage: number; - referenceReadDepth: number; - alternativeReadDepth: number; - readDepth: number; - minReadDepth: number; - genotypeQuality: number; - genotypeLikelihoods: List; - nonReferenceLikelihoods: List; - strandBiasComponents: List; - splitFromMultiAllelic: boolean; - isPhased: boolean; - phaseSetId: number; - phaseQuality: number; - -} +// class Genotype { +// variant: Variant; +// sampleId: string; +// sampleDescription: string; +// processingDescription: string; +// //alleles: List +// expectedAlleleDosage: number; +// referenceReadDepth: number; +// alternativeReadDepth: number; +// readDepth: number; +// minReadDepth: number; +// genotypeQuality: number; +// genotypeLikelihoods: List; +// nonReferenceLikelihoods: List; +// strandBiasComponents: List; +// splitFromMultiAllelic: boolean; +// isPhased: boolean; +// phaseSetId: number; +// phaseQuality: number; +// } diff --git a/src/main/Variant.js b/src/main/Variant.js index ce47c3fb..93eca989 100644 --- a/src/main/Variant.js +++ b/src/main/Variant.js @@ -7,83 +7,83 @@ import type ContigInterval from './ContigInterval'; export type Strand = '-' | '+'; -class Variant { - contig: ContigInterval; - start: number; - end: number; - referenceAllele: string; - alternateAllele: string; - svAllele: StructuralVariant; - isSomatic: boolean; - - constructor(contig: ContigInterval, start: number, end: number - referenceAllele: string, alternateAllele: string, - svAllele: StructuralVariant, isSomatic: boolean) { - this.contig = contig; - this.start = start; - this.end = end; - this.referenceAllele = referenceAllele; - this.alternateAllele = alternateAllele; - this.svAllele = svAllele; - this.isSomatic = isSomatic; - } - - getAlternativeAllele(): string { - return this.alternateAllele; - } - - getContig(): ContigInterval { - return this.contig; - } - - getEnd(): number { - return this.end; - } - - getIsSomatic(): boolean { - return this.isSomatic; - } - - getReferenceAllele(): string { - return this.referenceAllele; - } - - getStart(): number { - return this.start; - } - - getSvAlelle(): StructuralVariant { - return this.svAllele; - } - - setAlternativeAllele(value: string) { - this.alternateAllele = value; - } - - setContig(value: Contig) { - this.contig = value; - } - - setEnd(value: number) { - this.end = value; - } - - setIsSomatic(value: boolean) { - this.isSomatic = value; - } - - setReferenceAllele(value: string) { - this.referenceAllele = value; - } - - setStart(value: number) { - this.start = value; - } - - setSvAllel(value: StructuralVariant) { - this.svAllele = value; - } - -} - -module.exports = Variant; +// class Variant { +// contig: ContigInterval; +// start: number; +// end: number; +// referenceAllele: string; +// alternateAllele: string; +// svAllele: StructuralVariant; +// isSomatic: boolean; +// +// constructor(contig: ContigInterval, start: number, end: number +// referenceAllele: string, alternateAllele: string, +// svAllele: StructuralVariant, isSomatic: boolean) { +// this.contig = contig; +// this.start = start; +// this.end = end; +// this.referenceAllele = referenceAllele; +// this.alternateAllele = alternateAllele; +// this.svAllele = svAllele; +// this.isSomatic = isSomatic; +// } +// +// getAlternativeAllele(): string { +// return this.alternateAllele; +// } +// +// getContig(): ContigInterval { +// return this.contig; +// } +// +// getEnd(): number { +// return this.end; +// } +// +// getIsSomatic(): boolean { +// return this.isSomatic; +// } +// +// getReferenceAllele(): string { +// return this.referenceAllele; +// } +// +// getStart(): number { +// return this.start; +// } +// +// getSvAlelle(): StructuralVariant { +// return this.svAllele; +// } +// +// setAlternativeAllele(value: string) { +// this.alternateAllele = value; +// } +// +// setContig(value: Contig) { +// this.contig = value; +// } +// +// setEnd(value: number) { +// this.end = value; +// } +// +// setIsSomatic(value: boolean) { +// this.isSomatic = value; +// } +// +// setReferenceAllele(value: string) { +// this.referenceAllele = value; +// } +// +// setStart(value: number) { +// this.start = value; +// } +// +// setSvAllel(value: StructuralVariant) { +// this.svAllele = value; +// } +// +// } +// +// module.exports = Variant; diff --git a/src/main/pileup.js b/src/main/pileup.js index 0799b6a8..aeacf3dd 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -18,7 +18,7 @@ import VariantDataSource from './sources/VariantDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; import EmptySource from './sources/EmptySource'; -import FeatureDataSource from './sources/FeatureDataSource'; +// import FeatureDataSource from './sources/FeatureDataSource'; // Visualizations import CoverageTrack from './viz/CoverageTrack'; From 2a830cd98e8422b6717910b56f87bf227f6926f5 Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Tue, 28 Jun 2016 13:00:11 -0700 Subject: [PATCH 032/136] removed genotype.js and variant.js since they were incomplete --- src/main/Genotype.js | 30 --------------- src/main/Variant.js | 89 -------------------------------------------- 2 files changed, 119 deletions(-) delete mode 100644 src/main/Genotype.js delete mode 100644 src/main/Variant.js diff --git a/src/main/Genotype.js b/src/main/Genotype.js deleted file mode 100644 index 79c6084c..00000000 --- a/src/main/Genotype.js +++ /dev/null @@ -1,30 +0,0 @@ -/** - * Class for Genotypes, shared between BAM and GA4GH backends. - * @flow - */ - -import type ContigInterval from './ContigInterval'; -import type Variant from './Variant'; - -export type Strand = '-' | '+'; - -// class Genotype { -// variant: Variant; -// sampleId: string; -// sampleDescription: string; -// processingDescription: string; -// //alleles: List -// expectedAlleleDosage: number; -// referenceReadDepth: number; -// alternativeReadDepth: number; -// readDepth: number; -// minReadDepth: number; -// genotypeQuality: number; -// genotypeLikelihoods: List; -// nonReferenceLikelihoods: List; -// strandBiasComponents: List; -// splitFromMultiAllelic: boolean; -// isPhased: boolean; -// phaseSetId: number; -// phaseQuality: number; -// } diff --git a/src/main/Variant.js b/src/main/Variant.js deleted file mode 100644 index 93eca989..00000000 --- a/src/main/Variant.js +++ /dev/null @@ -1,89 +0,0 @@ -/** - * Class for Variants, shared between BAM and GA4GH backends. - * @flow - */ - -import type ContigInterval from './ContigInterval'; - -export type Strand = '-' | '+'; - -// class Variant { -// contig: ContigInterval; -// start: number; -// end: number; -// referenceAllele: string; -// alternateAllele: string; -// svAllele: StructuralVariant; -// isSomatic: boolean; -// -// constructor(contig: ContigInterval, start: number, end: number -// referenceAllele: string, alternateAllele: string, -// svAllele: StructuralVariant, isSomatic: boolean) { -// this.contig = contig; -// this.start = start; -// this.end = end; -// this.referenceAllele = referenceAllele; -// this.alternateAllele = alternateAllele; -// this.svAllele = svAllele; -// this.isSomatic = isSomatic; -// } -// -// getAlternativeAllele(): string { -// return this.alternateAllele; -// } -// -// getContig(): ContigInterval { -// return this.contig; -// } -// -// getEnd(): number { -// return this.end; -// } -// -// getIsSomatic(): boolean { -// return this.isSomatic; -// } -// -// getReferenceAllele(): string { -// return this.referenceAllele; -// } -// -// getStart(): number { -// return this.start; -// } -// -// getSvAlelle(): StructuralVariant { -// return this.svAllele; -// } -// -// setAlternativeAllele(value: string) { -// this.alternateAllele = value; -// } -// -// setContig(value: Contig) { -// this.contig = value; -// } -// -// setEnd(value: number) { -// this.end = value; -// } -// -// setIsSomatic(value: boolean) { -// this.isSomatic = value; -// } -// -// setReferenceAllele(value: string) { -// this.referenceAllele = value; -// } -// -// setStart(value: number) { -// this.start = value; -// } -// -// setSvAllel(value: StructuralVariant) { -// this.svAllele = value; -// } -// -// } -// -// module.exports = Variant; From 5d0183ebb448dbef81e02e0133622967511bffb4 Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Tue, 28 Jun 2016 13:22:35 -0700 Subject: [PATCH 033/136] finished merge conflicts in RemoteRequestjs --- src/test/sources/FeatureDataSource-test.js | 1 + 1 file changed, 1 insertion(+) diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js index 4c40a8db..afe5f82f 100644 --- a/src/test/sources/FeatureDataSource-test.js +++ b/src/test/sources/FeatureDataSource-test.js @@ -46,6 +46,7 @@ describe('FeatureDataSource', function() { var contigs = source.contigList(); expect(contigs).to.deep.equal(['chrM','93']); }); + //call server.respond it('should normalize range', function() { var source = getTestSource(); From ed30b9d7c5a6b4dac4a5cd02323a74dc7aa25caf Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Wed, 29 Jun 2016 12:49:17 -0700 Subject: [PATCH 034/136] Started working on creating featuredatasource-test.js --- src/main/data/FeatureEndpoint.js | 2 +- src/main/sources/FeatureDataSource.js | 9 ++++----- src/{main/data => test}/samplefeature.json | 0 src/test/sources/FeatureDataSource-test.js | 18 +++++++++--------- src/test/sources/samplefeature.json | 12 ++++++++++++ 5 files changed, 26 insertions(+), 15 deletions(-) rename src/{main/data => test}/samplefeature.json (100%) create mode 100644 src/test/sources/samplefeature.json diff --git a/src/main/data/FeatureEndpoint.js b/src/main/data/FeatureEndpoint.js index 26b1400b..d13e8d58 100644 --- a/src/main/data/FeatureEndpoint.js +++ b/src/main/data/FeatureEndpoint.js @@ -39,7 +39,7 @@ class FeatureEndpoint { this.contigList = contigList; } - contigList(): string[] { + getContigList(): string[] { return this.contigList.map(seq => seq.name); } diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index f7aee5ba..9d14e0d9 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -15,7 +15,7 @@ var FEATURES_PER_REQUEST = 200; function createFromFeatureEndpoint(remoteSource: FeatureEndpoint): BigBedSource { // Collection of genes that have already been loaded. var features: {[key:string]: feature} = {}; //TODO features - + var contigList = remoteSource.getContigList(); // Ranges for which we have complete information -- no need to hit network. var coveredRanges: Array> = []; @@ -70,15 +70,14 @@ function createFromFeatureEndpoint(remoteSource: FeatureEndpoint): BigBedSource } }).done() }, - getRange, - getRangeAsString, + // getRange, + // getRangeAsString, contigList: () => contigList, - normalizeRange, + // normalizeRange, getFeaturesInRange, // These are here to make Flow happy. on: () => {}, - once: () -> {}, off: () => {}, trigger: () => {} }; diff --git a/src/main/data/samplefeature.json b/src/test/samplefeature.json similarity index 100% rename from src/main/data/samplefeature.json rename to src/test/samplefeature.json diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js index afe5f82f..a71249ec 100644 --- a/src/test/sources/FeatureDataSource-test.js +++ b/src/test/sources/FeatureDataSource-test.js @@ -15,7 +15,7 @@ describe('FeatureDataSource', function() { var server: any = null, response; before(function () { - return new RemoteFile('../../main/samplefeature').getAllString().then(data => { + return new RemoteFile('samplefeature.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); server.respondWith('GET', '/features/chrM?start=1011&end=1012', [200, { "Content-Type": "application/json" }, response]); @@ -44,17 +44,17 @@ describe('FeatureDataSource', function() { it('should fetch contigs', function() { var source = getTestSource(); var contigs = source.contigList(); - expect(contigs).to.deep.equal(['chrM','93']); + expect(contigs).to.deep.equal(['chrM','93']); //Modify this to match actual data }); //call server.respond - it('should normalize range', function() { - var source = getTestSource(); - var range = {contig: 'chrM', start: 1011, stop: 1012}; - source.normalizeRange(range).then(normalized => { - expect(normalized.to.deep.equal(range)); - }).done(); - }); + // it('should normalize range', function() { + // var source = getTestSource(); + // var range = {contig: 'chrM', start: 1011, stop: 1012}; + // source.normalizeRange(range).then(normalized => { + // expect(normalized.to.deep.equal(range)); + // }).done(); + // }); it('should extract features in a range from a given endpoint', function(done) { this.timeout(5000); diff --git a/src/test/sources/samplefeature.json b/src/test/sources/samplefeature.json new file mode 100644 index 00000000..cee3e7a3 --- /dev/null +++ b/src/test/sources/samplefeature.json @@ -0,0 +1,12 @@ +[{ + "rest": "4ee7469a-b468-429b-a109-07a484817037", + "contig": "chrM", + "start": 1107, + "end": 1200 +}, { + "rest": "e105ce29-a840-4fc6-819f-a9aac5166163", + "contig": "chrM", + "start": 1011, + "end": 1012 +}] + From c9eb7381b2f3c8b0f8f7bca61d9e2a02bea9ada2 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Fri, 1 Jul 2016 17:24:57 -0700 Subject: [PATCH 035/136] completed generic feature visualization --- src/main/data/FeatureEndpoint.js | 72 ++++------ src/main/pileup.js | 13 +- src/main/sources/FeatureDataSource.js | 149 ++++++++++++-------- src/main/viz/FeatureTrack.js | 112 +++++++++++++++ src/test/samplefeature.json | 12 -- src/test/sources/FeatureDataSource-test.js | 105 ++++++-------- src/test/sources/GenotypeDataSource-test.js | 1 - src/test/sources/samplefeature.json | 12 -- test-data/features-chrM-1000-1200.json | 6 +- 9 files changed, 282 insertions(+), 200 deletions(-) create mode 100644 src/main/viz/FeatureTrack.js delete mode 100644 src/test/samplefeature.json delete mode 100644 src/test/sources/samplefeature.json diff --git a/src/main/data/FeatureEndpoint.js b/src/main/data/FeatureEndpoint.js index d13e8d58..d31f0861 100644 --- a/src/main/data/FeatureEndpoint.js +++ b/src/main/data/FeatureEndpoint.js @@ -7,56 +7,36 @@ // import Q from 'q'; import type RemoteRequest from '../RemoteRequest'; -//TODO import bedrow here - -export type FeatureRecord = { - featureId: string; - featureType: string; - start: number; - end: number; - range: ContigInterval + +type Feature = { + id: string; + featureType: string; + contig: string; + start: number; + stop: number; } -function unpackFeatures(dataView: DataView, start: number, end: number): Array { - // TODO: use jBinary bitfield for this - var features: Array = []; - // basePairs.length = dataView.byteLength * 4; // pre-allocate - for (var i = 0; i < dataView.byteLength; i++) { - var packed = dataView.getUint8(i); - features[i] = String.fromCharCode(packed); - } - // Remove base pairs from the end if the sequence terminated mid-byte. - // features.length = numBasePairs; //TODO Determine length +function extractFeatures(features: Object): Feature[] { return features; } class FeatureEndpoint { - remoteRequest: RemoteRequest; - contigList: FeatureRecord[]; - - constructor(remoteRequest: RemoteRequest, contigList: FeatureRecord[]) { - this.remoteRequest = remoteRequest; - this.contigList = contigList; - } - - getContigList(): string[] { - return this.contigList.map(seq => seq.name); - } - - /** - * Returns the Features in contig:start-stop. - * The range is inclusive and zero-based. - * Returns empty string if no data is available on this range. - */ - - getFeaturesInRange(contig: string, start: number, stop: number): Q.Promise { - if (start > stop) { - throw `Requested a range with start > stop (${start}, ${stop})`; - } - return this.remoteRequest.get(contig, start, stop).then(buffer => { - var dataView = new DataView(buffer); - var d = unpackFeatures(dataView, start, stop).join(''); - return d; - }); - } + remoteRequest: RemoteRequest; + + constructor(remoteRequest: RemoteRequest) { + this.remoteRequest = remoteRequest; + } + + getFeaturesInRange(range: ContigInterval): Q.Promise { + var contig = range.contig; + var start = range.interval.start; + var stop = range.interval.stop; + + return this.remoteRequest.get(contig, start, stop).then(object => { + var d = extractFeatures(object); + return d; + }); + } } + +module.exports = FeatureEndpoint; diff --git a/src/main/pileup.js b/src/main/pileup.js index aeacf3dd..06f24873 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -12,9 +12,11 @@ import ReactDOM from 'react-dom'; // Data sources import TwoBitDataSource from './sources/TwoBitDataSource'; +import ReferenceDataSource from './sources/ReferenceDataSource'; import BigBedDataSource from './sources/BigBedDataSource'; import VcfDataSource from './sources/VcfDataSource'; import VariantDataSource from './sources/VariantDataSource'; +import GenotypeDataSource from './sources/GenotypeDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; import EmptySource from './sources/EmptySource'; @@ -23,11 +25,13 @@ import EmptySource from './sources/EmptySource'; // Visualizations import CoverageTrack from './viz/CoverageTrack'; import GenomeTrack from './viz/GenomeTrack'; -import GeneTrack from './viz/GeneTrack'; //use this for features +import GeneTrack from './viz/GeneTrack'; +import FeatureTrack from './viz/FeatureTrack'; import LocationTrack from './viz/LocationTrack'; import PileupTrack from './viz/PileupTrack'; import ScaleTrack from './viz/ScaleTrack'; import VariantTrack from './viz/VariantTrack'; +import GenotypeTrack from './viz/GenotypeTrack'; import Root from './Root'; type GenomeRange = { @@ -126,7 +130,10 @@ var pileup = { ga4gh: GA4GHDataSource.create, vcf: VcfDataSource.create, variants: VariantDataSource.create, + genotypes: GenotypeDataSource.create, + features: FeatureDataSource.create, twoBit: TwoBitDataSource.create, + reference: ReferenceDataSource.create, bigBed: BigBedDataSource.create, empty: EmptySource.create }, @@ -134,12 +141,14 @@ var pileup = { coverage: makeVizObject(CoverageTrack), genome: makeVizObject(GenomeTrack), genes: makeVizObject(GeneTrack), + features: makeVizObject(FeatureTrack), location: makeVizObject(LocationTrack), scale: makeVizObject(ScaleTrack), variants: makeVizObject(VariantTrack), + genotypes: makeVizObject(GenotypeTrack), pileup: makeVizObject(PileupTrack) }, - version: '0.6.8' + version: '0.6.6' }; module.exports = pileup; diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index 9d14e0d9..e63b0465 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -1,79 +1,99 @@ - /** @flow */ +/** + * The "glue" between TwoBit.js and GenomeTrack.js. + * + * GenomeTrack is pure view code -- it renders data which is already in-memory + * in the browser. + * + * TwoBit is purely for data parsing and fetching. It only knows how to return + * promises for various genome features. + * + * This code acts as a bridge between the two. It maintains a local version of + * the data, fetching remote data and informing the view when it becomes + * available. + * + * @flow + */ 'use strict'; -import BigBedSource from './BigBedDataSource'; +import Q from 'q'; +import _ from 'underscore'; +import {Events} from 'backbone'; + import ContigInterval from '../ContigInterval'; import RemoteRequest from '../RemoteRequest'; import FeatureEndpoint from '../data/FeatureEndpoint'; -import Interval from '../Interval'; -import Q from 'q'; -import _ from 'underscore'; -import { Events } from 'backbone'; +import type {Feature} from '../data/FeatureEndPoint'; + +// Flow type for export. +export type FeatureDataSource = { + rangeChanged: (newRange: GenomeRange) => void; + getFeaturesInRange: (range: ContigInterval) => Feature[]; + on: (event: string, handler: Function) => void; + off: (event: string) => void; + trigger: (event: string, ...args:any) => void; +} + + +// Requests for 2bit ranges are expanded to begin & end at multiples of this +// constant. Doing this means that panning typically won't require +// additional network requests. +var BASE_PAIRS_PER_FETCH = 1000; -var FEATURES_PER_REQUEST = 200; +function expandRange(range: ContigInterval) { + var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; + var newStart = Math.max(1, roundDown(range.start())), + newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); + + return new ContigInterval(range.contig, newStart, newStop); +} + +function featureKey(f: Feature): string { + return `${f.contig}:${f.start}`; +} + + +function createFromFeatureUrl(remoteSource: FeatureEndpoint): FeatureDataSource { + var features: {[key: string]: Feature} = {}; -function createFromFeatureEndpoint(remoteSource: FeatureEndpoint): BigBedSource { - // Collection of genes that have already been loaded. - var features: {[key:string]: feature} = {}; //TODO features - var contigList = remoteSource.getContigList(); // Ranges for which we have complete information -- no need to hit network. - var coveredRanges: Array> = []; + var coveredRanges: ContigInterval[] = []; - function addFeature(newfeature) { - if (!feature[newFeature.featureId]) { - feature[newFeature.featureId] = newFeature; + function addFeature(f: Feature) { + var key = featureKey(f); + if (!features[key]) { + features[key] = f; } } - function getFeaturesInRange(range: ContigInterval): Feature[] { - if (!range) return []; - var results = []; - _.each(Feature, feature => { - if (range.intersects(feature.range)) { - results.push(feature); - } - }); - return results; - } - - function fetch(range: ContigInterval) { + function fetch(range: GenomeRange) { + var interval = new ContigInterval(range.contig, range.start, range.stop); // Check if this interval is already in the cache. - if (range.isCoveredBy(coveredRanges)) { + if (interval.isCoveredBy(coveredRanges)) { return Q.when(); } - coveredRanges.push(range); - coveredRanges = ContigInterval.coalesce(coveredRanges); + interval = expandRange(interval); - /** Modify URL */ - remoteSource.remoteRequest.url += range.contig.contig + "?start=" + range.start + "&end=" + range.stop; + // "Cover" the range immediately to prevent duplicate fetches. + coveredRanges.push(interval); + coveredRanges = ContigInterval.coalesce(coveredRanges); + return remoteSource.getFeaturesInRange(interval).then(features => { + features.forEach(feature => addFeature(feature)); + o.trigger('newdata', interval); + }); + } - return remoteSource.getFeaturesInRange(range.contig.contig, range.start, range.end); + function getFeaturesInRange(range: ContigInterval): Feature[] { + if (!range) return []; // XXX why would this happen? + var x = _.filter(features, f => range.chrContainsLocus(f.contig, f.start)); + return x; } var o = { rangeChanged: function(newRange: GenomeRange) { - normalizeRange(newRange).then(r => { - var range = new ContigInterval(r.contig, r.start, r.stop); - - if (range.isCoveredBy(coveredRanges)) { - return; - } - - var newRanges = range.complementIntervals(coveredRanges); - coveredRanges.push(range); - coveredRanges = ContigInterval.coalesce(coveredRanges); - - for (var newRange of newRanges) { - fetch(newRange); - } - }).done() + fetch(newRange).done(); }, - // getRange, - // getRangeAsString, - contigList: () => contigList, - // normalizeRange, getFeaturesInRange, // These are here to make Flow happy. @@ -81,20 +101,27 @@ function createFromFeatureEndpoint(remoteSource: FeatureEndpoint): BigBedSource off: () => {}, trigger: () => {} }; - _.extend(o, Events); // Make this an event emitter return o; -}; +} -function create(data: {url: string}): BigBedSource { - var url = data.url; - if (!url) { - throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); - } - return createFromFeatureEndpoint(new RemoteRequest(url)); +function create(data: {url?:string, key?:string}): FeatureDataSource { + var {url, key} = data; + if (!url) { + throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); + } + // verify key was correctly set + if (!key) { + throw new Error(`Missing key from track: ${JSON.stringify(data)}`); + } + var request = new RemoteRequest(url, key); + var endpoint = new FeatureEndpoint(request); + return createFromFeatureUrl(endpoint); } + module.exports = { - create + create, + createFromFeatureUrl }; diff --git a/src/main/viz/FeatureTrack.js b/src/main/viz/FeatureTrack.js new file mode 100644 index 00000000..4e9e87e6 --- /dev/null +++ b/src/main/viz/FeatureTrack.js @@ -0,0 +1,112 @@ +/** + * Visualization of features, including exons and coding regions. + * @flow + */ +'use strict'; + +import type {FeatureDataSource} from '../sources/FeatureDataSource'; +import type {Feature} from '../data/FeatureEndpoint'; + +import type {VizProps} from '../VisualizationWrapper'; +import type {Scale} from './d3utils'; + +import React from 'react'; +import ReactDOM from 'react-dom'; +import _ from 'underscore'; +import shallowEquals from 'shallow-equals'; + +import Interval from '../Interval'; +import d3utils from './d3utils'; +import scale from '../scale'; +import ContigInterval from '../ContigInterval'; +import canvasUtils from './canvas-utils'; +import dataCanvas from 'data-canvas'; +import style from '../style'; + + +class FeatureTrack extends React.Component { + props: VizProps & { source: FeatureDataSource }; + state: {features: Feature[]}; + + constructor(props: VizProps) { + super(props); + this.state = { + features: [] + }; + } + + render(): any { + return ; + } + + componentDidMount() { + // Visualize new reference data as it comes in from the network. + this.props.source.on('newdata', (range) => { + this.setState({ + features: this.props.source.getFeaturesInRange(range) + }); + }); + + this.updateVisualization(); + } + + getScale(): Scale { + return d3utils.getTrackScale(this.props.range, this.props.width); + } + + componentDidUpdate(prevProps: any, prevState: any) { + if (!shallowEquals(prevProps, this.props) || + !shallowEquals(prevState, this.state)) { + this.updateVisualization(); + } + } + + updateVisualization() { + var canvas = ReactDOM.findDOMNode(this), + {width, height} = this.props, + genomeRange = this.props.range; + + var range = new ContigInterval(genomeRange.contig, genomeRange.start, genomeRange.stop); + var y = height - style.VARIANT_HEIGHT - 1; + + // Hold off until height & width are known. + if (width === 0) return; + + var sc = this.getScale(), + // We can't clamp scale directly because of offsetPx. + clampedScale = scale.linear() + .domain([sc.invert(0), sc.invert(width)]) + .range([0, width]) + .clamp(true); + + d3utils.sizeCanvas(canvas, width, height); + + var ctx = dataCanvas.getDataContext(canvasUtils.getContext(canvas)); + ctx.reset(); + ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); + + var featureLineY = Math.round(height / 4); + var textIntervals = []; // x-intervals with rendered feature names, to avoid over-drawing. + // TODO: don't pull in features via state. + ctx.font = `${style.GENE_FONT_SIZE}px ${style.GENE_FONT}`; + ctx.textAlign = 'center'; + this.state.features.forEach(feature => { + var position = new ContigInterval(feature.contig, feature.start, feature.stop); + if (!position.chrIntersects(range)) return; + ctx.pushObject(feature); + ctx.lineWidth = 1; + ctx.strokeStyle = style.GENE_COLOR; + ctx.fillStyle = style.GENE_COLOR; + + var x = Math.round(sc(feature.start)); + var width = Math.round(sc(feature.stop) - sc(feature.start)); + ctx.fillRect(x - 0.5, y - 0.5, width, style.VARIANT_HEIGHT); + ctx.strokeRect(x - 0.5, y - 0.5, width, style.VARIANT_HEIGHT); + ctx.popObject(); + }); + } +} + +FeatureTrack.displayName = 'features'; + +module.exports = FeatureTrack; diff --git a/src/test/samplefeature.json b/src/test/samplefeature.json deleted file mode 100644 index cee3e7a3..00000000 --- a/src/test/samplefeature.json +++ /dev/null @@ -1,12 +0,0 @@ -[{ - "rest": "4ee7469a-b468-429b-a109-07a484817037", - "contig": "chrM", - "start": 1107, - "end": 1200 -}, { - "rest": "e105ce29-a840-4fc6-819f-a9aac5166163", - "contig": "chrM", - "start": 1011, - "end": 1012 -}] - diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js index a71249ec..6c5224b2 100644 --- a/src/test/sources/FeatureDataSource-test.js +++ b/src/test/sources/FeatureDataSource-test.js @@ -8,76 +8,53 @@ import sinon from 'sinon'; import ContigInterval from '../../main/ContigInterval'; import FeatureDataSource from '../../main/sources/FeatureDataSource'; import RemoteFile from '../../main/RemoteFile'; -// import sample from '../../main/samplefeature'; -// var url = "http://localhost:8080/features/chrM?start=0&end=1000"; describe('FeatureDataSource', function() { - var server: any = null, response; + var server: any = null, response; - before(function () { - return new RemoteFile('samplefeature.json').getAllString().then(data => { - response = data; - server = sinon.fakeServer.create(); - server.respondWith('GET', '/features/chrM?start=1011&end=1012', [200, { "Content-Type": "application/json" }, response]); - server.respondWith('GET', '/features/chrM?start=1107&end=1200', [200, { "Content-Type": "application/json" }, response]); - }); + before(function () { + return new RemoteFile('/test-data/features-chrM-1000-1200.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/features/chrM?start=1000&end=2000&key=test', [200, { "Content-Type": "application/json" }, response]); }); + }); - after(function () { - server.restore(); - }); - - function getTestSource() { - var source = FeatureDataSource.create({ - url: '/features', - contigList: [{ - name:"chrM", - length: 93 - }, { - name:"chrM", - length: 1 - }] - }); - return source; - } + after(function () { + server.restore(); + }); - it('should fetch contigs', function() { - var source = getTestSource(); - var contigs = source.contigList(); - expect(contigs).to.deep.equal(['chrM','93']); //Modify this to match actual data + function getTestSource() { + var source = FeatureDataSource.create({ + url: '/features', + key: 'test' }); - //call server.respond - - // it('should normalize range', function() { - // var source = getTestSource(); - // var range = {contig: 'chrM', start: 1011, stop: 1012}; - // source.normalizeRange(range).then(normalized => { - // expect(normalized.to.deep.equal(range)); - // }).done(); - // }); - - it('should extract features in a range from a given endpoint', function(done) { - this.timeout(5000); - var source = getTestSource(); - - // No features fetched initially - var testrange = new ContigInterval('chrM', 1011, 1012); - var test = source.getFeaturesInRange(testrange[0], testrange[1], testrange[2]); - expect(test).to.deep.equal([]); - - // Fetching that one feature should cache its entire block. - source.on('newdata', () => { - var tests = source.getFeaturesInRange(testrange[0], testrange[1], testrange[2]); - expect(tests).to.have.length(1); - - var test = tests[0]; - expect(test.name).to.equal('chrM'); - done(); - }); - source.rangeChanged({ - contig: testrange.contig, - start: testrange.start(), - stop: testrange.stop() - }); + return source; + } + + it('should extract features in a range', function(done) { + var source = getTestSource(); + + // No genes fetched initially + var range = new ContigInterval('chrM', 1000, 1200); + var emptyFeatures = source.getFeaturesInRange(range); + expect(emptyFeatures).to.deep.equal([]); + + // Fetching that one gene should cache its entire block. + source.on('newdata', () => { + var features = source.getFeaturesInRange(range); + expect(features).to.have.length(2); + + var feature = features[0]; + expect(feature.start).to.equal(1107); + expect(feature.contig).to.equal('chrM'); + done(); + }); + source.rangeChanged({ + contig: range.contig, + start: range.start(), + stop: range.stop() }); + server.respond(); + }); }); diff --git a/src/test/sources/GenotypeDataSource-test.js b/src/test/sources/GenotypeDataSource-test.js index 67ca5162..74c7cc4c 100644 --- a/src/test/sources/GenotypeDataSource-test.js +++ b/src/test/sources/GenotypeDataSource-test.js @@ -41,7 +41,6 @@ describe('GenotypeDataSource', function() { source.on('newdata', () => { var genotypes = source.getFeaturesInRange(range); - console.log(genotypes); expect(genotypes).to.have.length(3); expect(genotypes[1].sampleIds).to.contain('sample1'); expect(genotypes[1].variant.contig).to.equal('chrM'); diff --git a/src/test/sources/samplefeature.json b/src/test/sources/samplefeature.json deleted file mode 100644 index cee3e7a3..00000000 --- a/src/test/sources/samplefeature.json +++ /dev/null @@ -1,12 +0,0 @@ -[{ - "rest": "4ee7469a-b468-429b-a109-07a484817037", - "contig": "chrM", - "start": 1107, - "end": 1200 -}, { - "rest": "e105ce29-a840-4fc6-819f-a9aac5166163", - "contig": "chrM", - "start": 1011, - "end": 1012 -}] - diff --git a/test-data/features-chrM-1000-1200.json b/test-data/features-chrM-1000-1200.json index 2ba90728..c6285852 100644 --- a/test-data/features-chrM-1000-1200.json +++ b/test-data/features-chrM-1000-1200.json @@ -1,10 +1,12 @@ [{ - "rest": "4ee7469a-b468-429b-a109-07a484817037", + "id": "4ee7469a-b468-429b-a109-07a484817037", + "featureType": "peak", "contig": "chrM", "start": 1107, "end": 1200 }, { - "rest": "e105ce29-a840-4fc6-819f-a9aac5166163", + "id": "e105ce29-a840-4fc6-819f-a9aac5166163", + "featureType": "peak", "contig": "chrM", "start": 1011, "end": 1012 From b9011d50ccdd0c007dc20c25cbdce54b5d3dc355 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Mon, 4 Jul 2016 11:20:49 -0700 Subject: [PATCH 036/136] added check for negative values and restricted alignment fetch size --- src/main/sources/GA4GHDataSource.js | 6 ++++++ src/main/viz/FeatureTrack.js | 11 +---------- 2 files changed, 7 insertions(+), 10 deletions(-) diff --git a/src/main/sources/GA4GHDataSource.js b/src/main/sources/GA4GHDataSource.js index bf3396c4..e978fdf6 100644 --- a/src/main/sources/GA4GHDataSource.js +++ b/src/main/sources/GA4GHDataSource.js @@ -14,6 +14,7 @@ import ContigInterval from '../ContigInterval'; import GA4GHAlignment from '../GA4GHAlignment'; var ALIGNMENTS_PER_REQUEST = 200; // TODO: explain this choice. +var MAX_BASE_PAIRS_TO_FETCH = 40000; // Genome ranges are rounded to multiples of this for fetching. @@ -86,6 +87,11 @@ function create(spec: GA4GHSpec): AlignmentDataSource { function fetchAlignmentsForInterval(range: ContigInterval, pageToken: ?string, numRequests: number) { + + var span = range.length(); + if (span > MAX_BASE_PAIRS_TO_FETCH) { + return Q.when(); // empty promise + } var xhr = new XMLHttpRequest(); var endpoint = url + "/" + range.contig + "?start=" + range.start() + "&end=" + range.stop()+"&key="+spec.readGroupId; diff --git a/src/main/viz/FeatureTrack.js b/src/main/viz/FeatureTrack.js index 4e9e87e6..fc780fcf 100644 --- a/src/main/viz/FeatureTrack.js +++ b/src/main/viz/FeatureTrack.js @@ -12,10 +12,8 @@ import type {Scale} from './d3utils'; import React from 'react'; import ReactDOM from 'react-dom'; -import _ from 'underscore'; import shallowEquals from 'shallow-equals'; -import Interval from '../Interval'; import d3utils from './d3utils'; import scale from '../scale'; import ContigInterval from '../ContigInterval'; @@ -72,12 +70,7 @@ class FeatureTrack extends React.Component { // Hold off until height & width are known. if (width === 0) return; - var sc = this.getScale(), - // We can't clamp scale directly because of offsetPx. - clampedScale = scale.linear() - .domain([sc.invert(0), sc.invert(width)]) - .range([0, width]) - .clamp(true); + var sc = this.getScale(); d3utils.sizeCanvas(canvas, width, height); @@ -85,8 +78,6 @@ class FeatureTrack extends React.Component { ctx.reset(); ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); - var featureLineY = Math.round(height / 4); - var textIntervals = []; // x-intervals with rendered feature names, to avoid over-drawing. // TODO: don't pull in features via state. ctx.font = `${style.GENE_FONT_SIZE}px ${style.GENE_FONT}`; ctx.textAlign = 'center'; From 021b34e0e186d2964895335239788359d4f836bf Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Mon, 11 Jul 2016 20:27:59 -0700 Subject: [PATCH 037/136] completed gene endpoint --- src/main/data/GeneEndpoint.js | 62 ++ src/main/pileup.js | 4 +- src/main/sources/GeneDataSource.js | 105 +++ src/main/sources/ReferenceDataSource.js | 2 +- src/main/sources/VariantDataSource.js | 4 - src/test/sources/GeneDataSource-test.js | 58 ++ src/test/sources/GenotypeDataSource-test.js | 2 +- test-data/genes-chrM-0-30000.json | 855 ++++++++++++++++++++ 8 files changed, 1085 insertions(+), 7 deletions(-) create mode 100644 src/main/data/GeneEndpoint.js create mode 100644 src/main/sources/GeneDataSource.js create mode 100644 src/test/sources/GeneDataSource-test.js create mode 100644 test-data/genes-chrM-0-30000.json diff --git a/src/main/data/GeneEndpoint.js b/src/main/data/GeneEndpoint.js new file mode 100644 index 00000000..aebb6964 --- /dev/null +++ b/src/main/data/GeneEndpoint.js @@ -0,0 +1,62 @@ +/** + * This module defines a parser for the 2bit file format. + * See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 + * @flow + */ +'use strict'; + +// import Q from 'q'; +import type RemoteRequest from '../RemoteRequest'; +import Interval from '../Interval'; +import ContigInterval from '../../main/ContigInterval'; + +function extractGenes(genes: Object): Gene[] { + var mapped = genes.map(g => extractGene(g)); + return mapped; +} + +function extractGene(f: Object): Gene { + var pos = new ContigInterval(f.position.referenceName, Number(f.position.start), Number(f.position.end)); + // parse out exon intervals + var exons = f.exons + .map(ex => new Interval(ex.region.start, ex.region.end)); + + // parse strand to positive or negative boolean + var strand; + if (f.strand === false) { + strand = "-"; + } else { + strand = "+"; + } + return { + position: pos, + id: f.id, + strand: strand, // either + or - + codingRegion: new Interval(Number(f.codingRegion.start), Number(f.codingRegion.end)), + geneId: f.geneId, + name: f.name, + exons + }; +} + + +class GeneEndpoint { + remoteRequest: RemoteRequest; + + constructor(remoteRequest: RemoteRequest) { + this.remoteRequest = remoteRequest; + } + + getGenesInRange(range: ContigInterval): Q.Promise { + var contig = range.contig; + var start = range.interval.start; + var stop = range.interval.stop; + + return this.remoteRequest.get(contig, start, stop).then(object => { + var d = extractGenes(object); + return d; + }); + } +} + +module.exports = GeneEndpoint; diff --git a/src/main/pileup.js b/src/main/pileup.js index 06f24873..c8145627 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -16,6 +16,7 @@ import ReferenceDataSource from './sources/ReferenceDataSource'; import BigBedDataSource from './sources/BigBedDataSource'; import VcfDataSource from './sources/VcfDataSource'; import VariantDataSource from './sources/VariantDataSource'; +import GeneDataSource from './sources/GeneDataSource'; import GenotypeDataSource from './sources/GenotypeDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; @@ -26,7 +27,7 @@ import EmptySource from './sources/EmptySource'; import CoverageTrack from './viz/CoverageTrack'; import GenomeTrack from './viz/GenomeTrack'; import GeneTrack from './viz/GeneTrack'; -import FeatureTrack from './viz/FeatureTrack'; +import FeatureTrack from './viz/FeatureTrack'; import LocationTrack from './viz/LocationTrack'; import PileupTrack from './viz/PileupTrack'; import ScaleTrack from './viz/ScaleTrack'; @@ -135,6 +136,7 @@ var pileup = { twoBit: TwoBitDataSource.create, reference: ReferenceDataSource.create, bigBed: BigBedDataSource.create, + genes: GeneDataSource.create, empty: EmptySource.create }, viz: { diff --git a/src/main/sources/GeneDataSource.js b/src/main/sources/GeneDataSource.js new file mode 100644 index 00000000..fb1935e1 --- /dev/null +++ b/src/main/sources/GeneDataSource.js @@ -0,0 +1,105 @@ +/* @flow */ +'use strict'; + +import type {Strand} from '../Alignment'; + +import _ from 'underscore'; +import Q from 'q'; +import {Events} from 'backbone'; + +import ContigInterval from '../ContigInterval'; +import Interval from '../Interval'; +import type { BigBedSource, Gene } from './BigBedDataSource'; +import RemoteRequest from '../RemoteRequest'; +import GeneEndpoint from '../data/GeneEndpoint'; + +var BASE_PAIRS_PER_FETCH = 5000; + +function expandRange(range: ContigInterval) { + var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; + var newStart = Math.max(1, roundDown(range.start())), + newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); + + return new ContigInterval(range.contig, newStart, newStop); +} + +function createFromGeneUrl(remoteSource: GeneEndpoint): BigBedSource { + // Collection of genes that have already been loaded. + var genes: {[key:string]: Gene} = {}; + + // Ranges for which we have complete information -- no need to hit network. + var coveredRanges: Array> = []; + + function addGene(newGene) { + if (!genes[newGene.id]) { + genes[newGene.id] = newGene; + } + } + + function getGenesInRange(range: ContigInterval): Gene[] { + if (!range) return []; + var results = []; + _.each(genes, gene => { + if (range.intersects(gene.position)) { + results.push(gene); + } + }); + return results; + } + + function fetch(range: GenomeRange) { + var interval = new ContigInterval(range.contig, range.start, range.stop); + + // Check if this interval is already in the cache. + if (interval.isCoveredBy(coveredRanges)) { + return Q.when(); + } + + interval = expandRange(interval); + + coveredRanges.push(interval); + coveredRanges = ContigInterval.coalesce(coveredRanges); + + return remoteSource.getGenesInRange(interval).then(genes => { + genes.forEach(gene => addGene(gene)); + //we have new data from our internal block range + o.trigger('newdata', interval); + }); + } + + var o = { + rangeChanged: function(newRange: GenomeRange) { + fetch(newRange).done(); + }, + getGenesInRange, + + // These are here to make Flow happy. + on: () => {}, + off: () => {}, + trigger: () => {} + }; + _.extend(o, Events); // Make this an event emitter + + return o; +} + +function create(data: {url?:string, key?:string}): BigBedSource { + var url = data.url; + var key = data.key; + if (!url) { + throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); + } + // verify key was correctly set + if (!key) { + throw new Error(`Missing key from track: ${JSON.stringify(data)}`); + } + + var request = new RemoteRequest(url, key); + var endpoint = new GeneEndpoint(request); + return createFromGeneUrl(endpoint); +} + +module.exports = { + create, + createFromGeneUrl +}; diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index 1ded0b77..5e67c760 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -31,7 +31,7 @@ import utils from '../utils'; // Requests for 2bit ranges are expanded to begin & end at multiples of this // constant. Doing this means that panning typically won't require // additional network requests. -var BASE_PAIRS_PER_FETCH = 10000; +var BASE_PAIRS_PER_FETCH = 15000; var MAX_BASE_PAIRS_TO_FETCH = 100000; diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index 59a3539e..b1cad7fc 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -26,10 +26,6 @@ import type {VcfDataSource} from './VcfDataSource'; import RemoteRequest from '../RemoteRequest'; import VariantEndpoint from '../data/VariantEndpoint'; - -// Requests for 2bit ranges are expanded to begin & end at multiples of this -// constant. Doing this means that panning typically won't require -// additional network requests. var BASE_PAIRS_PER_FETCH = 1000; function expandRange(range: ContigInterval) { diff --git a/src/test/sources/GeneDataSource-test.js b/src/test/sources/GeneDataSource-test.js new file mode 100644 index 00000000..5a565d37 --- /dev/null +++ b/src/test/sources/GeneDataSource-test.js @@ -0,0 +1,58 @@ +/* @flow */ +'use strict'; + +import {expect} from 'chai'; + +import sinon from 'sinon'; + +import ContigInterval from '../../main/ContigInterval'; +import RemoteFile from '../../main/RemoteFile'; +import GeneDataSource from '../../main/sources/GeneDataSource'; + +describe('GeneDataSource', function() { + var server: any = null, response; + + before(function () { + return new RemoteFile('/test-data/genes-chrM-0-30000.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/genes/chrM?start=1&end=100000&key=test', [200, { "Content-Type": "application/json" }, response]); + }); + }); + + after(function () { + server.restore(); + }); + + function getTestSource() { + var source = GeneDataSource.create({ + url: '/genes', + key: 'test' + }); + return source; + } + + it('should extract genes in a range', function(done) { + var source = getTestSource(); + + // No genes fetched initially + var range = new ContigInterval('chrM', 0, 100000); + var emptyGenes = source.getGenesInRange(range); + expect(emptyGenes).to.deep.equal([]); + + // Fetching that one gene should cache its entire block. + source.on('newdata', () => { + var genes = source.getGenesInRange(range); + console.log(genes); + + expect(genes).to.have.length(9); + done(); + }); + source.rangeChanged({ + contig: range.contig, + start: range.start(), + stop: range.stop() + }); + server.respond(); + }); +}); diff --git a/src/test/sources/GenotypeDataSource-test.js b/src/test/sources/GenotypeDataSource-test.js index 74c7cc4c..78e1b572 100644 --- a/src/test/sources/GenotypeDataSource-test.js +++ b/src/test/sources/GenotypeDataSource-test.js @@ -6,7 +6,7 @@ import {expect} from 'chai'; import sinon from 'sinon'; -import VariantDataSource from '../../main/sources/GenotypeDataSource'; +import VariantDataSource from '../../main/sources/VariantDataSource'; import ContigInterval from '../../main/ContigInterval'; import RemoteFile from '../../main/RemoteFile'; diff --git a/test-data/genes-chrM-0-30000.json b/test-data/genes-chrM-0-30000.json new file mode 100644 index 00000000..13bf39e9 --- /dev/null +++ b/test-data/genes-chrM-0-30000.json @@ -0,0 +1,855 @@ +[{ + "position": { + "referenceName": "chrM", + "start": 14362, + "end": 24886, + "orientation": {} + }, + "id": "ENST00000541675", + "strand": false, + "codingRegion": { + "start": 14362, + "end": 24886 + }, + "exons": [{ + "exonId": "ENSE00002254515", + "transcriptId": "ENST00000541675", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 24733, + "end": 24886, + "orientation": {} + } + }, { + "exonId": "ENSE00002303227", + "transcriptId": "ENST00000541675", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 18267, + "end": 18369, + "orientation": {} + } + }, { + "exonId": "ENSE00003638984", + "transcriptId": "ENST00000541675", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17914, + "end": 18061, + "orientation": {} + } + }, { + "exonId": "ENSE00003629019", + "transcriptId": "ENST00000541675", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17605, + "end": 17742, + "orientation": {} + } + }, { + "exonId": "ENSE00002285713", + "transcriptId": "ENST00000541675", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17497, + "end": 17504, + "orientation": {} + } + }, { + "exonId": "ENSE00001656010", + "transcriptId": "ENST00000541675", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17232, + "end": 17364, + "orientation": {} + } + }, { + "exonId": "ENSE00001760358", + "transcriptId": "ENST00000541675", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 16853, + "end": 17055, + "orientation": {} + } + }, { + "exonId": "ENSE00003497546", + "transcriptId": "ENST00000541675", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 14969, + "end": 15038, + "orientation": {} + } + }, { + "exonId": "ENSE00003511598", + "transcriptId": "ENST00000541675", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 14362, + "end": 14829, + "orientation": {} + } + }], + "geneId": "ENSG00000227232", + "name": "ENST00000541675" +}, { + "position": { + "referenceName": "chrM", + "start": 14403, + "end": 29570, + "orientation": {} + }, + "id": "ENST00000488147", + "strand": false, + "codingRegion": { + "start": 14403, + "end": 29570 + }, + "exons": [{ + "exonId": "ENSE00001890219", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 29533, + "end": 29570, + "orientation": {} + } + }, { + "exonId": "ENSE00003507205", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 24737, + "end": 24891, + "orientation": {} + } + }, { + "exonId": "ENSE00003477500", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 18267, + "end": 18366, + "orientation": {} + } + }, { + "exonId": "ENSE00003565697", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17914, + "end": 18061, + "orientation": {} + } + }, { + "exonId": "ENSE00003475637", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17605, + "end": 17742, + "orientation": {} + } + }, { + "exonId": "ENSE00003502542", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17232, + "end": 17368, + "orientation": {} + } + }, { + "exonId": "ENSE00003553898", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 16857, + "end": 17055, + "orientation": {} + } + }, { + "exonId": "ENSE00003621279", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 16606, + "end": 16765, + "orientation": {} + } + }, { + "exonId": "ENSE00002030414", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 15795, + "end": 15947, + "orientation": {} + } + }, { + "exonId": "ENSE00001935574", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 15004, + "end": 15038, + "orientation": {} + } + }, { + "exonId": "ENSE00001843071", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 14403, + "end": 14501, + "orientation": {} + } + }], + "geneId": "ENSG00000227232", + "name": "ENST00000488147" +}, { + "position": { + "referenceName": "chrM", + "start": 14362, + "end": 29370, + "orientation": {} + }, + "id": "ENST00000423562", + "strand": false, + "codingRegion": { + "start": 14362, + "end": 29370 + }, + "exons": [{ + "exonId": "ENSE00001718035", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 29320, + "end": 29370, + "orientation": {} + } + }, { + "exonId": "ENSE00003603734", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 24737, + "end": 24891, + "orientation": {} + } + }, { + "exonId": "ENSE00003513603", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17914, + "end": 18061, + "orientation": {} + } + }, { + "exonId": "ENSE00003565315", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17605, + "end": 17742, + "orientation": {} + } + }, { + "exonId": "ENSE00003685767", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17232, + "end": 17368, + "orientation": {} + } + }, { + "exonId": "ENSE00003553898", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 16857, + "end": 17055, + "orientation": {} + } + }, { + "exonId": "ENSE00003621279", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 16606, + "end": 16765, + "orientation": {} + } + }, { + "exonId": "ENSE00002030414", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 15795, + "end": 15947, + "orientation": {} + } + }, { + "exonId": "ENSE00003591210", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 14969, + "end": 15038, + "orientation": {} + } + }, { + "exonId": "ENSE00003693168", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 14362, + "end": 14829, + "orientation": {} + } + }], + "geneId": "ENSG00000227232", + "name": "ENST00000423562" +}, { + "position": { + "referenceName": "chrM", + "start": 14362, + "end": 29370, + "orientation": {} + }, + "id": "ENST00000438504", + "strand": false, + "codingRegion": { + "start": 14362, + "end": 29370 + }, + "exons": [{ + "exonId": "ENSE00001718035", + "transcriptId": "ENST00000438504", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 29320, + "end": 29370, + "orientation": {} + } + }, { + "exonId": "ENSE00003624050", + "transcriptId": "ENST00000438504", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 24737, + "end": 24891, + "orientation": {} + } + }, { + "exonId": "ENSE00001642865", + "transcriptId": "ENST00000438504", + "strand": false, + "region": { + 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"ENSE00002234632", + "transcriptId": "ENST00000515242", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 11871, + "end": 12227, + "orientation": {} + } + }, { + "exonId": "ENSE00003608237", + "transcriptId": "ENST00000515242", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 12612, + "end": 12721, + "orientation": {} + } + }, { + "exonId": "ENSE00002306041", + "transcriptId": "ENST00000515242", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 13224, + "end": 14412, + "orientation": {} + } + }], + "geneId": "ENSG00000223972", + "name": "ENST00000515242" +}, { + "position": { + "referenceName": "chrM", + "start": 11868, + "end": 14409, + "orientation": {} + }, + "id": "ENST00000456328", + "strand": true, + "codingRegion": { + "start": 11868, + "end": 14409 + }, + "exons": [{ + "exonId": "ENSE00002234944", + "transcriptId": "ENST00000456328", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 11868, + "end": 12227, + "orientation": {} + } + }, { + "exonId": "ENSE00003582793", + "transcriptId": "ENST00000456328", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 12612, + "end": 12721, + "orientation": {} + } + }, { + "exonId": "ENSE00002312635", + "transcriptId": "ENST00000456328", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 13220, + "end": 14409, + "orientation": {} + } + }], + "geneId": "ENSG00000223972", + "name": "ENST00000456328" +}, { + "position": { + "referenceName": "chrM", + "start": 12009, + "end": 13670, + "orientation": {} + }, + "id": "ENST00000450305", + "strand": true, + "codingRegion": { + "start": 12009, + "end": 13670 + }, + "exons": [{ + "exonId": "ENSE00001948541", + "transcriptId": "ENST00000450305", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 12009, + "end": 12057, + "orientation": {} + } + }, { + "exonId": "ENSE00001671638", + "transcriptId": "ENST00000450305", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 12178, + "end": 12227, + "orientation": {} + } + }, { + "exonId": "ENSE00001758273", + "transcriptId": "ENST00000450305", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 12612, + "end": 12697, + "orientation": {} + } + }, { + "exonId": "ENSE00001799933", + "transcriptId": "ENST00000450305", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 12974, + "end": 13052, + "orientation": {} + } + }, { + "exonId": "ENSE00001746346", + "transcriptId": "ENST00000450305", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 13220, + "end": 13374, + "orientation": {} + } + }, { + "exonId": "ENSE00001863096", + "transcriptId": "ENST00000450305", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 13452, + "end": 13670, + "orientation": {} + } + }], + "geneId": "ENSG00000223972", + "name": "ENST00000450305" +}] From 43aaca9c9102f979f00b16b209baf70c75ba50ec Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sat, 20 Aug 2016 14:46:23 -0700 Subject: [PATCH 038/136] removed prepush hooks --- package.json | 4 ---- 1 file changed, 4 deletions(-) diff --git a/package.json b/package.json index ee1217a8..8df01cad 100644 --- a/package.json +++ b/package.json @@ -46,9 +46,6 @@ "url": "https://github.com/hammerlab/pileup.js/issues" }, "homepage": "https://github.com/hammerlab/pileup.js", - "prepush": [ - "lint" - ], "dependencies": { "backbone": "1.1.2", "d3": "^3.5.5", @@ -86,7 +83,6 @@ "number-to-locale-string": "^1.0.0", "parse-data-uri": "^0.2.0", "phantomjs": "1.9.17", - "prepush-hook": "^0.1.0", "react-addons-test-utils": "^0.14.0", "sinon": "^1.12.2", "smash": "0.0.14", From ee44f1878c8b1612fe7d38c17844feecd86a9905 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 24 Aug 2016 14:42:11 -0700 Subject: [PATCH 039/136] Passing more tests --- src/main/GA4GHAlignment.js | 2 +- src/main/data/FeatureEndpoint.js | 12 ++++-------- src/main/data/GeneEndpoint.js | 3 ++- src/main/data/GenotypeEndpoint.js | 10 ++-------- src/main/data/VariantEndpoint.js | 10 ++++------ src/main/sources/FeatureDataSource.js | 13 ++++--------- src/main/sources/GA4GHDataSource.js | 1 + src/main/sources/GeneDataSource.js | 13 +++---------- src/main/sources/GenotypeDataSource.js | 11 +++-------- src/main/sources/ReferenceDataSource.js | 5 ++--- src/main/sources/VariantDataSource.js | 18 +++++++----------- src/test/sources/FeatureDataSource-test.js | 5 ++--- src/test/sources/GeneDataSource-test.js | 7 ++----- src/test/sources/GenotypeDataSource-test.js | 15 +++++++-------- src/test/sources/VariantDataSource-test.js | 15 ++++----------- 15 files changed, 48 insertions(+), 92 deletions(-) diff --git a/src/main/GA4GHAlignment.js b/src/main/GA4GHAlignment.js index 6287c643..10ddd18f 100644 --- a/src/main/GA4GHAlignment.js +++ b/src/main/GA4GHAlignment.js @@ -80,7 +80,7 @@ class GA4GHAlignment /* implements Alignment */ { } getMateProperties(): ?MateProperties { - var next = this.nextMatePosition; + var next = this.alignment.nextMatePosition; return next && { ref: next.referenceName, pos: next.position, diff --git a/src/main/data/FeatureEndpoint.js b/src/main/data/FeatureEndpoint.js index d31f0861..631debd8 100644 --- a/src/main/data/FeatureEndpoint.js +++ b/src/main/data/FeatureEndpoint.js @@ -5,10 +5,11 @@ */ 'use strict'; -// import Q from 'q'; +import Q from 'q'; +import ContigInterval from '../ContigInterval'; import type RemoteRequest from '../RemoteRequest'; -type Feature = { +export type Feature = { id: string; featureType: string; contig: string; @@ -16,10 +17,6 @@ type Feature = { stop: number; } -function extractFeatures(features: Object): Feature[] { - return features; -} - class FeatureEndpoint { remoteRequest: RemoteRequest; @@ -33,8 +30,7 @@ class FeatureEndpoint { var stop = range.interval.stop; return this.remoteRequest.get(contig, start, stop).then(object => { - var d = extractFeatures(object); - return d; + return object; }); } } diff --git a/src/main/data/GeneEndpoint.js b/src/main/data/GeneEndpoint.js index aebb6964..a34e7e7a 100644 --- a/src/main/data/GeneEndpoint.js +++ b/src/main/data/GeneEndpoint.js @@ -5,7 +5,8 @@ */ 'use strict'; -// import Q from 'q'; +import Q from 'q'; +import type {Gene} from '../sources/BigBedDataSource'; import type RemoteRequest from '../RemoteRequest'; import Interval from '../Interval'; import ContigInterval from '../../main/ContigInterval'; diff --git a/src/main/data/GenotypeEndpoint.js b/src/main/data/GenotypeEndpoint.js index 5726d89f..dd88c1ba 100644 --- a/src/main/data/GenotypeEndpoint.js +++ b/src/main/data/GenotypeEndpoint.js @@ -5,21 +5,16 @@ */ 'use strict'; +import ContigInterval from '../ContigInterval'; import Q from 'q'; import type RemoteRequest from '../RemoteRequest'; import type {Variant} from './vcf'; - export type Genotype = { sampleIds: string, variant: Variant } - -function extractGenotypes(genotypes: Object): Genotype[] { - return genotypes; -} - class GenotypeEndpoint { remoteRequest: RemoteRequest; @@ -34,8 +29,7 @@ class GenotypeEndpoint { return this.remoteRequest.get(contig, start, stop).then(object => { - var d = extractGenotypes(object); - return d; + return object; }); } } diff --git a/src/main/data/VariantEndpoint.js b/src/main/data/VariantEndpoint.js index 59425dda..fdfa13d4 100644 --- a/src/main/data/VariantEndpoint.js +++ b/src/main/data/VariantEndpoint.js @@ -5,12 +5,10 @@ */ 'use strict'; +import ContigInterval from '../ContigInterval'; import Q from 'q'; import type RemoteRequest from '../RemoteRequest'; - -function extractVariants(variants: Object): Variant[] { - return variants; -} +import type {Variant} from './vcf'; class VariantEndpoint { remoteRequest: RemoteRequest; @@ -25,8 +23,8 @@ class VariantEndpoint { var stop = range.interval.stop; return this.remoteRequest.get(contig, start, stop).then(object => { - var d = extractVariants(object); // TODO: should parts to Variant[] - return d; + console.log("variant endpoint", object); + return object; }); } } diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index e63b0465..b84ea697 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -22,7 +22,7 @@ import {Events} from 'backbone'; import ContigInterval from '../ContigInterval'; import RemoteRequest from '../RemoteRequest'; import FeatureEndpoint from '../data/FeatureEndpoint'; -import type {Feature} from '../data/FeatureEndPoint'; +import type {Feature} from '../data/FeatureEndpoint'; // Flow type for export. export type FeatureDataSource = { @@ -106,16 +106,11 @@ function createFromFeatureUrl(remoteSource: FeatureEndpoint): FeatureDataSource return o; } -function create(data: {url?:string, key?:string}): FeatureDataSource { - var {url, key} = data; - if (!url) { +function create(data: {url?:string}): FeatureDataSource { + if (!data.url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } - // verify key was correctly set - if (!key) { - throw new Error(`Missing key from track: ${JSON.stringify(data)}`); - } - var request = new RemoteRequest(url, key); + var request = new RemoteRequest(data.url); var endpoint = new FeatureEndpoint(request); return createFromFeatureUrl(endpoint); } diff --git a/src/main/sources/GA4GHDataSource.js b/src/main/sources/GA4GHDataSource.js index e978fdf6..4fe58a4d 100644 --- a/src/main/sources/GA4GHDataSource.js +++ b/src/main/sources/GA4GHDataSource.js @@ -9,6 +9,7 @@ import type {Alignment, AlignmentDataSource} from '../Alignment'; import _ from 'underscore'; import {Events} from 'backbone'; +import Q from 'q'; import ContigInterval from '../ContigInterval'; import GA4GHAlignment from '../GA4GHAlignment'; diff --git a/src/main/sources/GeneDataSource.js b/src/main/sources/GeneDataSource.js index fb1935e1..1a027bdd 100644 --- a/src/main/sources/GeneDataSource.js +++ b/src/main/sources/GeneDataSource.js @@ -83,18 +83,11 @@ function createFromGeneUrl(remoteSource: GeneEndpoint): BigBedSource { return o; } -function create(data: {url?:string, key?:string}): BigBedSource { - var url = data.url; - var key = data.key; - if (!url) { +function create(data: {url?:string}): BigBedSource { + if (!data.url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } - // verify key was correctly set - if (!key) { - throw new Error(`Missing key from track: ${JSON.stringify(data)}`); - } - - var request = new RemoteRequest(url, key); + var request = new RemoteRequest(data.url); var endpoint = new GeneEndpoint(request); return createFromGeneUrl(endpoint); } diff --git a/src/main/sources/GenotypeDataSource.js b/src/main/sources/GenotypeDataSource.js index 7c0c140c..c32274b3 100644 --- a/src/main/sources/GenotypeDataSource.js +++ b/src/main/sources/GenotypeDataSource.js @@ -105,16 +105,11 @@ function createFromGenotypeUrl(remoteSource: GenotypeEndpoint): GenotypeDataSour return o; } -function create(data: {url?:string, key?:string}): GenotypeDataSource { - var {url, key} = data; - if (!url) { +function create(data: {url?:string}): GenotypeDataSource { + if (!data.url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } - // verify key was correctly set - if (!key) { - throw new Error(`Missing key from track: ${JSON.stringify(data)}`); - } - var request = new RemoteRequest(url, key); + var request = new RemoteRequest(data.url); var endpoint = new GenotypeEndpoint(request); return createFromGenotypeUrl(endpoint); } diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index 5e67c760..05551ff6 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -31,7 +31,7 @@ import utils from '../utils'; // Requests for 2bit ranges are expanded to begin & end at multiples of this // constant. Doing this means that panning typically won't require // additional network requests. -var BASE_PAIRS_PER_FETCH = 15000; +var BASE_PAIRS_PER_FETCH = 10000; var MAX_BASE_PAIRS_TO_FETCH = 100000; @@ -149,8 +149,7 @@ function create(data: {url:string, contigList: SequenceRecord[]}): TwoBitSource if (!contigList) { throw new Error(`Missing ContigList from track: ${JSON.stringify(data)}`); } - var key = "reference"; // key is not required for reference but required for Remote Request - return createFromReferenceUrl(new Sequence(new RemoteRequest(urlPrefix, key), contigList)); + return createFromReferenceUrl(new Sequence(new RemoteRequest(urlPrefix), contigList)); } // Getter/setter for base pairs per fetch. diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index b1cad7fc..3338fe41 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -67,13 +67,15 @@ function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { // "Cover" the range immediately to prevent duplicate fetches. coveredRanges.push(interval); coveredRanges = ContigInterval.coalesce(coveredRanges); - return remoteSource.getFeaturesInRange(interval).then(variants => { - variants.forEach(variant => addVariant(variant)); + return remoteSource.getFeaturesInRange(interval).then(object => { + console.log(object, variants); + object.forEach(variant => addVariant(variant)); o.trigger('newdata', interval); }); } function getFeaturesInRange(range: ContigInterval): Variant[] { + console.log("getFeaturesinRange", range); if (!range) return []; // XXX why would this happen? return _.filter(variants, v => range.chrContainsLocus(v.contig, v.position)); } @@ -94,17 +96,11 @@ function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { return o; } -function create(data: {url:string, contigList: SequenceRecord[]}): VcfDataSource { - var url = data.url; - var contigList = data.contigList; - if (!url) { +function create(data: {url?:string}): VcfDataSource { + if (!data.url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } - // verify contiglist was correctly set - if (!contigList) { - throw new Error(`Missing ContigList from track: ${JSON.stringify(data)}`); - } - var request = new RemoteRequest(url, contigList); + var request = new RemoteRequest(data.url); var endpoint = new VariantEndpoint(request); return createFromVariantUrl(endpoint); } diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js index 6c5224b2..4fb56cf1 100644 --- a/src/test/sources/FeatureDataSource-test.js +++ b/src/test/sources/FeatureDataSource-test.js @@ -16,7 +16,7 @@ describe('FeatureDataSource', function() { return new RemoteFile('/test-data/features-chrM-1000-1200.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); - server.respondWith('GET', '/features/chrM?start=1000&end=2000&key=test', [200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/features/chrM?start=1000&end=2000', [200, { "Content-Type": "application/json" }, response]); }); }); @@ -26,8 +26,7 @@ describe('FeatureDataSource', function() { function getTestSource() { var source = FeatureDataSource.create({ - url: '/features', - key: 'test' + url: '/features' }); return source; } diff --git a/src/test/sources/GeneDataSource-test.js b/src/test/sources/GeneDataSource-test.js index 5a565d37..5a11e478 100644 --- a/src/test/sources/GeneDataSource-test.js +++ b/src/test/sources/GeneDataSource-test.js @@ -16,7 +16,7 @@ describe('GeneDataSource', function() { return new RemoteFile('/test-data/genes-chrM-0-30000.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); - server.respondWith('GET', '/genes/chrM?start=1&end=100000&key=test', [200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/genes/chrM?start=1&end=100000', [200, { "Content-Type": "application/json" }, response]); }); }); @@ -26,8 +26,7 @@ describe('GeneDataSource', function() { function getTestSource() { var source = GeneDataSource.create({ - url: '/genes', - key: 'test' + url: '/genes' }); return source; } @@ -43,8 +42,6 @@ describe('GeneDataSource', function() { // Fetching that one gene should cache its entire block. source.on('newdata', () => { var genes = source.getGenesInRange(range); - console.log(genes); - expect(genes).to.have.length(9); done(); }); diff --git a/src/test/sources/GenotypeDataSource-test.js b/src/test/sources/GenotypeDataSource-test.js index 78e1b572..3133a989 100644 --- a/src/test/sources/GenotypeDataSource-test.js +++ b/src/test/sources/GenotypeDataSource-test.js @@ -6,7 +6,7 @@ import {expect} from 'chai'; import sinon from 'sinon'; -import VariantDataSource from '../../main/sources/VariantDataSource'; +import GenotypeDataSource from '../../main/sources/GenotypeDataSource'; import ContigInterval from '../../main/ContigInterval'; import RemoteFile from '../../main/RemoteFile'; @@ -17,7 +17,7 @@ describe('GenotypeDataSource', function() { return new RemoteFile('/test-data/genotypes-chrM-0-100.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); - server.respondWith('GET', '/genotypes/chrM?start=1&end=1000&key=test',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/genotypes/chrM?start=1&end=1000',[200, { "Content-Type": "application/json" }, response]); }); }); @@ -26,9 +26,8 @@ describe('GenotypeDataSource', function() { }); function getTestSource() { - var source = VariantDataSource.create({ - url: '/genotypes', - key: 'test' + var source = GenotypeDataSource.create({ + url: '/genotypes' }); return source; } @@ -36,12 +35,12 @@ describe('GenotypeDataSource', function() { var source = getTestSource(); var range = new ContigInterval('chrM', 0, 25); // No variants are cached yet. - var variants = source.getFeaturesInRange(range); - expect(variants).to.deep.equal([]); + var genotypes = source.getFeaturesInRange(range); + expect(genotypes).to.deep.equal([]); source.on('newdata', () => { var genotypes = source.getFeaturesInRange(range); - expect(genotypes).to.have.length(3); + expect(genotypes).to.have.length(2); expect(genotypes[1].sampleIds).to.contain('sample1'); expect(genotypes[1].variant.contig).to.equal('chrM'); expect(genotypes[1].variant.position).to.equal(20); diff --git a/src/test/sources/VariantDataSource-test.js b/src/test/sources/VariantDataSource-test.js index b074909f..1cf08079 100644 --- a/src/test/sources/VariantDataSource-test.js +++ b/src/test/sources/VariantDataSource-test.js @@ -17,7 +17,6 @@ describe('VariantDataSource', function() { return new RemoteFile('/test-data/variants-chrM-0-100.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); - // server.respondWith('GET', '/variants',[200, { "Content-Type": "application/json" }, response]); server.respondWith('GET', '/variants/chrM?start=1&end=1000',[200, { "Content-Type": "application/json" }, response]); }); }); @@ -28,27 +27,21 @@ describe('VariantDataSource', function() { function getTestSource() { var source = VariantDataSource.create({ - url: '/variants', - contigList: [{ - name:"chrM", - length: 1000 - },{ - name:"22", - length: 1000 - }] + url: '/variants' }); return source; } it('should extract features in a range', function(done) { var source = getTestSource(); - var range = new ContigInterval('chrM', 0, 25); + var range = new ContigInterval('chrM', 0, 50); // No variants are cached yet. var variants = source.getFeaturesInRange(range); expect(variants).to.deep.equal([]); source.on('newdata', () => { var variants = source.getFeaturesInRange(range); - expect(variants).to.have.length(2); + console.log(variants); + expect(variants).to.have.length(3); expect(variants[1].contig).to.equal('chrM'); expect(variants[1].position).to.equal(20); expect(variants[1].ref).to.equal('G'); From f794b81456dbd211766578d051bdc7a0c81172e7 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 24 Aug 2016 18:00:34 -0700 Subject: [PATCH 040/136] merge in main pileup updates and modified RemoteRequest --- src/main/RemoteRequest.js | 63 ++++--- src/main/ResolutionCache.js | 168 +++++++++++++++++++ src/main/data/FeatureEndpoint.js | 6 +- src/main/data/GeneEndpoint.js | 6 +- src/main/data/GenotypeEndpoint.js | 7 +- src/main/data/Sequence.js | 7 +- src/main/data/VariantEndpoint.js | 7 +- src/main/pileup.js | 2 +- src/main/sources/CoverageDataSource.js | 103 ++++++++++++ src/main/sources/GA4GHDataSource.js | 4 +- src/main/sources/ReferenceDataSource.js | 2 +- src/main/sources/VariantDataSource.js | 4 +- src/test/RemoteRequest-test.js | 29 +--- src/test/ResolutionCache-test.js | 88 ++++++++++ src/test/sources/CoverageDataSource-test.js | 99 +++++++++++ src/test/sources/GA4GHDataSource-test.js | 8 +- src/test/sources/ReferenceDataSource-test.js | 14 +- src/test/sources/VariantDataSource-test.js | 1 - test-data/chrM-coverage.json | 49 ++++++ test-data/variants-chrM-0-100.json | 2 +- 20 files changed, 574 insertions(+), 95 deletions(-) create mode 100644 src/main/ResolutionCache.js create mode 100644 src/main/sources/CoverageDataSource.js create mode 100644 src/test/ResolutionCache-test.js create mode 100644 src/test/sources/CoverageDataSource-test.js create mode 100644 test-data/chrM-coverage.json diff --git a/src/main/RemoteRequest.js b/src/main/RemoteRequest.js index 7fc9b269..d5a1fcf2 100644 --- a/src/main/RemoteRequest.js +++ b/src/main/RemoteRequest.js @@ -9,60 +9,69 @@ import Q from 'q'; import ContigInterval from './ContigInterval'; +var BASE_PAIRS_PER_FETCH = 1000; class RemoteRequest { url: string; - cache: Object; + basePairsPerFetch: number; numNetworkRequests: number; // track this for debugging/testing - constructor(url: string) { - this.cache = require('memory-cache'); + constructor(url: string, basePairsPerFetch?: number) { this.url = url; + if (!basePairsPerFetch) + this.basePairsPerFetch = BASE_PAIRS_PER_FETCH; + else + this.basePairsPerFetch = basePairsPerFetch; this.numNetworkRequests = 0; } - get(contig: string, start: number, stop: number): Q.Promise { - var length = stop - start; + expandRange(range: ContigInterval): ContigInterval { + var roundDown = x => x - x % this.basePairsPerFetch; + var newStart = Math.max(1, roundDown(range.start())), + newStop = roundDown(range.stop() + this.basePairsPerFetch - 1); + + return new ContigInterval(range.contig, newStart, newStop); + } + + getFeaturesInRange(range: ContigInterval, modifier: string = ""): Q.Promise { + var expandedRange = this.expandRange(range); + return this.get(expandedRange, modifier); + } + + get(range: ContigInterval, modifier: string = ""): Q.Promise { + + var length = range.stop() - range.start(); if (length <= 0) { return Q.reject(`Requested <0 interval (${length}) from ${this.url}`); + } else if (length > 5000000) { + throw `Monster request: Won't fetch ${length} sized ranges from ${this.url}`; } - - // First check the cache. - var contigInterval = new ContigInterval(contig, start, stop); - var buf = this.cache.get(contigInterval); - if (buf) { - return Q.when(buf); - } - - // Need to fetch from the network. - return this.getFromNetwork(contig, start, stop); + // get endpoint + var endpoint = this.getEndpointFromContig(range.contig, range.start(), range.stop(), modifier); + // Fetch from the network + return this.getFromNetwork(endpoint); } /** * Request must be of form "url/contig?start=start&end=stop" */ - getFromNetwork(contig: string, start: number, stop: number): Q.Promise { - var length = stop - start; - if (length > 5000000) { - throw `Monster request: Won't fetch ${length} sized ranges from ${this.url}`; - } + getFromNetwork(endpoint: string): Q.Promise { var xhr = new XMLHttpRequest(); - var endpoint = this.getEndpointFromContig(contig, start, stop); xhr.open('GET', endpoint); xhr.responseType = 'json'; xhr.setRequestHeader('Content-Type', 'application/json'); return this.promiseXHR(xhr).then(json => { // extract response from promise - var buffer = json[0]; - var contigInterval = new ContigInterval(contig, start, stop); - this.cache.put(contigInterval, buffer); - return buffer; + return json[0]; }); } - getEndpointFromContig(contig: string, start: number, stop: number): string { - return `${this.url}/${contig}?start=${start}&end=${stop}`; + getEndpointFromContig(contig: string, start: number, stop: number, modifier: string = ""): string { + if (modifier.length < 1) + return `${this.url}/${contig}?start=${start}&end=${stop}`; + else + return `${this.url}/${contig}?start=${start}&end=${stop}&${modifier}`; } // Wrapper to convert XHRs to Promises. diff --git a/src/main/ResolutionCache.js b/src/main/ResolutionCache.js new file mode 100644 index 00000000..8e347136 --- /dev/null +++ b/src/main/ResolutionCache.js @@ -0,0 +1,168 @@ +/** + * Cache for any Data Sources that rely on resolution. For example, + * this is used by coverage to keep track of the difference resolutions + * that have been fetched already. + * + * @flow + */ +'use strict'; + +import _ from 'underscore'; +import Interval from './Interval'; +import ContigInterval from './ContigInterval'; + +class ResolutionCache { + coveredRanges: ResolutionCacheKey[]; + cache: {[key: string]: T}; + filterFunction: Function; // should take form (range: ContigInterval, T) => boolean; + keyFunction: Function; // should take form (d: T) => string; + + constructor(filterFunction: Function, keyFunction: Function) { + this.coveredRanges = []; + this.cache = {}; + this.filterFunction = filterFunction; + this.keyFunction = keyFunction; + } + + // gets data from cache at the Resolution defined by the interval + get(range: ContigInterval): T[] { + if (this.coversRange(range)) { + if (!range) return []; + return _.filter(this.cache, d => this.filterFunction(range, d)); + } else { + return []; + } + } + + // puts new ranges into list of ranges covered by cache + coverRange(range: ContigInterval) { + var resolution = ResolutionCache.getResolution(range.interval); + var resolvedRange = new ResolutionCacheKey(range, resolution); + this.coveredRanges.push(resolvedRange); + // coalesce new contigIntervals + this.coveredRanges = ResolutionCacheKey.coalesce(this.coveredRanges); + } + + // puts data in cache + put(value: T) { + var key = this.keyFunction(value); + if (!this.cache[key]) { + this.cache[key] = value; + } + } + + // checks weather cache contains data for the + // specified interval and its corresponding resolution + coversRange(range: ContigInterval): boolean { + var resolution = ResolutionCache.getResolution(range.interval); + if (range.isCoveredBy(this.coveredRanges.map(r => r.contigInterval))) { + // if covered by the data, verify that the correct base pair density is + // available + var correctResolution = true; + for (var i = 0; i < this.coveredRanges.length; i++) { + var r: ContigInterval = this.coveredRanges[i].contigInterval; + var thisRes = this.coveredRanges[i].resolution; + if (r.intersects(range)) { + if (thisRes > resolution) { // resolution not fine enough for query + correctResolution = false; + break; + } + } + } + return correctResolution; + } else { + return false; + } + } + + // clears out all content in cache + clear() { + this.coveredRanges = []; + this.cache = {}; + } + + /** + * Gets the Base Pairs per bin given a specified interval + * This is used to bin coverage when viewing large regions + * + * Values were chosen based on a 1000 pixel screen (a conservative estimate): + * - For regions < 10,000 base pairs, no binning is performed (return 1) + * - For regions >= 10,000 and < 100,000, bin 10 bp into 1 (return 10) + * - For regions >= 100,000 and < 1,000,000, bin 100 bp into 1 (return 100) + * - For regions >= 1,000,000, bin 1000 bp into 1 (return 1000) + */ + static getResolution(range: Interval): number { + if (range.length() < 10000) + return 1; + else if (range.length() >= 10000 && range.length() < 100000 ) + return 10; + else if (range.length() >= 100000 && range.length() < 1000000 ) + return 100; + else + return 1000; + } +} + +/** + * Class holds a ContigInterval and resolution that designates whether + * a contig interval represents data at a certain resolution. The + * parameters for choosing a resolution based on interval length are set + * in getResolution. + * + */ +class ResolutionCacheKey { + contigInterval: ContigInterval; + resolution: number; + + constructor(contigInterval: ContigInterval, resolution: number) { + this.contigInterval = contigInterval; + this.resolution = resolution; + } + + clone(): ResolutionCacheKey { + return new ResolutionCacheKey(this.contigInterval.clone(), this.resolution); + } + + // Sort an array of intervals & coalesce adjacent/overlapping ranges. + // NB: this may re-order the intervals parameter + static coalesce(intervals: ResolutionCacheKey[]): ResolutionCacheKey[] { + intervals.sort(ResolutionCacheKey.compare); + + var rs = []; + intervals.forEach(r => { + if (rs.length === 0) { + rs.push(r); + return; + } + + var lastR: ResolutionCacheKey = rs[rs.length - 1]; + if (r.contigInterval.intersects(lastR.contigInterval) || + r.contigInterval.isAdjacentTo(lastR.contigInterval) && + r.resolution == lastR.resolution) { + lastR = rs[rs.length - 1] = lastR.clone(); + lastR.contigInterval.interval.stop = + Math.max(r.contigInterval.interval.stop, lastR.contigInterval.interval.stop); + } else { + rs.push(r); + } + }); + + return rs; + } + + // Comparator for use with Array.prototype.sort + static compare(a: ResolutionCacheKey, b: ResolutionCacheKey): number { + if (a.contigInterval.contig > b.contigInterval.contig) { + return -1; + } else if (a.contigInterval.contig < b.contigInterval.contig) { + return +1; + } else { + return a.contigInterval.start() - b.contigInterval.start(); + } + } + +} + +module.exports = { + ResolutionCache +}; diff --git a/src/main/data/FeatureEndpoint.js b/src/main/data/FeatureEndpoint.js index 631debd8..d0de28f3 100644 --- a/src/main/data/FeatureEndpoint.js +++ b/src/main/data/FeatureEndpoint.js @@ -25,11 +25,7 @@ class FeatureEndpoint { } getFeaturesInRange(range: ContigInterval): Q.Promise { - var contig = range.contig; - var start = range.interval.start; - var stop = range.interval.stop; - - return this.remoteRequest.get(contig, start, stop).then(object => { + return this.remoteRequest.get(range).then(object => { return object; }); } diff --git a/src/main/data/GeneEndpoint.js b/src/main/data/GeneEndpoint.js index a34e7e7a..a63f954a 100644 --- a/src/main/data/GeneEndpoint.js +++ b/src/main/data/GeneEndpoint.js @@ -49,11 +49,7 @@ class GeneEndpoint { } getGenesInRange(range: ContigInterval): Q.Promise { - var contig = range.contig; - var start = range.interval.start; - var stop = range.interval.stop; - - return this.remoteRequest.get(contig, start, stop).then(object => { + return this.remoteRequest.get(range).then(object => { var d = extractGenes(object); return d; }); diff --git a/src/main/data/GenotypeEndpoint.js b/src/main/data/GenotypeEndpoint.js index dd88c1ba..01e0dad0 100644 --- a/src/main/data/GenotypeEndpoint.js +++ b/src/main/data/GenotypeEndpoint.js @@ -23,12 +23,7 @@ class GenotypeEndpoint { } getFeaturesInRange(range: ContigInterval): Q.Promise { - var contig = range.contig; - var start = range.interval.start; - var stop = range.interval.stop; - - - return this.remoteRequest.get(contig, start, stop).then(object => { + return this.remoteRequest.get(range).then(object => { return object; }); } diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index 4d5562ad..8532831b 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -6,6 +6,7 @@ 'use strict'; import Q from 'q'; +import ContigInterval from '../ContigInterval'; import type RemoteRequest from '../RemoteRequest'; export type SequenceRecord = { @@ -32,11 +33,13 @@ class Sequence { * The range is inclusive and zero-based. * Returns empty string if no data is available on this range. */ - getFeaturesInRange(contig: string, start: number, stop: number): Q.Promise { + getFeaturesInRange(range: ContigInterval): Q.Promise { + var start = range.start(); + var stop = range.stop(); if (start > stop) { throw `Requested a range with start > stop (${start}, ${stop})`; } - return this.remoteRequest.get(contig, start, stop).then(sequence => { + return this.remoteRequest.get(range).then(sequence => { var d = sequence.substring(start, (stop-start + 1)); return d; }); diff --git a/src/main/data/VariantEndpoint.js b/src/main/data/VariantEndpoint.js index fdfa13d4..cf6447c0 100644 --- a/src/main/data/VariantEndpoint.js +++ b/src/main/data/VariantEndpoint.js @@ -18,12 +18,7 @@ class VariantEndpoint { } getFeaturesInRange(range: ContigInterval): Q.Promise { - var contig = range.contig; - var start = range.interval.start; - var stop = range.interval.stop; - - return this.remoteRequest.get(contig, start, stop).then(object => { - console.log("variant endpoint", object); + return this.remoteRequest.get(range).then(object => { return object; }); } diff --git a/src/main/pileup.js b/src/main/pileup.js index c8145627..afb726ce 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -150,7 +150,7 @@ var pileup = { genotypes: makeVizObject(GenotypeTrack), pileup: makeVizObject(PileupTrack) }, - version: '0.6.6' + version: '0.6.7' }; module.exports = pileup; diff --git a/src/main/sources/CoverageDataSource.js b/src/main/sources/CoverageDataSource.js new file mode 100644 index 00000000..4f428f0e --- /dev/null +++ b/src/main/sources/CoverageDataSource.js @@ -0,0 +1,103 @@ +/** + * Remote Endpoint for coverage. + * + * CoverageDataSource is purely for data parsing and fetching. + * Coverage for CoverageDataSource can be calculated from any source, + * including, but not limited to, Alignment Records, + * variants or features. + * + * @flow + */ +'use strict'; + +import Q from 'q'; +import _ from 'underscore'; +import {Events} from 'backbone'; +import {ResolutionCache} from '../ResolutionCache'; +import ContigInterval from '../ContigInterval'; +import RemoteRequest from '../RemoteRequest'; + +export type CoverageDataSource = { + rangeChanged: (newRange: GenomeRange) => void; + getCoverageInRange: (range: ContigInterval) => PositionCount[]; + on: (event: string, handler: Function) => void; + off: (event: string) => void; + trigger: (event: string, ...args:any) => void; +}; + +var BASE_PAIRS_PER_FETCH = 1000; + +export type PositionCount = { + contig: string; + position: number; + count: number; +} + +function keyFunction(p: PositionCount): string { + return `${p.contig}:${p.position}`; +} + +function filterFunction(range: ContigInterval, p: PositionCount): boolean { + return range.chrContainsLocus(p.contig, p.position); +} + +function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource { + var cache: ResolutionCache = + new ResolutionCache(filterFunction, keyFunction); + + function fetch(range: GenomeRange) { + var interval = new ContigInterval(range.contig, range.start, range.stop); + + // Check if this interval is already in the cache. + if (cache.coversRange(interval)) { + return Q.when(); + + } + + // modify endpoint to calculate coverage using binning + var basePairsPerBin = ResolutionCache.getResolution(interval.interval); + var endpointModifier = `binning=${basePairsPerBin}`; + + // Cover the range immediately to prevent duplicate fetches. + cache.coverRange(interval); + return remoteSource.getFeaturesInRange(interval, endpointModifier).then(positions => { + positions.forEach(p => cache.put(p)); + o.trigger('newdata', interval); + }); + } + + function getCoverageInRange(range: ContigInterval): PositionCount[] { + if (!range) return []; + return cache.get(range); + } + + var o = { + rangeChanged: function(newRange: GenomeRange) { + fetch(newRange).done(); + }, + getCoverageInRange, + + // These are here to make Flow happy. + on: () => {}, + off: () => {}, + trigger: () => {} + }; + _.extend(o, Events); + + return o; +} + +function create(data: {url?:string}): CoverageDataSource { + if (!data.url) { + throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); + } + + var endpoint = new RemoteRequest(data.url, BASE_PAIRS_PER_FETCH); + return createFromCoverageUrl(endpoint); +} + + +module.exports = { + create, + createFromCoverageUrl +}; diff --git a/src/main/sources/GA4GHDataSource.js b/src/main/sources/GA4GHDataSource.js index 4fe58a4d..ad0caa43 100644 --- a/src/main/sources/GA4GHDataSource.js +++ b/src/main/sources/GA4GHDataSource.js @@ -42,7 +42,7 @@ type GA4GHSpec = { }; function create(spec: GA4GHSpec): AlignmentDataSource { - var url = spec.endpoint ; + var url = spec.endpoint; var reads: {[key:string]: Alignment} = {}; @@ -95,7 +95,7 @@ function create(spec: GA4GHSpec): AlignmentDataSource { } var xhr = new XMLHttpRequest(); - var endpoint = url + "/" + range.contig + "?start=" + range.start() + "&end=" + range.stop()+"&key="+spec.readGroupId; + var endpoint = `${url}/${spec.readGroupId}/${range.contig}?start=${range.start()}&end=${range.stop()}`; xhr.open('GET', endpoint); xhr.responseType = 'json'; diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index 05551ff6..1982b998 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -59,7 +59,7 @@ var createFromReferenceUrl = function(remoteSource: Sequence): TwoBitSource { } // TODO remote Source - remoteSource.getFeaturesInRange(range.contig, range.start(), range.stop()) + remoteSource.getFeaturesInRange(range) .then(letters => { if (!letters) return; if (letters.length < range.length()) { diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index 3338fe41..d7d13649 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -68,14 +68,12 @@ function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { coveredRanges.push(interval); coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getFeaturesInRange(interval).then(object => { - console.log(object, variants); object.forEach(variant => addVariant(variant)); o.trigger('newdata', interval); }); } function getFeaturesInRange(range: ContigInterval): Variant[] { - console.log("getFeaturesinRange", range); if (!range) return []; // XXX why would this happen? return _.filter(variants, v => range.chrContainsLocus(v.contig, v.position)); } @@ -100,7 +98,7 @@ function create(data: {url?:string}): VcfDataSource { if (!data.url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } - var request = new RemoteRequest(data.url); + var request = new RemoteRequest(data.url, BASE_PAIRS_PER_FETCH); var endpoint = new VariantEndpoint(request); return createFromVariantUrl(endpoint); } diff --git a/src/test/RemoteRequest-test.js b/src/test/RemoteRequest-test.js index b24dec91..9b5b1a99 100644 --- a/src/test/RemoteRequest-test.js +++ b/src/test/RemoteRequest-test.js @@ -7,6 +7,7 @@ import sinon from 'sinon'; import RemoteRequest from '../main/RemoteRequest'; import RemoteFile from '../main/RemoteFile'; +import ContigInterval from '../main/ContigInterval'; describe('RemoteRequest', function() { var server: any = null, response; @@ -14,6 +15,8 @@ describe('RemoteRequest', function() { var contig = 'chr17'; var start = 10; var stop = 20; + var interval = new ContigInterval(contig, start, stop); + var basePairsPerFetch = 1000; before(function () { return new RemoteFile('/test-data/chr17.1-250.json').getAllString().then(data => { @@ -27,12 +30,12 @@ describe('RemoteRequest', function() { }); it('should fetch json from a server', function(done) { - var remoteRequest = new RemoteRequest(url); + var remoteRequest = new RemoteRequest(url, basePairsPerFetch); var endpoint = remoteRequest.getEndpointFromContig(contig, start, stop); server.respondWith('GET', endpoint, [200, { "Content-Type": "application/json" }, response]); - var promisedData = remoteRequest.get(contig, start, stop); + var promisedData = remoteRequest.get(interval); promisedData.then(obj => { var ret = obj.alignments; expect(remoteRequest.numNetworkRequests).to.equal(1); @@ -42,26 +45,4 @@ describe('RemoteRequest', function() { server.respond(); }); - - it('should cache data after server response', function(done) { - var remoteRequest = new RemoteRequest(url); - // verify cache is cleared for testing - remoteRequest.cache.clear(); - var endpoint = remoteRequest.getEndpointFromContig(contig, start, stop); - server.respondWith('GET', endpoint, - [200, { "Content-Type": "application/json" }, response]); - - var promisedData = remoteRequest.get(contig, start, stop); - promisedData.then(obj => { - var promisedData2 = remoteRequest.get(contig, start, stop); - promisedData2.then(obj2 => { - var ret = obj2.alignments; - expect(remoteRequest.numNetworkRequests).to.equal(1); - expect(ret.length).to.equal(14); - done(); - }); - }); - - server.respond(); - }); }); diff --git a/src/test/ResolutionCache-test.js b/src/test/ResolutionCache-test.js new file mode 100644 index 00000000..07a94d2a --- /dev/null +++ b/src/test/ResolutionCache-test.js @@ -0,0 +1,88 @@ +/** @flow */ +'use strict'; + +import {expect} from 'chai'; + +import ContigInterval from '../main/ContigInterval'; +import {ResolutionCache} from '../main/ResolutionCache'; + +describe('ResolutionCache', function() { + + // Type used for testing cache + type Position = { + contig: string; + position: number; + } + + var smRange = new ContigInterval("chrM", 0, 100); + var smRange2 = new ContigInterval("chrM", 100, 200); + var smRange3 = new ContigInterval("chrM", 300, 400); + + var bigRange = new ContigInterval("chrM", 0, 1000000); + var data: Position[] = [{contig:'chrM',position:2}, + {contig:'chrM',position:3}, + {contig:'chrM',position:6}, + {contig:'chrM',position:107}]; + + function filterFunction(range: ContigInterval, p: Position): boolean { + return range.chrContainsLocus(p.contig, p.position); + } + + function keyFunction(p: Position): string { + return `${p.contig}:${p.position}`; + } + + function createCache(): ResolutionCache { + var cache = new ResolutionCache(filterFunction, keyFunction); + return cache; + } + + + it('should create cache', function() { + var cache: ResolutionCache = createCache(); + expect(cache == {}); + }); + + it('should put and get data in range', function() { + var cache: ResolutionCache = createCache(); + cache.coverRange(smRange); + data.forEach(p => cache.put(p)); + var d = cache.get(smRange); + expect(d.length == 3); + }); + + it('should cover ranges after put', function() { + var cache: ResolutionCache = createCache(); + cache.coverRange(smRange); + data.forEach(p => cache.put(p)); + var covered = cache.coversRange(smRange); + expect(covered === true); + }); + + it('should clear the cache', function() { + var cache: ResolutionCache = createCache(); + cache.coverRange(smRange); + data.forEach(p => cache.put(p)); + cache.clear(); + expect(cache.cache == {}); + expect(cache.coveredRanges == []); + }); + + it('should return false when finer resolution was not yet loaded', function() { + var cache: ResolutionCache = createCache(); + cache.coverRange(bigRange); + var covered = cache.coversRange(smRange); + expect(covered === false); + }); + + it('should coalesce the covered ranges', function() { + var cache: ResolutionCache = createCache(); + cache.coverRange(smRange); + cache.coverRange(smRange3); + expect(cache.coveredRanges.length == 2); + + cache.coverRange(smRange2); + expect(cache.coveredRanges.length == 2); + }); + +}); diff --git a/src/test/sources/CoverageDataSource-test.js b/src/test/sources/CoverageDataSource-test.js new file mode 100644 index 00000000..2c4ec87b --- /dev/null +++ b/src/test/sources/CoverageDataSource-test.js @@ -0,0 +1,99 @@ +/** @flow */ +'use strict'; + +import {expect} from 'chai'; + +import sinon from 'sinon'; + +import ContigInterval from '../../main/ContigInterval'; +import CoverageDataSource from '../../main/sources/CoverageDataSource'; +import RemoteFile from '../../main/RemoteFile'; + +describe('CoverageDataSource', function() { + var server: any = null, response; + + before(function () { + return new RemoteFile('/test-data/chrM-coverage.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/coverage/chrM?start=1&end=1000&binning=1',[200, { "Content-Type": "application/json" }, response]); + }); + }); + + after(function () { + server.restore(); + }); + + it('should fetch coverage points from a server', function(done) { + + var source = CoverageDataSource.create({ + url: '/coverage' + }); + + var requestInterval = new ContigInterval('chrM', 10, 30); + expect(source.getCoverageInRange(requestInterval)) + .to.deep.equal([]); + + source.on('newdata', () => { + var coverage = source.getCoverageInRange(requestInterval); + expect(coverage).to.have.length(12); + done(); + }); + + source.rangeChanged({contig: 'chrM', start: 10, stop: 30}); + server.respond(); + }); + + it('should cache coverage after first call', function(done) { + + var source = CoverageDataSource.create({ + url: '/coverage' + }); + var requestCount = 0; + var requestInterval = new ContigInterval('chrM', 10, 20); + expect(source.getCoverageInRange(requestInterval)) + .to.deep.equal([]); + + var progress = []; + source.on('networkprogress', e => { progress.push(e); }); + source.on('networkdone', e => { progress.push('done'); }); + source.on('newdata', () => { + requestCount += 1; + expect(requestCount == 1); + done(); + }); + + source.rangeChanged({contig: 'chrM', start: 1, stop: 30}); + source.rangeChanged({contig: 'chrM', start: 2, stop: 8}); + + server.respond(); + + }); + + it('should bin coverage over large regions', function(done) { + + var source = CoverageDataSource.create({ + url: '/coverage' + }); + var requestCount = 0; + var requestInterval = new ContigInterval('chrM', 10, 20); + expect(source.getCoverageInRange(requestInterval)) + .to.deep.equal([]); + + var progress = []; + source.on('networkprogress', e => { progress.push(e); }); + source.on('networkdone', e => { progress.push('done'); }); + source.on('newdata', () => { + requestCount += 1; + expect(requestCount == 1); + done(); + }); + + source.rangeChanged({contig: 'chrM', start: 1, stop: 30}); + source.rangeChanged({contig: 'chrM', start: 2, stop: 8}); + + server.respond(); + + }); + +}); diff --git a/src/test/sources/GA4GHDataSource-test.js b/src/test/sources/GA4GHDataSource-test.js index e6fd6467..c507cfad 100644 --- a/src/test/sources/GA4GHDataSource-test.js +++ b/src/test/sources/GA4GHDataSource-test.js @@ -8,7 +8,7 @@ import sinon from 'sinon'; import ContigInterval from '../../main/ContigInterval'; import GA4GHDataSource from '../../main/sources/GA4GHDataSource'; import RemoteFile from '../../main/RemoteFile'; - + describe('GA4GHDataSource', function() { var server: any = null, response; @@ -24,12 +24,12 @@ describe('GA4GHDataSource', function() { }); it('should fetch alignments from a server', function(done) { - server.respondWith('POST', '/v0.5.1/reads/search', + server.respondWith('POST', '/v0.5.1/reads/search/chr17?start=1&end=1000', [200, { "Content-Type": "application/json" }, response]); var source = GA4GHDataSource.create({ - endpoint: '/v0.5.1', - readGroupId: 'some-group-set:some-read-group', + endpoint: '/v0.5.1/reads', + readGroupId: 'search', killChr: false }); diff --git a/src/test/sources/ReferenceDataSource-test.js b/src/test/sources/ReferenceDataSource-test.js index c8b7f25c..ab1c86d4 100644 --- a/src/test/sources/ReferenceDataSource-test.js +++ b/src/test/sources/ReferenceDataSource-test.js @@ -63,13 +63,13 @@ it('should fetch base pairs', function(done) { var range = {contig: 'chrM', start: 0, stop: 3}; // Before data has been fetched, all base pairs are null. - expect(source.getRange(range)).to.deep.equal({ - 'chrM:0': null, - 'chrM:1': null, - 'chrM:2': null, - 'chrM:3': null - }); - expect(source.getRangeAsString(range)).to.equal('....'); + expect(source.getRange(range)).to.deep.equal({ + 'chrM:0': null, + 'chrM:1': null, + 'chrM:2': null, + 'chrM:3': null + }); + expect(source.getRangeAsString(range)).to.equal('....'); source.on('newdata', () => { expect(source.getRange(range)).to.deep.equal({ diff --git a/src/test/sources/VariantDataSource-test.js b/src/test/sources/VariantDataSource-test.js index 1cf08079..bedbc400 100644 --- a/src/test/sources/VariantDataSource-test.js +++ b/src/test/sources/VariantDataSource-test.js @@ -40,7 +40,6 @@ describe('VariantDataSource', function() { source.on('newdata', () => { var variants = source.getFeaturesInRange(range); - console.log(variants); expect(variants).to.have.length(3); expect(variants[1].contig).to.equal('chrM'); expect(variants[1].position).to.equal(20); diff --git a/test-data/chrM-coverage.json b/test-data/chrM-coverage.json new file mode 100644 index 00000000..caaeab28 --- /dev/null +++ b/test-data/chrM-coverage.json @@ -0,0 +1,49 @@ +[{ + "contig": "chrM", + "position": 10, + "count": 50 +}, { + "contig": "chrM", + "position": 11, + "count": 52 +}, { + "contig": "chrM", + "position": 12, + "count": 54 +}, { + "contig": "chrM", + "position": 13, + "count": 56 +}, { + "contig": "chrM", + "position": 14, + "count": 58 +}, { + "contig": "chrM", + "position": 15, + "count": 58 +}, { + "contig": "chrM", + "position": 16, + "count": 58 +}, { + "contig": "chrM", + "position": 17, + "count": 58 +}, { + "contig": "chrM", + "position": 18, + "count": 68 +}, { + "contig": "chrM", + "position": 19, + "count": 72 +}, { + "contig": "chrM", + "position": 20, + "count": 75 +}, { + "contig": "chrM", + "position": 21, + "count": 62 +}] diff --git a/test-data/variants-chrM-0-100.json b/test-data/variants-chrM-0-100.json index c48c5b03..44598dae 100644 --- a/test-data/variants-chrM-0-100.json +++ b/test-data/variants-chrM-0-100.json @@ -10,7 +10,7 @@ "alt": "T" }, { "contig": "chrM", - "position": 20, + "position": 23, "ref": "A", "alt": "C" }] From ad3c79914ea103756db73db649fd6f1d39a01002 Mon Sep 17 00:00:00 2001 From: dorislee0309 Date: Fri, 1 Jul 2016 09:28:18 -0700 Subject: [PATCH 041/136] customized ALT REF colors for variants, greyed genotype --- src/main/style.js | 4 +--- src/main/viz/VariantTrack.js | 8 ++++---- 2 files changed, 5 insertions(+), 7 deletions(-) diff --git a/src/main/style.js b/src/main/style.js index e1e3d40a..a1fcd216 100644 --- a/src/main/style.js +++ b/src/main/style.js @@ -62,12 +62,10 @@ module.exports = { LOC_FONT_COLOR: 'black', // Variant Track - VARIANT_STROKE: 'blue', - VARIANT_FILL: 'blue', VARIANT_HEIGHT: 14, // Genotype Track GENOTYPE_SPACING: 1, - GENOTYPE_FILL: 'red', + GENOTYPE_FILL: '#9494b8', GENOTYPE_HEIGHT: 10, }; diff --git a/src/main/viz/VariantTrack.js b/src/main/viz/VariantTrack.js index 45ebe2c6..d19b8c8c 100644 --- a/src/main/viz/VariantTrack.js +++ b/src/main/viz/VariantTrack.js @@ -77,14 +77,14 @@ class VariantTrack extends React.Component { ctx.reset(); ctx.save(); - ctx.fillStyle = style.VARIANT_FILL; - ctx.strokeStyle = style.VARIANT_STROKE; variants.forEach(variant => { ctx.pushObject(variant); + ctx.fillStyle = style.BASE_COLORS[variant.alt]; + ctx.strokeStyle = style.BASE_COLORS[variant.ref]; var x = Math.round(scale(variant.position)); var width = Math.round(scale(variant.position + 1)) - 1 - x; - ctx.fillRect(x - 0.5, y - 0.5, width, style.VARIANT_HEIGHT); - ctx.strokeRect(x - 0.5, y - 0.5, width, style.VARIANT_HEIGHT); + ctx.fillRect(x - 0.2, y - 0.2, width, style.VARIANT_HEIGHT); + ctx.strokeRect(x - 0.2, y - 0.2, width, style.VARIANT_HEIGHT); ctx.popObject(); }); From f65ebcd13e2b58a9871e732d8e14f96ae74f57a0 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 4 Oct 2016 09:04:20 -0700 Subject: [PATCH 042/136] fixed versions, shorted build time --- scripts/test.sh | 3 - src/main/pileup.js | 4 +- src/test/sources/ReferenceDataSource-test.js | 210 +++++++++---------- 3 files changed, 104 insertions(+), 113 deletions(-) diff --git a/scripts/test.sh b/scripts/test.sh index 2b734566..9914fba4 100755 --- a/scripts/test.sh +++ b/scripts/test.sh @@ -3,9 +3,6 @@ # Note that you must run `npm run build` or `npm run watch` before running this. set -o errexit -# compile files for test -./scripts/quick-build.sh - # Run http-server and save its PID http-server -p 8081 > /dev/null & SERVER_PID=$! diff --git a/src/main/pileup.js b/src/main/pileup.js index afb726ce..b7328eeb 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -21,7 +21,7 @@ import GenotypeDataSource from './sources/GenotypeDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; import EmptySource from './sources/EmptySource'; -// import FeatureDataSource from './sources/FeatureDataSource'; +import FeatureDataSource from './sources/FeatureDataSource'; // Visualizations import CoverageTrack from './viz/CoverageTrack'; @@ -150,7 +150,7 @@ var pileup = { genotypes: makeVizObject(GenotypeTrack), pileup: makeVizObject(PileupTrack) }, - version: '0.6.7' + version: '0.6.8' }; module.exports = pileup; diff --git a/src/test/sources/ReferenceDataSource-test.js b/src/test/sources/ReferenceDataSource-test.js index ab1c86d4..eba5bd39 100644 --- a/src/test/sources/ReferenceDataSource-test.js +++ b/src/test/sources/ReferenceDataSource-test.js @@ -24,132 +24,126 @@ describe('ReferenceDataSource', function() { after(function () { server.restore(); }); -}); -after(function () { - server.restore(); -}); + function getTestSource() { + var source = ReferenceDataSource.create({ + url: '/reference', + contigList: [{ + name:"chrM", + length: 1000 + },{ + name:"22", + length: 1000 + }] + }); + return source; + } -function getTestSource() { - var source = ReferenceDataSource.create({ - url: '/reference', - contigList: [{ - name:"chrM", - length: 1000 - },{ - name:"22", - length: 1000 - }] + it('should fetch contigs', function() { + var source = getTestSource(); + var contigs = source.contigList(); + expect(contigs).to.deep.equal(['chrM','22']); }); - return source; -} - -it('should fetch contigs', function() { - var source = getTestSource(); - var contigs = source.contigList(); - expect(contigs).to.deep.equal(['chrM','22']); -}); - -it('should normalize range', function() { - var source = getTestSource(); - var range = {contig: 'chrM', start: 0, stop: 3}; - source.normalizeRange(range).then(normalized => { - expect(normalized.to.deep.equal(range)); - }).done(); -}); -it('should fetch base pairs', function(done) { - var source = getTestSource(); - var range = {contig: 'chrM', start: 0, stop: 3}; - - // Before data has been fetched, all base pairs are null. - expect(source.getRange(range)).to.deep.equal({ - 'chrM:0': null, - 'chrM:1': null, - 'chrM:2': null, - 'chrM:3': null + it('should normalize range', function() { + var source = getTestSource(); + var range = {contig: 'chrM', start: 0, stop: 3}; + source.normalizeRange(range).then(normalized => { + expect(normalized.to.deep.equal(range)); + }).done(); }); - expect(source.getRangeAsString(range)).to.equal('....'); - source.on('newdata', () => { + it('should fetch base pairs', function(done) { + var source = getTestSource(); + var range = {contig: 'chrM', start: 0, stop: 3}; + + // Before data has been fetched, all base pairs are null. expect(source.getRange(range)).to.deep.equal({ - 'chrM:0': 'N', - 'chrM:1': 'G', - 'chrM:2': 'T', - 'chrM:3': 'T' + 'chrM:0': null, + 'chrM:1': null, + 'chrM:2': null, + 'chrM:3': null }); - expect(source.getRangeAsString(range)).to.equal('NGTT'); + expect(source.getRangeAsString(range)).to.equal('....'); - done(); - }); - source.rangeChanged(range); - server.respond(); -}); + source.on('newdata', () => { + expect(source.getRange(range)).to.deep.equal({ + 'chrM:0': 'N', + 'chrM:1': 'G', + 'chrM:2': 'T', + 'chrM:3': 'T' + }); + expect(source.getRangeAsString(range)).to.equal('NGTT'); -it('should fetch nearby base pairs', function(done) { - var source = getTestSource(); - - source.on('newdata', () => { - expect(source.getRange({contig: 'chrM', start: 0, stop: 14})) - .to.deep.equal({ - 'chrM:0': 'N', - 'chrM:1': 'G', - 'chrM:2': 'T', - 'chrM:3': 'T', - 'chrM:4': 'A', // start of actual request - 'chrM:5': 'A', - 'chrM:6': 'T', - 'chrM:7': 'G', - 'chrM:8': 'T', - 'chrM:9': 'A', // end of actual requuest - 'chrM:10': 'G', - 'chrM:11': 'C', - 'chrM:12': 'T', - 'chrM:13': 'T', - 'chrM:14': 'A' - }); - done(); + done(); + }); + source.rangeChanged(range); + server.respond(); }); - source.rangeChanged({contig: 'chrM', start: 4, stop: 9}); - server.respond(); -}); - -it('should add chr', function(done) { - var source = getTestSource(); - var range = {contig: '22', start: 0, stop: 3}; - source.on('newdata', () => { - expect(source.getRange(range)).to.deep.equal({ - '22:0': 'N', - '22:1': 'G', - '22:2': 'T', - '22:3': 'T' + it('should fetch nearby base pairs', function(done) { + var source = getTestSource(); + + source.on('newdata', () => { + expect(source.getRange({contig: 'chrM', start: 0, stop: 14})) + .to.deep.equal({ + 'chrM:0': 'N', + 'chrM:1': 'G', + 'chrM:2': 'T', + 'chrM:3': 'T', + 'chrM:4': 'A', // start of actual request + 'chrM:5': 'A', + 'chrM:6': 'T', + 'chrM:7': 'G', + 'chrM:8': 'T', + 'chrM:9': 'A', // end of actual requuest + 'chrM:10': 'G', + 'chrM:11': 'C', + 'chrM:12': 'T', + 'chrM:13': 'T', + 'chrM:14': 'A' + }); + done(); }); - expect(source.getRangeAsString(range)).to.equal('NGTT'); - done(); + source.rangeChanged({contig: 'chrM', start: 4, stop: 9}); + server.respond(); }); - source.rangeChanged(range); - server.respond(); -}); - -it('should only report newly-fetched ranges', function(done) { - ReferenceDataSource.testBasePairsToFetch(10); - var initRange = {contig: 'chrM', start: 5, stop: 8}, - secondRange = {contig: 'chrM', start: 8, stop: 15}; - var source = getTestSource(); - source.once('newdata', newRange => { - expect(newRange.toString()).to.equal('chrM:0-10'); // expanded range - source.once('newdata', newRange => { - // This expanded range excludes previously-fetched data. - expect(newRange.toString()).to.equal('chrM:11-20'); + it('should add chr', function(done) { + var source = getTestSource(); + var range = {contig: '22', start: 0, stop: 3}; + + source.on('newdata', () => { + expect(source.getRange(range)).to.deep.equal({ + '22:0': 'N', + '22:1': 'G', + '22:2': 'T', + '22:3': 'T' + }); + expect(source.getRangeAsString(range)).to.equal('NGTT'); done(); }); - source.rangeChanged(secondRange); + source.rangeChanged(range); server.respond(); }); - source.rangeChanged(initRange); - server.respond(); -}); + it('should only report newly-fetched ranges', function(done) { + ReferenceDataSource.testBasePairsToFetch(10); + var initRange = {contig: 'chrM', start: 5, stop: 8}, + secondRange = {contig: 'chrM', start: 8, stop: 15}; + var source = getTestSource(); + source.once('newdata', newRange => { + expect(newRange.toString()).to.equal('chrM:0-10'); // expanded range + + source.once('newdata', newRange => { + // This expanded range excludes previously-fetched data. + expect(newRange.toString()).to.equal('chrM:11-20'); + done(); + }); + source.rangeChanged(secondRange); + server.respond(); + }); + source.rangeChanged(initRange); + server.respond(); + }); }); From 0c5c4a4683fb65f9bb4d8d90d3cf2860edb0f192 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 5 Oct 2016 09:42:56 -0700 Subject: [PATCH 043/136] small formatting nits and removing double 'strict' statement --- examples/data.js | 127 +++++++++++++++------------------ scripts/quick-build.sh | 19 ----- src/main/data/TwoBit.js | 2 +- src/main/data/VirtualOffset.js | 2 - src/main/style.js | 2 - 5 files changed, 57 insertions(+), 95 deletions(-) delete mode 100755 scripts/quick-build.sh diff --git a/examples/data.js b/examples/data.js index 86b0f074..77d16e35 100644 --- a/examples/data.js +++ b/examples/data.js @@ -1,83 +1,68 @@ // Some data for the demo. -//// We are going to use the same data source for multiple tracks -//var bamSource = pileup.formats.bam({ -// url: '/test-data/synth3.normal.17.7500000-7515000.bam', -// indexUrl: '/test-data/synth3.normal.17.7500000-7515000.bam.bai' -//}); +// We are going to use the same data source for multiple tracks +var bamSource = pileup.formats.bam({ + url: '/test-data/synth3.normal.17.7500000-7515000.bam', + indexUrl: '/test-data/synth3.normal.17.7500000-7515000.bam.bai' +}); var sources = [ { viz: pileup.viz.genome(), isReference: true, - data: pileup.formats.reference({ - url: '/reference', - contigList: [{ - name:"chrM", - length: 1000 - },{ - name:"22", - length: 1000 - }] + data: pileup.formats.twoBit({ + url: 'http://www.biodalliance.org/datasets/hg19.2bit' }), name: 'Reference' + }, + { + viz: pileup.viz.scale(), + name: 'Scale' + }, + { + viz: pileup.viz.location(), + name: 'Location' + }, + { + viz: pileup.viz.variants(), + data: pileup.formats.vcf({ + url: '/test-data/snv.chr17.vcf' + }), + name: 'Variants' + }, + { + viz: pileup.viz.genes(), + data: pileup.formats.bigBed({ + url: 'http://www.biodalliance.org/datasets/ensGene.bb' + }), + name: 'Genes' + }, + { + viz: pileup.viz.coverage(), + data: bamSource, + cssClass: 'normal', + name: 'Coverage' + }, + { + viz: pileup.viz.pileup(), + data: bamSource, + cssClass: 'normal', + name: 'Alignments' + }, + { + viz: pileup.viz.coverage(), + data: bamSource, + cssClass: 'tumor', + name: 'Coverage' + }, + { + viz: pileup.viz.pileup({ + viewAsPairs: true + }), + data: bamSource, + cssClass: 'tumor', + name: 'Alignments' } -// { -// viz: pileup.viz.genome(), -// isReference: true, -// data: pileup.formats.reference({ -// prefix:"../json/" -// }), -// name: 'Reference' -// } -// { -// viz: pileup.viz.scale(), -// name: 'Scale' -// }, -// { -// viz: pileup.viz.location(), -// name: 'Location' -// }, -// { -// viz: pileup.viz.variants(), -// data: pileup.formats.vcf({ -// url: '/test-data/snv.chr17.vcf' -// }), -// name: 'Variants' -// }, -// { -// viz: pileup.viz.genes(), -// data: pileup.formats.bigBed({ -// url: 'http://www.biodalliance.org/datasets/ensGene.bb' -// }), -// name: 'Genes' -// }, -// { -// viz: pileup.viz.coverage(), -// data: bamSource, -// cssClass: 'normal', -// name: 'Coverage' -// }, -// { -// viz: pileup.viz.pileup(), -// data: bamSource, -// cssClass: 'normal', -// name: 'Alignments' -// }, -// { -// viz: pileup.viz.coverage(), -// data: bamSource, -// cssClass: 'tumor', -// name: 'Coverage' -// }, -// { -// viz: pileup.viz.pileup({ -// viewAsPairs: true -// }), -// data: bamSource, -// cssClass: 'tumor', -// name: 'Alignments' -// } ]; -var range = {contig: 'chrM', start: 0, stop: 10}; +var range = {contig: 'chr17', start: 7512284, stop: 7512644}; diff --git a/scripts/quick-build.sh b/scripts/quick-build.sh deleted file mode 100755 index 1c617c78..00000000 --- a/scripts/quick-build.sh +++ /dev/null @@ -1,19 +0,0 @@ -#!/bin/bash -# Build require-ale and minified assets for distribution. -set -o errexit -# ./scripts/make-mini-d3.sh # TODO: remove - -# Transpile individual files. This is useful if another module, -# e.g. cycledash, wants to require('pileup'). -# The dist/test files are required for code coverage -mkdir -p dist/test/{data,source,viz} -babel src --retain-lines --ignore src/lib --out-dir dist -cp -r src/lib dist/ - -# Create dist/tests -browserify \ - -v \ - -t [ babelify --ignore src/lib ] \ - --debug \ - -o dist/tests.js \ - $(find src/test -name '*.js') diff --git a/src/main/data/TwoBit.js b/src/main/data/TwoBit.js index 1858da08..ca0231f4 100644 --- a/src/main/data/TwoBit.js +++ b/src/main/data/TwoBit.js @@ -270,4 +270,4 @@ class TwoBit { } } -module.exports = TwoBit; \ No newline at end of file +module.exports = TwoBit; diff --git a/src/main/data/VirtualOffset.js b/src/main/data/VirtualOffset.js index b3136b40..5d3dcc78 100644 --- a/src/main/data/VirtualOffset.js +++ b/src/main/data/VirtualOffset.js @@ -8,8 +8,6 @@ */ 'use strict'; -"use strict"; - class VirtualOffset { coffset: number; uoffset: number; diff --git a/src/main/style.js b/src/main/style.js index a1fcd216..b3b77a01 100644 --- a/src/main/style.js +++ b/src/main/style.js @@ -6,8 +6,6 @@ */ 'use strict'; -"use strict"; - module.exports = { // Colors for individual base pairs BASE_COLORS: { From c9ebcb548df1d4e08064aede41012a4e2db394aa Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 5 Oct 2016 09:43:15 -0700 Subject: [PATCH 044/136] fixed genotype samples and added unit tests --- src/main/data/GenotypeEndpoint.js | 2 +- src/main/viz/GenotypeTrack.js | 3 +- src/test/viz/GenotypeTrack-test.js | 84 ++++++++++++++++++++++++++++++ 3 files changed, 87 insertions(+), 2 deletions(-) create mode 100644 src/test/viz/GenotypeTrack-test.js diff --git a/src/main/data/GenotypeEndpoint.js b/src/main/data/GenotypeEndpoint.js index 01e0dad0..d5c04431 100644 --- a/src/main/data/GenotypeEndpoint.js +++ b/src/main/data/GenotypeEndpoint.js @@ -11,7 +11,7 @@ import type RemoteRequest from '../RemoteRequest'; import type {Variant} from './vcf'; export type Genotype = { - sampleIds: string, + sampleIds: string[], variant: Variant } diff --git a/src/main/viz/GenotypeTrack.js b/src/main/viz/GenotypeTrack.js index 56297a78..f43c6d9a 100644 --- a/src/main/viz/GenotypeTrack.js +++ b/src/main/viz/GenotypeTrack.js @@ -94,7 +94,8 @@ class GenotypeTrack extends React.Component { // This is a hack to adjust parent div for resize var el = d3utils.findParent(canvas, 'track-content'); - if (el) el.style.height = newHeight; + console.log("el", el); + // if (el) el.style.height = newHeight; ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); ctx.reset(); diff --git a/src/test/viz/GenotypeTrack-test.js b/src/test/viz/GenotypeTrack-test.js new file mode 100644 index 00000000..71cd1395 --- /dev/null +++ b/src/test/viz/GenotypeTrack-test.js @@ -0,0 +1,84 @@ +/** + * This tests that the Controls and reference track render correctly, even when + * an externally-set range uses a different chromosome naming system (e.g. '17' + * vs 'chr17'). See https://github.com/hammerlab/pileup.js/issues/146 + * @flow + */ + +'use strict'; + +import {expect} from 'chai'; + +import sinon from 'sinon'; + +import pileup from '../../main/pileup'; +import dataCanvas from 'data-canvas'; +import {waitFor} from '../async'; +import RemoteFile from '../../main/RemoteFile'; + +describe('GenotypeTrack', function() { + var server: any = null, response; + + before(function () { + return new RemoteFile('/test-data/genotypes-17.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/genotypes/17?start=1&end=1000',[200, { "Content-Type": "application/json" }, response]); + }); + }); + + var testDiv = document.getElementById('testdiv'); + + beforeEach(() => { + testDiv.style.width = '800px'; + dataCanvas.RecordingContext.recordAll(); + }); + + afterEach(() => { + dataCanvas.RecordingContext.reset(); + // avoid pollution between tests. + testDiv.innerHTML = ''; + }); + var {drawnObjects, callsOf} = dataCanvas.RecordingContext; + + function ready() { + return testDiv.querySelector('canvas') && + drawnObjects(testDiv, '.genotypes').length > 0; + } + + it('should render genotypes', function() { + var p = pileup.create(testDiv, { + // range: {contig: 'chrM', start: 0, stop: 30}, + range: {contig: '17', start: 9386380, stop: 9537420}, + tracks: [ + { + viz: pileup.viz.genome(), + data: pileup.formats.twoBit({ + url: '/test-data/test.2bit' + }), + isReference: true + }, + { + data: pileup.formats.genotypes({ + url: '/test-data/genotypes-17.json' + }), + viz: pileup.viz.genotypes(), + } + ] + }); + + return waitFor(ready, 2000) + .then(() => { + var genotypes = drawnObjects(testDiv, '.genotypes'); + var sampleIds = ["sample1", "sample2", "sample3"]; + expect(genotypes).to.have.length(3); + expect(genotypes.map(g => g.variant.position)).to.deep.equal( + [10, 20, 30]); + expect(genotypes.map(g => g.sampleIds)).to.deep.equal( + [sampleIds, sampleIds, sampleIds]); + + p.destroy(); + }); + }); + +}); From 24160efe543ad309cc19617de719aa510f6851c5 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 5 Oct 2016 09:43:59 -0700 Subject: [PATCH 045/136] Removed alignment test file and renamed Alignment test suite --- src/test/ADAMAlignment-test.js | 4 +- src/test/sources/GA4GHDataSource-test.js | 3 +- test-data/adam-alignments.json | 33390 --------------------- 3 files changed, 4 insertions(+), 33393 deletions(-) delete mode 100644 test-data/adam-alignments.json diff --git a/src/test/ADAMAlignment-test.js b/src/test/ADAMAlignment-test.js index 07191353..9edda342 100644 --- a/src/test/ADAMAlignment-test.js +++ b/src/test/ADAMAlignment-test.js @@ -7,11 +7,11 @@ import GA4GHAlignment from '../main/GA4GHAlignment'; import RemoteFile from '../main/RemoteFile'; import Bam from '../main/data/bam'; -describe('GA4GHAlignment', function() { +describe('ADAMAlignment', function() { var sampleAlignments = []; before(function() { - return new RemoteFile('/test-data/adam-alignments.json').getAllString().then(data => { + return new RemoteFile('/test-data/chr17.1-250.json').getAllString().then(data => { sampleAlignments = JSON.parse(data).alignments; }); }); diff --git a/src/test/sources/GA4GHDataSource-test.js b/src/test/sources/GA4GHDataSource-test.js index c507cfad..5d85a63b 100644 --- a/src/test/sources/GA4GHDataSource-test.js +++ b/src/test/sources/GA4GHDataSource-test.js @@ -24,7 +24,8 @@ describe('GA4GHDataSource', function() { }); it('should fetch alignments from a server', function(done) { - server.respondWith('POST', '/v0.5.1/reads/search/chr17?start=1&end=1000', + // ALYSSA: TODO: should move back to POST as in original API + server.respondWith('GET', '/v0.5.1/reads/search/chr17?start=1&end=1000', [200, { "Content-Type": "application/json" }, response]); var source = GA4GHDataSource.create({ diff --git a/test-data/adam-alignments.json b/test-data/adam-alignments.json deleted file mode 100644 index e8866aa4..00000000 --- a/test-data/adam-alignments.json +++ /dev/null @@ -1,33390 +0,0 @@ -{ - "alignments": [{ - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:47:2891:8862", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 0, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 59, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 42, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATCATTGTATCCCATAAACACAAAGTTTTGGTCCTGGCCTTATAATTACTTAG", - "alignedQuality": [17, 28, 10, 23, 27, 28, 17, 31, 22, 10, 16, 19, 9, 15, 16, 22, 15, 14, 15, 20, 15, 9, 15, 15, 9, 32, 32, 25, 27, 9, 21, 25, 32, 28, 28, 31, 31, 23, 22, 22, 9, 17, 22, 12, 25, 24, 14, 10, 26, 26, 10, 32, 26, 30, 32, 31, 25, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:40:17115:17222", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 154, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 1, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 31, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 70, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTCATGTAGCTTGATAACAGCGCAAAGAACTCCAAATGCTTAGATGGATAATTGTATCCCATAAAAACAAAGGATTGGGCCTGGCCTTATAANTATTTTGA", - "alignedQuality": [31, 31, 7, 30, 7, 11, 31, 7, 31, 7, 7, 11, 6, 28, 11, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:27:8808:3060", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 2, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATNAATTAGAG", - "alignedQuality": [38, 38, 38, 38, 35, 37, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 38, 37, 38, 38, 38, 38, 38, 38, 30, 37, 35, 38, 37, 37, 37, 37, 38, 38, 38, 35, 36, 37, 37, 36, 38, 38, 38, 35, 38, 36, 37, 36, 38, 36, 37, 36, 36, 37, 33, 33, 34, 35, 36, 36, 34, 35, 35, 35, 35, 35, 36, 25, 35, 36, 30, 35, 32, 25, 26, 0, 26, 6, 29, 26, 29, 28, 22, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.3", - "fragmentName": "613F0AAXX100423:3:93:11085:15551", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 138, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 2, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "CLIP_SOFT", - "operationLength": 47, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 54, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACCAAAACTCTAATCATACTCTATTACGCAATAAACATTAACAAGATAATGTAGCTTAATAACAAAGCAAAGCACTGCATATGCTTAGATGGGTAATTGT", - "alignedQuality": [23, 18, 23, 29, 18, 30, 27, 30, 24, 27, 26, 21, 21, 11, 18, 30, 29, 23, 11, 24, 29, 18, 23, 27, 27, 30, 23, 27, 30, 27, 24, 29, 32, 24, 29, 29, 31, 31, 32, 31, 33, 33, 28, 33, 33, 27, 7, 23, 23, 23, 32, 33, 33, 27, 31, 32, 25, 33, 33, 28, 31, 24, 29, 33, 31, 16, 32, 31, 31, 19, 16, 16, 27, 29, 17, 27, 30, 29, 10, 25, 9, 29, 29, 30, 29, 31, 21, 33, 18, 31, 33, 31, 10, 18, 31, 33, 32, 32, 19, 32, 25], - 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"fragmentName": "613F0AAXX100423:7:103:9796:21327", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 26, - "reverseStrand": false - }, - "mappingQuality": 25, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGCACTGAAAATGCTTAGATGGATAATTGTATCCNATAAACACAAAGGTTTGGTCCTGGCCTTATANTTAATTAGAGGTAAAATTACAAGANNGGNNNNNN", - "alignedQuality": [24, 26, 12, 26, 25, 26, 26, 24, 26, 26, 32, 29, 30, 31, 32, 30, 34, 32, 34, 34, 28, 28, 28, 31, 28, 20, 28, 33, 25, 30, 26, 26, 29, 12, 0, 26, 32, 26, 26, 26, 32, 32, 32, 32, 32, 34, 30, 34, 34, 25, 32, 34, 32, 30, 32, 35, 35, 35, 25, 35, 35, 35, 25, 35, 30, 33, 0, 28, 30, 29, 23, 27, 24, 25, 26, 31, 29, 24, 13, 29, 32, 30, 29, 32, 28, 35, 35, 20, 25, 30, 2, 0, 0, 2, 2, 0, 0, 0, 0, 0, 0], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:43:1543:11173", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 29, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACTGAAAATGCTTAGATGGATACTTGTATCCCATAAACACAAAGGTTTGGGCCTGGCCTTATACTTAATTAGAGGTAAAATCACACATGCAANACCTCTAT", - "alignedQuality": [32, 32, 15, 32, 9, 23, 28, 30, 20, 15, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - 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"properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 187, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 32, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCNCCCATAGA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 33, 38, 37, 38, 38, 38, 38, 36, 36, 38, 38, 38, 37, 38, 38, 37, 38, 37, 36, 38, 38, 38, 33, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 34, 38, 37, 38, 37, 38, 36, 38, 38, 35, 38, 38, 38, 37, 38, 38, 37, 38, 32, 30, 0, 7, 30, 25, 25, 27, 25, 28, 31], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:107:18142:17511", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 40, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGANCGGTGTAA", - "alignedQuality": [38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 34, 37, 38, 38, 37, 36, 38, 37, 33, 37, 37, 38, 38, 38, 37, 38, 36, 37, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 34, 34, 35, 36, 37, 37, 37, 37, 38, 36, 36, 36, 37, 36, 36, 38, 36, 35, 35, 36, 35, 35, 36, 35, 33, 35, 36, 26, 32, 0, 32, 27, 19, 15, 27, 18, 21, 34], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:100:2715:9259", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 164, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 41, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 22, - "referenceSequence": null - }, { - "operation": "DELETE", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 79, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAGATGGATAATTGTATCCCATAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAA", - "alignedQuality": [36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 36, 38, 35, 38, 38, 38, 38, 35, 35, 38, 38, 38, 35, 35, 37, 38, 33, 35, 37, 38, 38, 37, 38, 37, 38, 37, 36, 30, 38, 37, 35, 37, 37, 38, 36, 35, 38, 38, 28, 36, 37, 37, 37, 37, 36, 36, 34, 36, 34, 35, 35, 32, 33, 32, 36, 36, 36, 35, 35, 36, 34, 35, 33, 34, 32, 34, 32, 36, 34, 20, 29, 33, 27, 33, 33, 33, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:21:16353:12115", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 181, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 41, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 100, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 1, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCCTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 36, 37, 36, 38, 37, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 36, 38, 38, 36, 31, 36, 36, 38, 36, 34, 38, 37, 36, 36, 37, 38, 36, 9, 37, 37, 37, 33, 34, 35, 35, 34, 35, 37, 38, 33, 37, 36, 37, 36, 34, 37, 36, 37, 37, 38, 36, 38, 35, 37, 36, 38, 36, 30, 34, 37, 35, 36, 37, 35, 36, 36, 35, 37, 36, 37, 36, 37, 36, 35, 36, 34, 31, 32, 30, 25, 31, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:101:7284:15284", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 41, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 86, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 15, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGGAAAATTACACATGCAAACCTCCAAGATCGGAAGAGCG", - "alignedQuality": [31, 21, 18, 14, 31, 15, 15, 18, 31, 16, 24, 14, 32, 23, 11, 28, 21, 33, 26, 33, 34, 25, 34, 30, 34, 34, 34, 34, 34, 28, 34, 34, 25, 12, 28, 10, 17, 28, 16, 22, 22, 7, 17, 30, 22, 14, 17, 14, 28, 13, 32, 24, 24, 27, 33, 27, 23, 22, 34, 32, 30, 29, 15, 5, 33, 11, 26, 17, 15, 16, 33, 30, 33, 19, 32, 21, 22, 22, 29, 22, 30, 20, 22, 15, 11, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:16:11065:2362", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 177, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 43, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGNGTGTAAAA", - "alignedQuality": [37, 38, 38, 38, 38, 35, 37, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 37, 38, 38, 37, 35, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 37, 38, 38, 35, 38, 38, 36, 37, 38, 37, 37, 38, 37, 37, 37, 36, 36, 38, 38, 38, 38, 38, 37, 38, 37, 36, 38, 36, 34, 36, 37, 38, 36, 38, 35, 38, 37, 37, 36, 36, 36, 36, 35, 36, 36, 35, 36, 36, 35, 36, 35, 35, 33, 36, 35, 35, 35, 30, 34, 0, 21, 24, 22, 21, 23, 25, 15, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.8", - "fragmentName": "6141AAAXX100423:8:119:13184:13731", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGTGGCTAACGAAAAAGCTTTGAAATGCTTTCTGAAGGTCCTGAAACATGCCTTTAAAATTAAAAATAAGTTTAAATGAGTTTTACACACGTTTGTGGTGT", - "alignedQuality": [16, 19, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.8", - "fragmentName": "6141AAAXX100423:8:119:13184:13731", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 43, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 88, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 13, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GATGGATAATTGTATCCCATAAACACAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGAAGACAGGA", - "alignedQuality": [18, 11, 28, 26, 11, 18, 26, 26, 11, 18, 28, 11, 30, 27, 23, 33, 23, 30, 11, 29, 30, 30, 23, 23, 18, 23, 17, 26, 11, 32, 17, 9, 23, 30, 11, 19, 22, 10, 8, 15, 15, 9, 8, 8, 30, 21, 15, 22, 8, 8, 30, 32, 18, 9, 28, 9, 32, 29, 14, 21, 11, 31, 21, 18, 21, 22, 23, 28, 28, 11, 23, 23, 9, 33, 27, 32, 33, 28, 18, 31, 33, 25, 31, 25, 31, 31, 18, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:7:7712:11139", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 43, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAGT", - "alignedQuality": [38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 37, 37, 38, 38, 38, 38, 36, 38, 38, 38, 38, 35, 38, 37, 36, 38, 38, 37, 37, 38, 38, 38, 38, 36, 38, 37, 34, 38, 36, 36, 37, 38, 38, 38, 38, 37, 37, 38, 37, 36, 37, 37, 35, 36, 35, 36, 36, 36, 36, 36, 36, 38, 33, 35, 35, 35, 36, 34, 33, 36, 34, 35, 35, 30, 34, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:45:14089:3113", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 187, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 46, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 84, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 17, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGATAATTGTATCCCATAAACACAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCC", - "alignedQuality": [28, 25, 20, 20, 28, 26, 26, 30, 26, 17, 26, 20, 27, 26, 26, 32, 30, 30, 26, 30, 34, 34, 34, 34, 34, 30, 34, 34, 20, 34, 28, 28, 20, 18, 33, 28, 18, 29, 25, 25, 28, 28, 28, 20, 25, 34, 34, 34, 34, 34, 34, 32, 26, 34, 30, 28, 20, 28, 13, 33, 32, 29, 32, 26, 19, 34, 34, 34, 30, 34, 34, 25, 20, 28, 34, 34, 30, 19, 18, 32, 26, 17, 29, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.2", - "fragmentName": "6141AAAXX100423:2:106:17757:15738", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 46, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAATCTCCATAGACCGGTGTGGGTTGGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 37, 36, 37, 38, 37, 38, 38, 38, 35, 38, 38, 37, 38, 37, 38, 38, 38, 37, 37, 38, 38, 38, 38, 37, 38, 38, 33, 37, 37, 38, 38, 36, 37, 35, 38, 37, 36, 37, 36, 37, 37, 37, 36, 37, 37, 35, 36, 36, 35, 35, 36, 36, 36, 34, 34, 33, 36, 36, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 189, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 46, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 89, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 12, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGATAATTGTATCCCATAAACACAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCC", - "alignedQuality": [32, 32, 22, 19, 17, 23, 20, 31, 23, 17, 33, 26, 26, 20, 26, 24, 25, 26, 24, 31, 21, 26, 33, 33, 18, 28, 18, 20, 5, 21, 17, 13, 26, 28, 31, 28, 16, 34, 28, 22, 34, 25, 28, 25, 29, 22, 31, 24, 22, 33, 28, 25, 34, 34, 31, 16, 29, 26, 12, 29, 10, 14, 30, 22, 29, 25, 29, 30, 29, 29, 28, 29, 20, 20, 20, 32, 29, 31, 25, 31, 33, 21, 20, 30, 30, 32, 32, 30, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:4:11279:10553", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAAATTCCCAAATAAAGACATTAACACAGCTCTACAAAGTCCAAACTCTGCATTTCTACCTCTAATGACTAATAAGTCCACAACCAACCACTCCTGTTTC", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:4:11279:10553", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 50, - "reverseStrand": false - }, - "mappingQuality": 25, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATTGGATCCCATAAACACAAAGGATTGGTCCTGGCGTTATAATTAATTAGAGGAAAGATTAGACATGCAAACCTCTACAGACCGGTGTAAAATCCCTTAA", - "alignedQuality": [31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:50:14496:18474", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 52, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGTATCCCATAAACACAAAGGTTTGGTCCTAGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 37, 30, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 32, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 35, 38, 38, 37, 37, 38, 38, 36, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 34, 38, 37, 38, 37, 38, 38, 37, 34, 38, 36, 37, 37, 35, 38, 36, 38, 37, 38, 36, 35, 37, 36, 33, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:61:6403:21082", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTGGGGGTGTGGCTATAGACACAAACGAACACACATGTTATGTACTCTCTGATCCCCACCTATTCATCAAAGAAAGTGGAATACGCATATCACCACTCCCC", - "alignedQuality": [25, 32, 24, 29, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:61:6403:21082", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 52, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 65, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 36, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGTATCCCATAAACACAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCTAACCTCCATAGACCGGTGTAAAACCCCTTAAAC", - "alignedQuality": [25, 19, 29, 25, 27, 33, 28, 28, 33, 28, 29, 29, 11, 19, 25, 26, 26, 18, 18, 18, 17, 15, 8, 31, 28, 21, 9, 16, 32, 26, 31, 33, 21, 23, 33, 33, 32, 18, 31, 18, 20, 30, 26, 23, 22, 20, 33, 22, 10, 8, 26, 27, 30, 16, 20, 24, 9, 30, 30, 21, 20, 17, 20, 17, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:69:1823:1645", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 52, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATACCTTAAAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 36, 37, 38, 34, 37, 38, 38, 38, 36, 35, 38, 37, 38, 38, 36, 37, 38, 36, 37, 37, 37, 36, 38, 35, 37, 37, 38, 37, 35, 38, 35, 37, 33, 32, 35, 37, 34, 36, 37, 30, 37, 37, 37, 36, 30, 34, 35, 36, 36, 30, 34, 31, 28, 32, 34, 34, 34, 32, 28, 34, 31, 34, 34, 32, 28, 30, 32, 29, 32, 25, 34, 27, 17, 7, 25, 22, 28, 27, 32, 27, 32, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:99:18637:3397", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 100, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 52, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATNCCCTTAAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 38, 38, 38, 36, 38, 38, 38, 36, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 36, 37, 38, 38, 38, 36, 35, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 35, 38, 36, 37, 34, 37, 38, 33, 37, 37, 37, 38, 37, 38, 37, 36, 35, 38, 35, 38, 37, 30, 37, 36, 33, 37, 32, 36, 33, 37, 25, 25, 0, 19, 27, 30, 30, 27, 28, 26, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:78:6316:4697", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGAGTCCAGAAGGACAGCGCCCACAATCCCTCGCGCCTAGCCCTTTCTTCGCCTTCCTCTCTCCTCCCTCAATTTTAAGAACATAATTATAGCTGCAAAAC", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:78:6316:4697", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 52, - "reverseStrand": false - }, - "mappingQuality": 25, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGCATCCCATAAACACAAAGGTTTGGACCTGGCCTTATAATTCATTAGAGGTAAAATTACACATGCAAACGTCCATCGACTGGTGTAAAATCCCTCAAAC", - "alignedQuality": [28, 20, 26, 13, 20, 26, 20, 26, 28, 22, 20, 24, 28, 26, 24, 32, 29, 21, 21, 34, 32, 26, 34, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:26:1496:7922", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 53, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCNACTTAAAC", - "alignedQuality": [37, 37, 37, 37, 36, 37, 32, 32, 35, 35, 37, 32, 37, 37, 37, 37, 37, 33, 37, 35, 35, 36, 37, 37, 35, 37, 37, 37, 37, 32, 37, 37, 30, 37, 37, 35, 30, 37, 36, 37, 37, 37, 36, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 35, 28, 33, 37, 37, 37, 36, 37, 37, 35, 35, 37, 37, 33, 36, 37, 37, 36, 36, 36, 33, 36, 37, 37, 36, 37, 35, 25, 36, 36, 33, 28, 33, 33, 28, 33, 33, 18, 25, 0, 10, 22, 28, 26, 28, 25, 23, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:74:10712:3372", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 53, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCACTTAAAC", - "alignedQuality": [37, 35, 38, 36, 38, 37, 37, 36, 37, 37, 38, 37, 35, 38, 37, 38, 38, 35, 35, 37, 37, 35, 37, 37, 35, 36, 33, 36, 36, 34, 37, 38, 37, 38, 35, 32, 36, 36, 36, 36, 38, 36, 36, 38, 33, 37, 35, 35, 37, 35, 36, 32, 36, 36, 36, 28, 31, 31, 34, 32, 37, 36, 37, 32, 36, 36, 35, 35, 37, 37, 31, 35, 35, 32, 30, 36, 32, 33, 36, 33, 33, 35, 30, 31, 33, 32, 35, 28, 31, 35, 22, 20, 27, 6, 27, 27, 26, 25, 22, 23, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:84:2459:12292", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 54, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCNCTTAAACA", - "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 35, 38, 37, 38, 37, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 34, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 37, 37, 37, 37, 32, 37, 36, 36, 37, 35, 36, 36, 37, 35, 36, 34, 34, 36, 35, 33, 35, 34, 35, 35, 35, 35, 35, 24, 30, 0, 8, 18, 20, 23, 23, 20, 24, 30], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:37:8169:13015", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 55, - "reverseStrand": false - }, - "mappingQuality": 25, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATCCCATAAACACAAAGGTCTGGTCCTGGCCCTATAACTAATTAGAGGTAAAATTACACATGCACACCTCTATAGACCCGTGTCAAATCTTCTACACCTC", - "alignedQuality": [32, 11, 33, 32, 33, 24, 14, 30, 20, 13, 12, 8, 6, 29, 25, 12, 21, 14, 7, 30, 10, 31, 7, 32, 15, 32, 16, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 55, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 75, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 26, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGCAAAATTACACATGCAAACCTCCATAGCCCGGAGAAAAACCCCNATACACAT", - "alignedQuality": [22, 21, 25, 9, 28, 17, 22, 17, 27, 31, 26, 17, 26, 27, 26, 22, 17, 17, 17, 18, 32, 26, 15, 9, 9, 22, 22, 17, 8, 21, 14, 29, 33, 21, 30, 21, 13, 16, 17, 24, 27, 23, 11, 33, 18, 25, 14, 26, 9, 8, 9, 21, 21, 23, 29, 31, 31, 28, 28, 25, 32, 32, 33, 32, 33, 33, 33, 29, 11, 32, 20, 7, 15, 25, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:48:2158:5284", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGTGTGGCTAAAAAAAGGGGCTTTAACCATTTTTATTTGCTTGTTACCCCCTCCCTTTATTTTTAAAAAAAATTTATAGGATTTTTCACCCGGCTCTGGGG", - "alignedQuality": [31, 31, 28, 31, 30, 31, 32, 31, 30, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:45:14369:17254", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCGTGGGGGTGTGGCTAACTAAAGAATCGTTATGTCATTTTAAATTAATTTTACACTTTCCTCTAATTTTAAAGAAAAATTTTATGGGTTGTTTACAGCAC", - "alignedQuality": [26, 26, 26, 27, 23, 23, 27, 27, 23, 32, 31, 32, 33, 11, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:45:14369:17254", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 61, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGAGTAAAATCCCTTAAACATTTACTTA", - "alignedQuality": [30, 28, 24, 26, 25, 29, 28, 28, 30, 29, 17, 22, 22, 19, 22, 31, 31, 26, 34, 33, 25, 34, 34, 25, 32, 28, 28, 28, 31, 28, 31, 31, 31, 21, 30, 20, 26, 26, 26, 26, 25, 28, 20, 33, 30, 32, 33, 35, 33, 30, 30, 29, 26, 31, 31, 29, 29, 32, 32, 33, 32, 30, 28, 34, 34, 32, 32, 25, 32, 33, 34, 28, 12, 34, 34, 8, 22, 10, 20, 30, 28, 17, 23, 26, 11, 15, 31, 25, 28, 18, 15, 15, 23, 20, 32, 34, 25, 20, 32, 25, 28], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:97:6550:8373", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 179, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 61, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACGCATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACCTCTACTTC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 35, 38, 38, 38, 37, 37, 35, 36, 38, 38, 37, 38, 36, 36, 38, 38, 37, 38, 36, 36, 36, 37, 36, 33, 36, 37, 36, 37, 35, 33, 36, 36, 34, 36, 34, 36, 35, 33, 36, 36, 35, 36, 31, 35, 35, 32, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:8:19398:15767", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 97, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 61, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACNATTTAAGA", - "alignedQuality": [37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 35, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 35, 38, 38, 38, 38, 37, 38, 38, 37, 35, 38, 38, 38, 38, 38, 36, 38, 38, 35, 38, 33, 38, 38, 36, 37, 36, 38, 36, 37, 36, 37, 36, 37, 37, 38, 36, 38, 35, 36, 36, 36, 32, 37, 34, 36, 35, 36, 35, 35, 34, 35, 34, 35, 34, 36, 35, 21, 18, 0, 15, 24, 22, 22, 25, 23, 23, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.7", - "fragmentName": "6141AAAXX100423:7:116:1040:2014", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 180, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 61, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 64, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 37, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAAACACAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAAACTCCATAGATTGNAGNNNNNNNNNNNNNNNNNNNNNNNN", - "alignedQuality": [28, 16, 14, 28, 17, 21, 29, 26, 27, 28, 24, 26, 26, 17, 20, 24, 24, 20, 24, 32, 26, 24, 24, 30, 17, 24, 24, 20, 24, 26, 28, 28, 33, 28, 13, 25, 30, 18, 28, 29, 34, 34, 26, 25, 34, 32, 32, 30, 34, 29, 25, 10, 12, 33, 30, 30, 32, 34, 34, 32, 34, 21, 28, 34, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:83:17153:4354", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 62, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACANTTTACTTA", - "alignedQuality": [38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 38, 37, 35, 37, 37, 37, 37, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 35, 38, 37, 37, 35, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 36, 38, 36, 38, 38, 38, 36, 37, 38, 36, 38, 38, 38, 36, 33, 37, 33, 37, 30, 33, 38, 35, 36, 32, 36, 35, 35, 31, 36, 35, 35, 35, 36, 31, 33, 28, 20, 0, 9, 19, 18, 18, 23, 19, 21, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:38:19313:14863", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 177, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 63, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 75, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 26, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGCGTAAAATCCTTTAACAATTCACTTAAA", - "alignedQuality": [33, 36, 30, 35, 36, 36, 35, 30, 36, 33, 35, 36, 20, 36, 35, 30, 34, 36, 36, 33, 35, 32, 30, 33, 36, 37, 37, 37, 37, 37, 37, 35, 30, 35, 32, 36, 30, 36, 30, 33, 20, 29, 34, 25, 34, 30, 32, 34, 34, 34, 33, 36, 36, 36, 36, 35, 37, 35, 36, 32, 30, 33, 30, 31, 28, 33, 33, 33, 12, 20, 26, 30, 20, 8, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:113:6641:2087", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 105, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 64, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTNACTTAAAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 36, 35, 38, 38, 38, 36, 36, 37, 36, 37, 37, 37, 36, 37, 35, 33, 36, 37, 36, 35, 34, 37, 34, 36, 35, 28, 36, 35, 36, 35, 35, 35, 34, 35, 34, 35, 35, 35, 31, 31, 0, 31, 31, 29, 30, 29, 25, 29, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:103:10989:15255", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCCGTGGGGGTGTGGCTAAAAAAAGGGGCTTTAGACATTTTTATTTTCTTGGTACACTCTCCTTCAATTTTTAATAAAATTTTTTAGGGTTTTTTTACGGG", - "alignedQuality": [32, 31, 29, 32, 30, 32, 25, 31, 31, 31, 26, 32, 29, 31, 32, 32, 29, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:103:10989:15255", - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:94:5017:20924", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 66, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAACATT", - "alignedQuality": [37, 37, 37, 37, 37, 34, 36, 36, 36, 36, 37, 37, 37, 37, 37, 36, 38, 38, 37, 38, 38, 38, 38, 38, 35, 36, 37, 37, 38, 38, 38, 38, 38, 36, 36, 35, 37, 37, 35, 37, 38, 35, 38, 38, 37, 38, 38, 38, 38, 35, 37, 38, 38, 33, 37, 37, 35, 38, 37, 38, 36, 36, 35, 38, 36, 37, 35, 32, 35, 36, 28, 32, 33, 34, 32, 33, 37, 36, 30, 32, 36, 33, 35, 33, 12, 25, 32, 29, 23, 26, 33, 31, 32, 33, 32, 32, 20, 12, 33, 32, 33], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:90:5251:10922", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 168, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 67, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGCGTAAAATCCCTTAAACATTTACTTAAAATTT", - "alignedQuality": [38, 38, 38, 38, 37, 38, 36, 37, 38, 38, 38, 38, 36, 38, 38, 38, 36, 37, 38, 38, 38, 38, 38, 37, 35, 38, 38, 38, 38, 37, 38, 38, 38, 32, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 30, 37, 38, 38, 35, 35, 37, 38, 36, 37, 36, 38, 38, 37, 38, 35, 38, 37, 38, 36, 37, 37, 37, 12, 31, 30, 25, 31, 31, 36, 36, 36, 32, 32, 36, 35, 33, 28, 33, 36, 35, 35, 32, 31, 35, 35, 36, 35, 36, 30, 35, 30, 36, 35, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:13:1683:1249", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 178, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 67, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAACTTT", - "alignedQuality": [38, 38, 38, 38, 38, 37, 37, 34, 37, 37, 35, 36, 33, 36, 34, 36, 38, 37, 38, 38, 38, 38, 36, 38, 37, 37, 38, 36, 35, 38, 37, 37, 37, 37, 32, 37, 37, 34, 37, 37, 38, 38, 38, 33, 37, 36, 38, 36, 32, 38, 38, 33, 37, 36, 38, 36, 35, 35, 38, 36, 36, 36, 36, 36, 36, 34, 36, 35, 35, 33, 35, 32, 35, 34, 35, 34, 35, 30, 34, 34, 34, 34, 34, 34, 33, 34, 34, 34, 34, 30, 34, 30, 34, 32, 34, 30, 32, 8, 32, 25, 15], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.8", - "fragmentName": "6141AAAXX100423:8:30:1383:5864", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 168, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 67, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 80, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 21, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTACAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTCGCCCCCCCCC", - "alignedQuality": [29, 28, 29, 12, 20, 32, 32, 32, 32, 32, 25, 35, 33, 33, 35, 32, 30, 25, 32, 34, 35, 35, 25, 35, 25, 12, 32, 29, 30, 32, 26, 29, 20, 24, 24, 25, 22, 21, 9, 9, 21, 21, 17, 22, 22, 25, 22, 6, 23, 22, 35, 30, 32, 35, 32, 35, 35, 20, 33, 33, 28, 30, 12, 12, 20, 34, 31, 26, 26, 28, 21, 24, 29, 31, 31, 34, 30, 12, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:10:3803:7158", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 101, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 68, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 97, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 4, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGAAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCTCTAAACATTTACTNAAAATATA", - "alignedQuality": [22, 19, 9, 7, 19, 21, 11, 26, 24, 14, 24, 29, 20, 12, 15, 11, 11, 11, 18, 22, 24, 26, 26, 25, 16, 24, 24, 20, 23, 20, 11, 22, 18, 29, 17, 16, 10, 20, 20, 22, 25, 28, 28, 28, 13, 27, 26, 20, 12, 20, 18, 18, 28, 22, 17, 18, 31, 22, 21, 22, 18, 17, 22, 17, 14, 26, 26, 20, 31, 32, 16, 12, 33, 33, 21, 18, 9, 16, 8, 7, 32, 30, 10, 32, 21, 17, 29, 28, 33, 16, 15, 18, 0, 21, 18, 26, 32, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.6", - "fragmentName": "613F0AAXX100423:6:99:6691:8008", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 68, - "reverseStrand": false - }, - "mappingQuality": 17, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAAGGCTTGGTCCTGGCCTTATACTTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTA", - "alignedQuality": [32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:15:18178:9141", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 118, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 68, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 86, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 15, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGAACGGTGTAAAATCCCTTAAACATTTAGTTACTATTTC", - "alignedQuality": [35, 35, 35, 35, 32, 35, 30, 25, 35, 32, 28, 27, 29, 28, 27, 34, 28, 35, 33, 35, 35, 32, 28, 35, 33, 35, 34, 33, 25, 35, 28, 34, 29, 26, 29, 24, 12, 11, 32, 20, 16, 33, 33, 33, 21, 31, 31, 34, 32, 30, 25, 34, 32, 20, 12, 23, 23, 33, 15, 13, 19, 13, 18, 27, 4, 25, 33, 28, 18, 29, 25, 20, 29, 29, 25, 17, 29, 22, 19, 19, 23, 18, 22, 21, 19, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:84:13828:6520", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 163, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 70, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 91, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 10, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTCACAACTACAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 37, 35, 36, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 37, 38, 38, 37, 38, 38, 36, 38, 38, 36, 38, 37, 38, 38, 38, 38, 36, 38, 30, 38, 38, 38, 38, 36, 38, 32, 37, 36, 38, 36, 38, 35, 38, 35, 34, 25, 36, 34, 28, 20, 28, 28, 33, 30, 31, 25, 20, 30, 30, 27, 9, 25, 34, 12, 28, 11, 10, 23, 16, 24, 33, 30, 20, 36, 25, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:15:10605:11846", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 71, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAANAATTTAAG", - "alignedQuality": [36, 36, 36, 34, 36, 37, 37, 37, 35, 38, 37, 36, 37, 37, 37, 38, 38, 38, 36, 38, 37, 37, 38, 38, 38, 36, 38, 37, 38, 37, 36, 36, 37, 34, 38, 36, 37, 28, 38, 37, 37, 36, 36, 37, 37, 36, 38, 38, 38, 38, 36, 36, 35, 30, 36, 35, 35, 36, 36, 36, 36, 35, 34, 36, 35, 34, 36, 34, 36, 34, 33, 36, 34, 33, 34, 34, 34, 34, 32, 34, 34, 36, 35, 35, 25, 35, 34, 35, 34, 34, 28, 29, 0, 7, 26, 24, 26, 24, 27, 25, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:94:18554:7515", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 186, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 71, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGGTTTGGTCCTGGCCCTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGG", - "alignedQuality": [38, 37, 38, 36, 38, 38, 38, 38, 35, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 37, 38, 37, 38, 38, 36, 38, 37, 35, 38, 35, 38, 38, 37, 37, 38, 36, 38, 36, 35, 38, 37, 37, 36, 38, 37, 36, 36, 38, 35, 36, 35, 36, 37, 35, 35, 36, 36, 36, 35, 37, 35, 33, 36, 33, 36, 25, 36, 34, 34, 34, 36, 35, 35, 35, 35, 35, 28, 34, 35, 35, 34, 35, 33, 35, 36, 34, 36, 33, 35, 28, 35, 29, 32, 34, 28, 34, 22], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:56:8831:15599", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 72, - "reverseStrand": false - }, - "mappingQuality": 25, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAAAGATCGGA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 38, 38, 38, 37, 35, 38, 37, 38, 37, 38, 37, 38, 38, 37, 37, 37, 37, 38, 37, 38, 37, 38, 37, 36, 37, 36, 36, 37, 37, 37, 31, 35, 36, 36, 36, 34, 33, 35, 33, 35, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.3", - "fragmentName": "613F0AAXX100423:3:82:8502:16782", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 130, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 74, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCACACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGA", - "alignedQuality": [35, 33, 35, 20, 25, 33, 34, 33, 35, 25, 35, 25, 33, 35, 35, 30, 35, 25, 35, 35, 29, 32, 30, 34, 25, 35, 28, 33, 35, 35, 34, 30, 33, 35, 35, 34, 35, 25, 34, 35, 32, 34, 32, 28, 35, 34, 12, 28, 31, 25, 29, 29, 20, 30, 28, 20, 30, 32, 26, 30, 30, 20, 27, 32, 25, 29, 10, 11, 26, 30, 33, 33, 30, 20, 33, 17, 24, 12, 17, 15, 30, 20, 33, 30, 30, 25, 22, 26, 10, 26, 28, 28, 29, 29, 25, 30, 28, 12, 30, 20, 22], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:86:18532:14392", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 75, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTNAAGGAGAG", - "alignedQuality": [38, 38, 38, 37, 37, 38, 38, 38, 36, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 35, 38, 38, 38, 37, 38, 38, 30, 38, 38, 38, 38, 38, 38, 38, 35, 38, 37, 38, 37, 38, 38, 38, 38, 38, 36, 38, 38, 37, 37, 38, 38, 37, 37, 37, 35, 37, 36, 37, 38, 38, 32, 38, 37, 38, 37, 35, 37, 38, 33, 37, 38, 35, 38, 36, 37, 38, 38, 37, 38, 38, 37, 37, 37, 30, 32, 0, 26, 32, 17, 26, 23, 16, 22, 31], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:24:8390:5967", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 78, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAANGGAGAGGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 38, 38, 35, 37, 37, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 37, 37, 38, 38, 37, 38, 32, 38, 36, 38, 36, 37, 38, 38, 38, 38, 38, 38, 38, 36, 36, 36, 37, 37, 38, 36, 36, 37, 37, 38, 36, 38, 35, 36, 35, 37, 36, 36, 30, 28, 0, 16, 25, 26, 25, 18, 30, 25, 24], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:37:11670:10031", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 117, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 79, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 9, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCCTGGCCTTATAATTAATTGGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGNAAGAGGGT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 36, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 36, 38, 36, 38, 38, 38, 37, 38, 36, 38, 36, 37, 38, 37, 37, 36, 37, 37, 37, 36, 36, 37, 37, 35, 37, 36, 33, 28, 35, 38, 37, 37, 36, 26, 33, 0, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:68:10831:5608", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 82, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 80, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 21, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGGCCTTATAATTCATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGCAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGACACACAAC", - "alignedQuality": [33, 18, 28, 20, 28, 30, 31, 28, 31, 34, 34, 32, 34, 12, 28, 17, 24, 32, 25, 31, 34, 33, 32, 34, 34, 32, 34, 32, 34, 34, 30, 34, 32, 32, 34, 26, 30, 33, 19, 32, 26, 31, 34, 28, 32, 34, 34, 33, 25, 33, 34, 22, 24, 34, 32, 29, 8, 34, 22, 16, 23, 30, 30, 24, 25, 17, 20, 34, 34, 28, 23, 23, 8, 25, 30, 33, 23, 17, 27, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:2:12805:15961", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 82, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 9, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGGCCTTATAATTAATTAGAGGTAAAATTACACATGTAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGNAGGGTATC", - "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 37, 35, 38, 38, 38, 38, 35, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 37, 38, 37, 38, 38, 36, 38, 38, 38, 37, 38, 38, 38, 38, 38, 35, 38, 35, 38, 38, 37, 37, 38, 38, 38, 38, 38, 38, 38, 36, 28, 31, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:78:13618:8833", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 84, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGCGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGCGTATCAA", - "alignedQuality": [38, 35, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 20, 36, 36, 36, 36, 36, 38, 38, 36, 38, 38, 38, 36, 38, 38, 38, 38, 38, 35, 37, 38, 37, 38, 38, 38, 38, 37, 35, 12, 37, 35, 38, 36, 36, 37, 38, 38, 36, 38, 36, 36, 35, 28, 36, 37, 36, 37, 35, 37, 36, 37, 37, 37, 36, 34, 35, 35, 36, 35, 36, 36, 37, 35, 34, 33, 36, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:84:4613:3792", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 85, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGTATATCAAG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 38, 37, 36, 38, 38, 38, 38, 38, 36, 38, 36, 38, 37, 37, 36, 37, 38, 37, 38, 37, 33, 37, 37, 37, 36, 38, 37, 35, 35, 36, 36, 36, 28, 30, 30, 20, 11, 25, 20, 21, 24, 15, 20, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:107:6156:15270", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 116, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 85, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 9, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCTTATAATTAATTAGAGGTAAAATTACACATACAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGNATATCAAG", - "alignedQuality": [38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 35, 38, 38, 38, 35, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 20, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 32, 36, 36, 36, 36, 38, 38, 35, 38, 38, 38, 38, 38, 38, 25, 36, 28, 36, 28, 36, 36, 36, 28, 36, 36, 37, 37, 33, 30, 25, 36, 35, 36, 36, 36, 38, 35, 33, 36, 38, 33, 30, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:99:1424:17385", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 86, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTTTTAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCACGCA", - "alignedQuality": [38, 38, 38, 37, 38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 36, 38, 38, 38, 35, 35, 36, 38, 36, 38, 34, 37, 34, 37, 37, 37, 37, 38, 33, 38, 37, 37, 38, 28, 37, 37, 38, 37, 38, 38, 38, 37, 35, 38, 38, 38, 33, 35, 36, 33, 37, 25, 36, 38, 36, 36, 36, 37, 28, 25, 31, 25, 23, 15, 30, 30, 30], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:82:6224:14395", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 95, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCACGCACACACACAA", - "alignedQuality": [37, 37, 38, 38, 36, 37, 37, 37, 37, 34, 35, 36, 33, 36, 36, 38, 38, 36, 38, 38, 35, 35, 37, 38, 38, 38, 36, 38, 36, 37, 36, 38, 35, 38, 38, 37, 38, 33, 32, 38, 37, 32, 37, 35, 36, 35, 37, 37, 37, 37, 35, 36, 34, 36, 35, 28, 37, 34, 37, 36, 37, 35, 31, 36, 28, 32, 32, 34, 34, 34, 36, 35, 36, 20, 35, 32, 30, 25, 34, 34, 20, 31, 11, 7, 30, 27, 28, 28, 6, 21, 33, 15, 31, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:82:10630:4431", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 168, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 96, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACNTTTAAAAT", - "alignedQuality": [38, 38, 38, 38, 38, 36, 37, 38, 38, 38, 37, 36, 25, 37, 37, 38, 37, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 36, 38, 38, 38, 38, 38, 38, 37, 38, 37, 35, 38, 37, 37, 33, 36, 37, 38, 38, 38, 38, 36, 38, 37, 37, 38, 37, 38, 37, 38, 37, 38, 35, 36, 35, 37, 38, 36, 38, 36, 36, 37, 36, 36, 38, 36, 37, 36, 37, 33, 33, 37, 33, 28, 33, 34, 31, 27, 27, 0, 8, 18, 19, 22, 22, 18, 25, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:15:4665:11101", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 96, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTAGAGGAAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATATAAGGAGAGGGTATCAAGCACATTAAAATA", - "alignedQuality": [28, 20, 18, 30, 13, 7, 8, 12, 7, 21, 33, 14, 33, 33, 33, 33, 15, 20, 14, 18, 32, 16, 32, 32, 17, 12, 14, 12, 29, 26, 33, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:51:4149:16879", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 96, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTAGGGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 28, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 38, 38, 38, 38, 35, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 35, 38, 38, 38, 37, 38, 38, 37, 38, 38, 38, 38, 36, 38, 38, 36, 35, 37, 38, 37, 38, 35, 37, 35, 37, 37, 37, 38, 37, 37, 38, 33, 36, 35, 36, 30, 36, 36, 37, 35, 38, 38, 36, 35, 35, 37, 36, 37, 32, 37], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:87:8203:7507", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 96, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACNTTTAAAAT", - "alignedQuality": [38, 38, 38, 28, 35, 38, 38, 35, 37, 38, 35, 36, 30, 37, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 36, 36, 32, 36, 36, 36, 36, 37, 38, 38, 38, 34, 35, 37, 37, 37, 33, 38, 36, 38, 38, 37, 38, 38, 38, 37, 38, 36, 35, 32, 36, 37, 36, 35, 36, 37, 36, 35, 36, 38, 36, 37, 37, 36, 33, 35, 36, 36, 36, 35, 35, 36, 28, 29, 0, 11, 25, 22, 23, 22, 16, 23, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:83:12309:12275", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 178, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 97, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACACTAAAATAG", - "alignedQuality": [37, 38, 37, 38, 38, 38, 38, 37, 38, 38, 36, 20, 36, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 36, 38, 37, 38, 38, 35, 38, 36, 36, 38, 36, 38, 38, 38, 38, 38, 37, 37, 38, 33, 38, 37, 37, 37, 33, 37, 37, 36, 37, 36, 35, 37, 38, 36, 36, 32, 36, 36, 32, 35, 36, 36, 35, 35, 35, 36, 35, 35, 35, 32, 33, 33, 25, 34, 34, 34, 34, 35, 35, 33, 33, 27, 33, 20, 28, 29, 29, 29, 31, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:99:2873:11239", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 180, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 98, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATNAAAATAGC", - "alignedQuality": [38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 30, 36, 36, 33, 36, 38, 37, 38, 38, 38, 38, 37, 35, 38, 38, 35, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 37, 35, 38, 36, 38, 37, 37, 38, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 37, 36, 37, 36, 37, 34, 38, 33, 33, 37, 37, 30, 37, 35, 37, 36, 37, 30, 35, 35, 37, 36, 36, 36, 36, 37, 35, 29, 31, 0, 29, 7, 17, 24, 21, 21, 17, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:89:9024:14985", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 99, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTNAAATAGCT", - "alignedQuality": [36, 38, 38, 38, 38, 38, 38, 37, 38, 25, 35, 36, 36, 36, 36, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 36, 38, 32, 38, 38, 38, 37, 35, 36, 37, 37, 38, 38, 30, 37, 36, 38, 36, 37, 38, 37, 38, 38, 35, 38, 38, 38, 36, 38, 37, 38, 38, 38, 38, 33, 36, 37, 38, 36, 38, 37, 38, 32, 37, 36, 37, 37, 37, 30, 35, 31, 28, 36, 36, 33, 36, 36, 38, 28, 36, 37, 24, 28, 0, 25, 15, 20, 20, 21, 26, 24, 37], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:7:14929:17117", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 99, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGAGGGAAAGTTACACATGCAAACCTCCATACACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCTAGCACATTGAAATAGCT", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:35:11834:16627", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 178, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 102, - "reverseStrand": false - }, - "mappingQuality": 17, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGCAAAATTACACATGCAAACCTCCATAGACCGGAGAAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGAGCATCACGCACATTACCATCGCTTAA", - "alignedQuality": [32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:103:2795:18322", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 103, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAANAGCTTAAG", - "alignedQuality": [38, 38, 38, 38, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 32, 35, 10, 35, 35, 36, 36, 36, 34, 36, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 38, 38, 36, 37, 38, 37, 36, 37, 37, 38, 37, 38, 33, 36, 36, 36, 36, 36, 36, 36, 36, 36, 35, 33, 36, 37, 36, 31, 33, 0, 18, 25, 23, 23, 26, 23, 27, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:18:16997:14849", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 167, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 103, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAANAGCTTAAG", - "alignedQuality": [36, 36, 36, 36, 36, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 36, 38, 36, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 37, 38, 38, 38, 36, 37, 38, 38, 36, 33, 38, 38, 38, 37, 38, 34, 38, 38, 38, 36, 37, 37, 37, 38, 38, 36, 36, 37, 38, 35, 32, 33, 0, 18, 27, 24, 23, 29, 24, 27, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:12:5463:17668", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 178, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 105, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATANACTTAAGA", - "alignedQuality": [38, 38, 38, 36, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 37, 37, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 35, 37, 36, 37, 37, 38, 37, 38, 37, 33, 35, 36, 36, 38, 37, 38, 36, 38, 33, 38, 37, 36, 36, 36, 37, 36, 30, 33, 38, 36, 36, 37, 30, 36, 37, 28, 31, 0, 15, 26, 28, 26, 27, 28, 27, 35], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.6", - "fragmentName": "613F0AAXX100423:6:81:2952:2378", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 178, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 106, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACG", - "alignedQuality": [37, 38, 30, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 36, 38, 38, 38, 38, 37, 38, 37, 38, 36, 38, 38, 38, 37, 38, 35, 37, 38, 38, 36, 36, 38, 35, 36, 38, 37, 36, 25, 34, 22, 32, 32, 34, 33, 34, 34, 36, 36, 35, 35, 36, 34, 36, 25, 36, 35, 36, 37, 35, 30, 33, 35, 35, 36, 36, 36, 35, 35], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.2", - "fragmentName": "6141AAAXX100423:2:83:5909:16925", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 168, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 110, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 91, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 10, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGGGGGTATCAAGCACATTAAAATAGCTTAAGACCCCCA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 35, 38, 35, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 37, 28, 31, 16, 34, 29, 34, 34, 32, 32, 34, 38, 37, 37, 35, 38, 37, 37, 38, 35, 34, 36, 37, 36, 36, 36, 35, 34, 38, 26, 35, 35, 35, 36, 35, 36, 36, 37, 37, 38, 35, 36, 35, 36, 36, 38, 35, 36, 33, 28, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:51:4491:5009", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 101, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 112, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CACATGCAAACCTCCATAGACCGATGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTACGAACACTAGC", - "alignedQuality": [37, 36, 37, 37, 35, 37, 35, 35, 32, 37, 35, 30, 36, 36, 33, 36, 36, 35, 35, 30, 36, 35, 34, 33, 34, 35, 37, 35, 37, 35, 37, 37, 33, 35, 35, 36, 28, 28, 36, 33, 37, 33, 30, 37, 37, 20, 29, 30, 30, 29, 19, 17, 24, 24, 29, 32, 26, 12, 20, 30, 27, 29, 29, 25, 29, 31, 14, 31, 31, 28, 32, 32, 30, 33, 31, 30, 33, 25, 31, 31, 25, 33, 31, 30, 30, 30, 25, 30, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.7", - "fragmentName": "613F0AAXX100423:7:89:1974:2032", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 179, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 113, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 95, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 6, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGGATCAAGCACATTAAAATAGCTTAAGACACCTTGCC", - "alignedQuality": [34, 34, 33, 34, 34, 28, 34, 34, 34, 30, 34, 34, 34, 34, 26, 26, 34, 34, 30, 21, 28, 28, 25, 20, 28, 34, 34, 34, 33, 34, 34, 34, 34, 25, 34, 34, 34, 25, 30, 33, 34, 34, 20, 25, 34, 23, 33, 32, 29, 30, 34, 33, 34, 34, 33, 33, 28, 33, 33, 20, 28, 21, 28, 17, 28, 10, 30, 33, 30, 18, 29, 24, 8, 16, 29, 30, 30, 30, 33, 12, 33, 32, 30, 33, 30, 19, 30, 33, 33, 33, 30, 28, 32, 28, 32, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:1:5113:6786", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 129, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 114, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 95, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 6, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACNCCTTGCCT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 36, 26, 36, 36, 36, 36, 38, 38, 37, 35, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 37, 38, 30, 37, 33, 33, 36, 36, 36, 34, 36, 38, 34, 37, 37, 38, 37, 38, 35, 38, 37, 37, 38, 36, 32, 33, 36, 37, 36, 25, 32, 32, 0, 25, 30, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:86:12263:12921", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 139, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 116, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACATTGCCTAG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 30, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 28, 38, 38, 38, 38, 38, 38, 38, 38, 34, 37, 38, 38, 36, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 36, 38, 37, 38, 37, 37, 37, 36, 35, 37, 36, 38, 37, 34, 35, 8, 32, 32, 33, 30, 33, 31, 33, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:10:3273:9196", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 116, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTATGACACCTTGCCTAG", - "alignedQuality": [28, 28, 29, 28, 28, 26, 33, 21, 29, 31, 35, 28, 35, 33, 30, 29, 26, 31, 31, 29, 28, 32, 30, 32, 25, 17, 9, 28, 25, 23, 35, 30, 33, 35, 33, 35, 32, 35, 35, 35, 30, 35, 33, 35, 34, 35, 30, 33, 35, 35, 33, 35, 25, 35, 35, 35, 25, 35, 34, 35, 35, 33, 22, 35, 35, 30, 28, 34, 34, 34, 35, 20, 33, 34, 32, 35, 30, 33, 35, 32, 25, 33, 30, 33, 30, 29, 11, 29, 31, 28, 32, 32, 20, 25, 29, 31, 25, 28, 9, 31, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:99:15593:8631", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 117, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 35, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 36, 38, 38, 38, 38, 36, 38, 37, 36, 38, 36, 38, 36, 37, 34, 37, 36, 37, 36, 36, 37, 38, 36, 37, 36, 37, 33, 32, 36, 35, 36, 36, 36, 33, 37, 25, 36, 33, 36, 35, 36, 37, 36, 35, 34, 35, 35, 35, 33, 35, 35, 36, 28, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:19:15882:10660", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 118, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTNGCCTAGCC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 37, 37, 36, 38, 37, 38, 35, 37, 38, 38, 37, 37, 37, 38, 38, 38, 38, 38, 38, 36, 38, 37, 36, 37, 37, 38, 38, 38, 36, 36, 38, 38, 38, 38, 37, 37, 38, 37, 36, 38, 37, 36, 38, 37, 33, 33, 36, 36, 37, 36, 35, 37, 37, 37, 37, 35, 37, 36, 37, 35, 37, 36, 36, 36, 36, 35, 36, 36, 36, 36, 36, 36, 36, 35, 29, 31, 0, 29, 28, 29, 25, 29, 29, 28, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:16:19656:17183", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 118, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTNGCCTAGCC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 30, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 34, 37, 38, 38, 35, 38, 38, 37, 37, 37, 37, 38, 37, 38, 37, 36, 38, 37, 38, 33, 35, 36, 37, 36, 38, 36, 36, 36, 33, 36, 31, 31, 0, 31, 20, 28, 27, 24, 27, 27, 37], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:120:2445:12049", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 186, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 119, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTNCCCTAGCC", - "alignedQuality": [38, 37, 38, 37, 38, 38, 38, 38, 37, 38, 35, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 35, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 37, 33, 38, 36, 37, 37, 37, 32, 37, 37, 37, 37, 35, 37, 37, 37, 36, 37, 37, 37, 37, 35, 36, 36, 35, 35, 36, 36, 35, 35, 36, 36, 35, 35, 33, 37, 36, 35, 23, 18, 0, 16, 24, 28, 22, 23, 23, 25, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:94:1337:1612", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 121, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGTACATTAAAATAGCTTAAGACACCTTGCCTAGCTACA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 36, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 37, 37, 38, 38, 36, 38, 36, 38, 37, 38, 35, 35, 37, 36, 35, 36, 34, 37, 33, 36, 32, 34, 35, 32, 33, 33, 33, 11, 34, 34, 36, 34, 34, 35, 33, 35, 35, 35, 35, 34, 26, 35, 34, 33, 20, 28, 30, 34, 34, 32, 27, 32, 32, 30, 23, 30, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:42:10426:16978", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 124, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCCATAGACCGGTGTAAAATCCATTAAACATTTACTTAAAATTTAAGGAGAGGGCATCAAGAAAATTAAAAAAGCTAAAGACACCTTGCCTCNCCACACCC", - "alignedQuality": [10, 21, 21, 10, 21, 16, 16, 16, 18, 16, 10, 23, 31, 22, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:2:5743:8006", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 188, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 125, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGNCCACACCC", - "alignedQuality": [38, 36, 37, 38, 32, 35, 37, 38, 38, 35, 28, 34, 36, 36, 36, 35, 32, 12, 35, 32, 37, 37, 37, 37, 37, 38, 37, 38, 38, 38, 33, 32, 36, 35, 36, 35, 37, 35, 28, 35, 36, 30, 28, 36, 36, 37, 35, 37, 28, 35, 36, 30, 35, 28, 34, 36, 30, 33, 36, 36, 36, 38, 38, 38, 36, 37, 37, 33, 37, 37, 36, 32, 37, 35, 34, 37, 37, 36, 25, 36, 37, 37, 28, 36, 36, 20, 30, 34, 30, 25, 20, 14, 0, 8, 25, 30, 30, 18, 25, 18, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.6", - "fragmentName": "613F0AAXX100423:6:11:2492:20081", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 125, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "CLIP_SOFT", - "operationLength": 3, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 31, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 67, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CGCCCATAGCCCGGTGTAACATCACTTACACATTAACTTAAAATTTAAGGAGAGGGAATCAAGCACATTAAAATAGCTTAAGACACCTCGCCTACCCACAC", - "alignedQuality": [32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:73:7585:2657", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 190, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 127, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCNCCACCCCC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 37, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 37, 32, 37, 37, 37, 38, 38, 37, 38, 38, 38, 35, 38, 35, 37, 38, 38, 36, 36, 37, 33, 37, 37, 38, 38, 38, 37, 33, 38, 38, 36, 38, 30, 35, 36, 32, 36, 34, 30, 36, 26, 33, 0, 5, 24, 30, 29, 29, 30, 17, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:84:9190:20996", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 127, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCNACACCCCC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 37, 38, 37, 37, 38, 38, 33, 34, 34, 36, 36, 37, 37, 38, 37, 36, 36, 37, 38, 38, 36, 37, 37, 38, 37, 37, 37, 36, 36, 36, 36, 35, 36, 36, 35, 36, 35, 35, 35, 35, 35, 37, 34, 35, 35, 35, 28, 28, 0, 22, 29, 27, 27, 28, 19, 22, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:80:18593:18950", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 179, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 128, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCGTAGCCACACCCCCAC", - "alignedQuality": [33, 30, 33, 36, 36, 33, 32, 28, 36, 35, 36, 36, 30, 36, 36, 35, 36, 36, 36, 33, 36, 36, 35, 36, 32, 35, 32, 32, 35, 35, 34, 32, 32, 30, 36, 25, 35, 36, 36, 35, 35, 33, 36, 36, 36, 36, 36, 36, 36, 33, 17, 32, 30, 34, 32, 32, 32, 32, 32, 32, 36, 36, 32, 33, 36, 28, 35, 35, 35, 28, 32, 20, 35, 34, 35, 32, 25, 32, 28, 34, 20, 8, 9, 11, 27, 4, 18, 26, 17, 23, 32, 29, 33, 30, 32, 35, 18, 30, 21, 29, 29], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:96:1093:15921", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 186, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 128, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 60, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 41, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "NAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAANATAGCTTAAGACNNCTTGCCTAGCNNNNCCCCNAC", - "alignedQuality": [0, 26, 23, 20, 21, 25, 25, 23, 25, 24, 33, 33, 33, 33, 33, 29, 32, 32, 32, 32, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 2, 2, 2, 2, 0, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:54:6541:15697", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 188, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 129, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGACCGGTGTAAAATCCATTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACG", - "alignedQuality": [32, 27, 10, 29, 28, 26, 31, 25, 26, 26, 35, 35, 35, 35, 35, 35, 35, 12, 35, 35, 35, 33, 35, 35, 32, 28, 30, 35, 35, 35, 36, 36, 36, 36, 35, 25, 33, 33, 34, 16, 32, 34, 32, 34, 34, 36, 36, 25, 36, 36, 36, 36, 36, 35, 35, 32, 36, 36, 36, 35, 36, 36, 36, 35, 36, 36, 36, 30, 36, 36, 36, 36, 36, 36, 34, 36, 36, 36, 36, 35, 36, 30, 36, 33, 33, 36, 34, 32, 36, 36, 36, 36, 36, 36, 36, 35, 35, 34, 32, 29, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:10:2043:20748", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 92, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 129, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 6, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 1, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACAGATCGGAA", - "alignedQuality": [37, 38, 38, 38, 38, 37, 37, 37, 37, 37, 37, 33, 37, 37, 37, 38, 38, 38, 38, 35, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 38, 36, 37, 38, 38, 38, 37, 38, 38, 37, 38, 32, 36, 36, 36, 30, 37, 37, 37, 35, 37, 38, 35, 38, 35, 33, 38, 38, 38, 36, 37, 36, 38, 37, 37, 37, 37, 36, 36, 34, 36, 35, 35, 35, 34, 36, 35, 35, 36, 20, 35, 33, 34, 34, 34, 26, 30, 33, 32, 33, 33, 31, 34, 34, 25, 32, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.1", - "fragmentName": "6141AAAXX100423:1:28:16844:17150", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 180, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 131, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTACCTAGCCACACCCNCACGGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 38, 38, 36, 38, 38, 38, 38, 37, 35, 37, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 35, 38, 37, 38, 36, 37, 34, 36, 37, 38, 38, 37, 38, 38, 35, 36, 34, 36, 30, 32, 34, 34, 34, 34, 36, 34, 36, 36, 36, 33, 33, 33, 2, 0, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:5:13257:10132", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 194, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 131, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 44, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 57, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACCGGTGTAAAATACCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTCGCATAGCCACACACCCACAGG", - "alignedQuality": [20, 28, 22, 22, 20, 15, 20, 7, 22, 30, 24, 23, 25, 9, 25, 27, 24, 24, 31, 30, 24, 8, 22, 24, 10, 18, 14, 29, 9, 23, 32, 31, 26, 32, 27, 32, 22, 23, 25, 22, 14, 30, 13, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:22:11409:13390", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 172, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 133, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 60, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 41, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CGGAGTAAAATCCCATAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAACAGCTTAAGACACCTTGACTAGGCACACCCTATACAGAC", - "alignedQuality": [15, 12, 20, 9, 9, 28, 14, 15, 9, 9, 15, 9, 15, 13, 9, 20, 9, 9, 15, 21, 9, 12, 28, 22, 31, 19, 22, 14, 27, 26, 15, 22, 31, 15, 13, 22, 32, 13, 29, 32, 32, 29, 29, 10, 23, 30, 32, 21, 15, 15, 29, 12, 32, 32, 18, 26, 16, 12, 29, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:20:2751:5355", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 204, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 133, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGGCACCTTGCCTAGCCACACCCCCACGGGAC", - "alignedQuality": [37, 37, 37, 37, 37, 38, 38, 38, 38, 38, 37, 37, 38, 36, 36, 38, 37, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 34, 37, 38, 38, 38, 37, 36, 38, 30, 36, 30, 35, 36, 36, 34, 38, 36, 38, 38, 37, 38, 38, 38, 37, 38, 38, 36, 35, 38, 37, 38, 38, 37, 35, 32, 36, 36, 37, 33, 36, 25, 38, 32, 38, 36, 37, 36, 37, 35, 37, 32, 35, 35, 37, 34, 37, 36, 35, 38, 34, 35, 36, 34, 34, 38, 28, 25, 25, 34, 36], - 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"duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 152, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 134, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 94, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCTCACGAACCA", - "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 38, 38, 38, 38, 34, 38, 38, 38, 37, 35, 38, 38, 37, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 37, 38, 38, 33, 38, 37, 38, 36, 36, 36, 35, 36, 37, 36, 37, 35, 36, 36, 35, 38, 36, 37, 36, 36, 32, 31, 7, 30, 30, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:77:6629:6612", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 137, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 97, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 4, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACAGGACTCAG", - "alignedQuality": [37, 33, 37, 37, 36, 37, 37, 37, 35, 33, 37, 37, 37, 37, 37, 37, 36, 37, 36, 36, 37, 35, 37, 37, 36, 37, 37, 25, 37, 37, 37, 33, 36, 37, 35, 37, 37, 37, 36, 37, 33, 30, 33, 36, 36, 37, 37, 37, 37, 34, 36, 37, 33, 35, 36, 36, 33, 36, 36, 36, 37, 35, 36, 33, 35, 32, 33, 20, 34, 34, 33, 31, 33, 33, 36, 36, 32, 32, 30, 28, 36, 31, 34, 33, 33, 35, 32, 32, 35, 19, 7, 13, 3, 20, 19, 30, 30, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:70:17800:2509", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 138, - "reverseStrand": false - }, - "mappingQuality": 17, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 34, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 67, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAAAATCCCTTAAACATTTTTTTAAGATTTAAGGCGAGGGAATCTAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACATTTCCACATGTTGTTGA", - "alignedQuality": [30, 7, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:14:10186:18032", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 139, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAAATCCCTTAAACATTTACTTAAAATTTAAGGAGGGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 35, 37, 38, 38, 36, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 36, 37, 35, 23, 37, 35, 37, 37, 37, 35, 30, 38, 36, 38, 35, 38, 38, 36, 38, 38, 38, 38, 38, 37, 35, 38, 33, 35, 35, 38, 38, 32, 38, 37, 38, 36, 38, 35, 38, 38, 32, 33, 37, 36, 37, 36, 37, 37, 37, 37, 37, 36, 36, 34, 34, 28, 28, 20, 32, 33, 32, 34, 34, 36, 28], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:25:10206:18665", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 189, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 139, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCA", - "alignedQuality": [38, 28, 38, 35, 38, 38, 38, 38, 38, 37, 38, 38, 38, 35, 37, 37, 38, 38, 38, 38, 37, 37, 38, 37, 38, 38, 38, 38, 37, 35, 38, 38, 38, 37, 36, 35, 36, 36, 36, 34, 38, 38, 37, 38, 36, 38, 38, 35, 36, 38, 38, 38, 33, 38, 37, 36, 36, 36, 36, 36, 11, 21, 23, 18, 29, 37, 37, 37, 37, 37, 37, 37, 36, 37, 36, 33, 35, 37, 34, 34, 35, 37, 38, 34, 37, 34, 37, 34, 33, 36, 32, 34, 33, 32, 35, 32, 35, 34, 35, 36, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:4:11968:13298", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 144, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCNCTCAGTGA", - "alignedQuality": [38, 35, 37, 38, 38, 38, 38, 37, 38, 38, 38, 36, 38, 37, 38, 38, 38, 38, 37, 35, 36, 37, 38, 38, 38, 38, 36, 38, 38, 38, 37, 32, 37, 37, 34, 37, 37, 37, 37, 37, 35, 37, 37, 38, 38, 38, 38, 38, 38, 37, 36, 38, 38, 38, 37, 38, 38, 38, 37, 38, 37, 36, 37, 38, 38, 37, 37, 38, 36, 38, 37, 37, 38, 32, 38, 38, 38, 38, 38, 35, 36, 37, 36, 36, 38, 34, 32, 36, 35, 35, 28, 29, 0, 11, 20, 23, 19, 26, 23, 22, 34], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.8", - "fragmentName": "6141AAAXX100423:8:89:15451:11285", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 145, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }, { - "operation": "DELETE", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 25, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 69, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCTTAAAATTTTATTAAAATTTAAGGGGGGGGGTATAAGGCACTTAAAAATAGTTAAAGACACTTTGCCTACCCACACCCCCACGGGCCTCCGCACTCTAA", - "alignedQuality": [31, 25, 31, 25, 4, 25, 22, 12, 8, 31, 25, 8, 19, 19, 17, 9, 30, 32, 32, 14, 33, 31, 9, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:55:11240:18646", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 146, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTTAAACATTTACTTAAAATTTAAGGAGAGGATATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAA", - "alignedQuality": [37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 27, 30, 36, 36, 36, 36, 36, 36, 36, 30, 34, 36, 36, 37, 37, 38, 38, 38, 38, 35, 38, 38, 38, 38, 35, 38, 37, 35, 37, 35, 38, 37, 37, 36, 38, 38, 38, 37, 38, 35, 38, 37, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 26, 34, 25, 33, 34, 34, 34, 33, 36, 36, 34, 34, 32, 36, 25, 36, 33, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:33:19510:10053", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 148, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCANGTGATAAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 35, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 37, 38, 38, 38, 38, 35, 38, 38, 37, 37, 38, 38, 37, 36, 38, 36, 37, 37, 37, 38, 35, 38, 36, 36, 37, 36, 34, 38, 34, 34, 34, 36, 37, 28, 37, 34, 35, 29, 27, 0, 18, 21, 22, 23, 22, 20, 18, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:23:19257:14002", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 150, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTNATAAATAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 38, 38, 38, 38, 38, 38, 38, 34, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 37, 36, 38, 34, 34, 36, 33, 34, 35, 34, 35, 32, 36, 32, 35, 35, 34, 30, 29, 0, 25, 28, 23, 25, 26, 26, 22, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:103:7190:1200", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 131, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 150, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCAGATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTNATAAATAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 34, 38, 38, 38, 38, 36, 38, 36, 36, 11, 36, 36, 35, 35, 35, 34, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 37, 38, 36, 37, 35, 37, 36, 37, 36, 38, 37, 37, 36, 37, 36, 35, 35, 35, 34, 33, 34, 33, 34, 33, 35, 35, 34, 34, 34, 35, 34, 33, 30, 25, 0, 28, 25, 25, 25, 20, 24, 20, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:106:16259:6089", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 131, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 150, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTNATAAATAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 34, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 37, 37, 38, 38, 38, 38, 38, 36, 36, 38, 38, 36, 38, 34, 35, 36, 35, 36, 35, 37, 35, 36, 36, 35, 31, 30, 0, 28, 28, 25, 26, 29, 21, 29, 35], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:12:6338:18527", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 177, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 151, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGNATAAATAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 38, 38, 38, 38, 38, 38, 38, 35, 37, 35, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 37, 38, 38, 32, 35, 38, 38, 33, 38, 36, 37, 36, 37, 35, 37, 36, 37, 36, 38, 37, 35, 36, 38, 35, 36, 37, 36, 36, 34, 34, 32, 34, 34, 35, 36, 35, 37, 35, 35, 35, 34, 35, 22, 23, 0, 18, 25, 22, 12, 25, 19, 19, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:71:11131:10038", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 152, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGANAAATATTA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 36, 37, 36, 34, 36, 34, 35, 35, 36, 37, 35, 36, 35, 36, 36, 35, 35, 33, 28, 29, 0, 27, 6, 24, 26, 30, 26, 23, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:84:17103:17682", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 152, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGANACATATTA", - "alignedQuality": [38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 37, 38, 38, 38, 36, 38, 37, 38, 37, 36, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 35, 37, 38, 35, 38, 38, 38, 36, 38, 35, 38, 38, 38, 38, 37, 38, 36, 38, 36, 38, 38, 36, 38, 38, 35, 38, 36, 36, 35, 35, 38, 35, 37, 36, 36, 36, 35, 35, 32, 30, 31, 0, 29, 6, 25, 28, 30, 26, 21, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:110:19637:9034", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 154, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 152, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 89, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 12, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACACCCACGGGACTCAGCAGTCCCCATCCCCT", - "alignedQuality": [29, 28, 21, 21, 29, 25, 34, 31, 34, 34, 35, 30, 32, 33, 35, 35, 35, 32, 28, 35, 35, 30, 35, 30, 35, 34, 20, 25, 30, 25, 35, 35, 33, 35, 33, 25, 35, 25, 25, 28, 35, 20, 35, 30, 35, 35, 12, 35, 32, 20, 26, 29, 31, 33, 30, 32, 35, 20, 35, 32, 32, 35, 35, 32, 35, 20, 35, 35, 28, 33, 25, 26, 30, 25, 30, 12, 31, 19, 29, 33, 33, 33, 12, 34, 30, 30, 29, 28, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:98:18822:1677", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 153, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTTACTAAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAAATATTAA", - "alignedQuality": [37, 37, 37, 37, 37, 37, 37, 20, 37, 37, 35, 35, 37, 37, 37, 37, 35, 37, 37, 37, 37, 37, 37, 37, 37, 35, 36, 37, 37, 36, 37, 37, 37, 37, 37, 37, 37, 37, 36, 37, 37, 34, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 36, 36, 35, 37, 37, 35, 35, 37, 37, 37, 36, 35, 34, 34, 34, 28, 20, 35, 33, 36, 33, 37, 30, 36, 36, 32, 36, 30, 36, 31, 33, 28, 31, 18, 31, 31, 30, 32, 25, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:14:16046:18217", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 180, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 153, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTTTCTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAAATATTCA", - "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 37, 37, 38, 38, 38, 30, 38, 38, 38, 37, 38, 38, 33, 37, 37, 37, 37, 37, 37, 38, 37, 38, 38, 37, 38, 38, 37, 35, 38, 37, 35, 36, 37, 36, 38, 38, 35, 38, 38, 38, 38, 36, 32, 38, 36, 38, 38, 38, 38, 38, 33, 33, 30, 37, 37, 35, 35, 37, 36, 36, 38, 37, 38, 38, 37, 37, 38, 35, 38, 34, 35, 33, 35, 36, 33, 36, 34, 35, 28, 32, 12, 30, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:112:17844:20285", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 154, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 154, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 41, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 60, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTTACTTAAAATTTAAGGAGAGGGGATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGCGACTCAGCAGTGATAAATATAAAG", - "alignedQuality": [18, 23, 27, 18, 30, 30, 26, 23, 28, 18, 17, 21, 11, 21, 21, 30, 18, 18, 21, 23, 13, 21, 11, 17, 6, 9, 21, 21, 31, 31, 11, 30, 11, 29, 21, 17, 31, 17, 15, 14, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.7", - "fragmentName": "6141AAAXX100423:7:39:5477:10548", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 112, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 154, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 61, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 40, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTTACTTAAAATTTAAGGAGAGGGCATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGAGATACATATTCAG", - "alignedQuality": [33, 28, 33, 33, 25, 26, 26, 32, 20, 32, 15, 24, 25, 24, 23, 33, 28, 27, 17, 33, 21, 23, 23, 21, 9, 32, 21, 19, 22, 32, 20, 22, 21, 31, 23, 34, 30, 28, 30, 31, 22, 30, 33, 16, 33, 22, 28, 24, 28, 28, 26, 20, 27, 30, 23, 25, 32, 25, 30, 29, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.2", - "fragmentName": "6141AAAXX100423:2:36:5277:2408", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 157, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGTCACACCCCCACGGGACTCAGCAGTGATAAATATTAAGCAA", - "alignedQuality": [38, 38, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 36, 38, 36, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 35, 37, 37, 36, 38, 38, 38, 37, 37, 38, 33, 37, 38, 34, 33, 32, 34, 32, 11, 35, 34, 34, 34, 36, 33, 33, 33, 27, 36, 36, 22, 34, 35, 34, 33, 35, 35, 34, 36, 35, 35, 36, 29, 34, 34, 33, 31, 34, 34, 32, 17, 14, 30, 23, 27, 27, 24, 25, 15], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:108:6919:14629", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 167, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 254, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 95, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 6, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GCAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGGTTAACCCAAACTAATTATCTTCGGCC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 35, 37, 35, 38, 38, 38, 37, 35, 38, 36, 38, 38, 38, 38, 37, 38, 38, 35, 38, 38, 38, 37, 37, 38, 38, 37, 36, 35, 38, 36, 34, 36, 35, 36, 35, 36, 35, 36, 35, 36, 35, 35, 37, 33, 35, 34, 36, 36, 36, 38, 35, 35, 35, 35, 35, 29, 34, 31, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:53:17789:18789", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 255, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 62, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 39, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGGTGGTAAATTTCGTGCCAGCCACCGCGACCATACGATTAACCCAAACTAATTATCTTCGGCGT", - "alignedQuality": [22, 29, 20, 15, 15, 9, 18, 15, 20, 7, 15, 29, 15, 29, 27, 31, 16, 31, 27, 17, 15, 7, 20, 11, 15, 32, 15, 23, 18, 28, 22, 8, 22, 9, 22, 12, 12, 16, 7, 31, 32, 32, 8, 25, 20, 29, 23, 23, 28, 32, 14, 17, 17, 28, 32, 23, 23, 10, 18, 20, 28, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 196, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 265, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 81, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 20, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGCCATACGATTAACCCAAACTAATTATCTTCGGCGTANAACGTGTC", - "alignedQuality": [25, 18, 29, 17, 21, 28, 28, 30, 28, 28, 34, 35, 35, 33, 35, 33, 25, 35, 30, 30, 34, 35, 33, 33, 34, 29, 29, 27, 27, 34, 35, 35, 30, 34, 35, 25, 33, 30, 20, 29, 34, 29, 32, 31, 32, 33, 28, 33, 33, 33, 34, 33, 32, 30, 33, 28, 8, 30, 30, 30, 30, 33, 32, 30, 30, 30, 30, 28, 30, 33, 31, 33, 12, 32, 31, 30, 31, 20, 20, 30, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - 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"supplementaryAlignment": false, - "alignedSequence": "GTTGGTAAATATCACTCCCACCACCGCGTAGATACGATCAAACCAAGCACAGTATCTCCGGCGAATAACATACCAAGCATAGATAGATAGATAGAAGTAAA", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:20:10777:15367", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 167, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 293, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATNATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATTAAAG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 37, 38, 38, 38, 38, 38, 35, 38, 38, 37, 37, 38, 38, 38, 38, 38, 35, 38, 38, 35, 0, 35, 35, 35, 35, 35, 35, 34, 31, 38, 37, 33, 38, 37, 38, 38, 37, 38, 35, 37, 37, 38, 37, 37, 38, 38, 38, 38, 38, 32, 33, 35, 35, 31, 31, 31, 36, 35, 29, 35, 38, 38, 34, 38, 33, 34, 35, 32, 35, 19], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:53:5706:6524", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 203, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 293, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAGCCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATTAAAA", - "alignedQuality": [38, 38, 38, 38, 37, 38, 38, 37, 38, 38, 38, 37, 38, 36, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 36, 37, 38, 34, 37, 38, 37, 37, 37, 38, 34, 36, 34, 36, 25, 31, 33, 31, 33, 33, 37, 36, 37, 37, 36, 37, 36, 36, 37, 35, 36, 36, 36, 36, 35, 35, 36, 34, 36, 35, 32, 36, 36, 35, 28, 35, 34, 35, 34, 35, 35, 35, 35, 35, 36, 35, 35, 35, 35, 34, 34, 34, 35, 35, 34, 31, 36, 34, 33, 35, 33, 35, 35, 34, 35, 25], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:54:14488:6889", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 177, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 295, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGANATTAAAAT", - "alignedQuality": [38, 36, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 37, 38, 38, 38, 38, 35, 37, 38, 37, 37, 38, 37, 38, 36, 38, 37, 38, 38, 38, 38, 38, 37, 37, 37, 35, 36, 35, 36, 37, 35, 35, 36, 36, 36, 35, 36, 33, 36, 34, 35, 35, 32, 35, 36, 36, 35, 36, 35, 35, 36, 36, 36, 36, 34, 37, 36, 34, 33, 35, 28, 29, 0, 6, 20, 26, 24, 24, 20, 24, 34], - 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"properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 309, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATTAAAATTCAACTTATATGTGA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 35, 35, 35, 37, 36, 35, 36, 36, 36, 36, 35, 34, 34, 35, 34, 36, 35, 35, 34, 34, 35, 35, 36, 34, 35, 34, 36, 35, 31, 28, 35, 35, 33, 12, 33, 34, 34, 34, 34, 35, 35, 33, 35, 34, 34, 30, 34, 34, 34, 32, 32, 34, 34, 32, 34, 32, 34, 22, 30, 34], - 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"fragmentName": "6141AAAXX100423:4:5:15800:2970", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 180, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 563, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 54, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 47, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACTAGCCATAGATTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGCGCCTGTTCTATAATCGATAACACCCGCTCTCCCTCACAGGCAGC", - "alignedQuality": [21, 17, 17, 26, 10, 26, 20, 25, 10, 10, 16, 8, 9, 14, 25, 25, 20, 27, 10, 17, 15, 15, 9, 27, 27, 32, 29, 31, 32, 29, 17, 31, 27, 32, 31, 9, 30, 15, 15, 15, 25, 25, 16, 25, 9, 31, 28, 16, 28, 30, 31, 17, 25, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:28:13247:4522", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 159, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 575, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTAAAACTCAAAGGACTTGGCGGTACTTTTTATTCCTTTTGAGGAGGCCGTTCTTTTATCGGTAAAACCCCCCCTACCCCACCCTCCCCTGCTAATTATGG", - "alignedQuality": [38, 37, 38, 38, 37, 38, 37, 38, 38, 36, 38, 38, 35, 35, 38, 35, 35, 37, 37, 37, 36, 35, 36, 31, 12, 16, 16, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:55:12324:18701", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 578, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 94, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCCCTACCTCACCATCTCTTGCTAATTCAGCCTA", - "alignedQuality": [37, 36, 37, 37, 37, 37, 37, 37, 37, 37, 37, 36, 37, 37, 36, 37, 37, 37, 37, 37, 31, 33, 33, 32, 35, 34, 31, 34, 32, 34, 33, 35, 25, 25, 30, 32, 20, 31, 29, 31, 34, 33, 30, 33, 36, 20, 25, 26, 30, 30, 33, 33, 33, 36, 36, 33, 33, 28, 33, 31, 36, 36, 36, 31, 35, 35, 37, 31, 36, 30, 29, 23, 20, 31, 33, 30, 31, 25, 30, 30, 8, 20, 24, 14, 21, 15, 18, 5, 20, 20, 27, 30, 25, 30, 2, 2, 2, 2, 2, 2, 2], - 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"supplementaryAlignment": false, - "alignedSequence": "AACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTAGATCGGA", - "alignedQuality": [37, 37, 37, 37, 33, 37, 37, 37, 37, 37, 36, 37, 37, 35, 36, 37, 37, 35, 37, 35, 35, 30, 35, 35, 36, 36, 32, 37, 37, 20, 37, 34, 37, 36, 36, 37, 37, 37, 30, 37, 35, 37, 33, 37, 37, 36, 35, 36, 36, 30, 34, 36, 36, 32, 33, 33, 33, 32, 33, 33, 35, 37, 35, 37, 30, 37, 35, 37, 32, 37, 33, 35, 35, 25, 25, 35, 35, 35, 35, 32, 20, 31, 20, 32, 31, 30, 10, 30, 20, 30, 33, 32, 25, 20, 33, 31, 8, 32, 30, 30, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:101:18850:4156", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 180, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 582, - "reverseStrand": false - }, - "mappingQuality": 50, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCAAAGGACTTGGCGGTACCTTATATCCCTCTAGAGGAGCCTGATCTATAATCGATAAACCCCGCTCTACCCCACCATCTCCTGCTCATTCANCCCTATCC", - "alignedQuality": [31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.6", - "fragmentName": "6141AAAXX100423:6:44:19703:8774", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 582, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCAAAGGACTTGGCGGTACTTTTTTTTCATCTAGAGGAGGCTGTTCTTTTATTGATAAAACCCCCCCTCCCCCCCCCCTCCCTCCTTTCTCACACCGTAAT", - "alignedQuality": [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:58:19645:7588", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 179, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 583, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 75, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 26, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAAACCCGCTCTACCTCACCATCTCTTGCTAATTCTACATCTCGTC", - "alignedQuality": [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 32, 32, 30, 32, 35, 33, 23, 29, 28, 29, 17, 31, 29, 29, 28, 34, 20, 31, 31, 32, 35, 28, 34, 20, 34, 28, 29, 26, 31, 21, 28, 18, 28, 15, 30, 30, 20, 30, 29, 30, 30, 34, 33, 9, 30, 34, 31, 20, 21, 28, 31, 30, 20, 30, 30, 30, 30, 25, 25, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.1", - "fragmentName": "6141AAAXX100423:1:30:6739:16634", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 187, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 583, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAAGGACTTGGCGGTACTTTTTTTTCCTCTTGAGGAGGCCGGTTTTTTATTGATAAAACCCCCCCCTCCCCCCCCACCCCTTCTTAATCCACCTNCTTTC", - "alignedQuality": [32, 32, 32, 32, 32, 31, 32, 32, 32, 31, 32, 31, 32, 31, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.6", - "fragmentName": "613F0AAXX100423:6:50:8271:8395", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 105, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 583, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAAGGACTTAGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATAC", - "alignedQuality": [38, 38, 38, 38, 38, 37, 37, 38, 38, 38, 38, 38, 37, 38, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 36, 37, 38, 35, 38, 38, 38, 38, 35, 38, 38, 28, 37, 38, 38, 37, 38, 38, 37, 35, 36, 38, 36, 37, 36, 38, 35, 37, 37, 36, 35, 35, 35, 35, 36, 35, 38, 36, 36, 34, 37, 36, 36, 37, 30, 32, 36, 30, 37, 35, 33, 36, 34, 35, 35, 32, 35, 32, 28, 37], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:52:11799:20332", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 124, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 583, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 34, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 67, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAAGGACTTGGCGGGACTTTTTATCCCTCTAGAGGAGGCTGGTCTATTATTGATAAAACCCGCTCTTACTTCCCATTTCCTTGTTAATTCACCCTCATAA", - "alignedQuality": [33, 23, 26, 23, 23, 26, 17, 15, 18, 28, 17, 28, 15, 21, 24, 17, 17, 17, 22, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:47:9825:4091", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 584, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAAGGACTTGGCGGTACTTTATATCCATCTCGAGGAGCCTGTTTTAGAATAGATAAACCCCGCTCTACCGCACCACGTCTTGCGAAATCATGCAGATTACG", - "alignedQuality": [26, 30, 30, 30, 31, 30, 29, 29, 29, 29, 31, 29, 24, 31, 32, 31, 10, 31, 31, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.1", - "fragmentName": "6141AAAXX100423:1:94:17716:11880", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 181, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 584, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAAGGACTTGGCGGGACTTTTTATTCATCTAGAGGGGGCCGTTTTTTTATAGATAAAACCCCCCCCACCCCACCACCTCTTTCTTTTTCTAGTTGGTTTTT", - "alignedQuality": [33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:6:19748:13634", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 584, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAAGGACTTGGCGGTACTTTTTATCCATCTAGAGGAGCCCGTTCTATTATAGATAAACCCCCCTCTCCCTCACCCTCTCTTTCTAATTTCAGTCATCCACC", - "alignedQuality": [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 30, 16, 18, 22, 28, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:111:18973:2067", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 168, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 585, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGGACTTGGCGGTACTTTATATCCATCTAGGGGAGCCTTTTCTATAATCTATAAACCCCTCTCTACCTCACCATCTCTTTCTAATTCTGTGTAGTGTTAT", - "alignedQuality": [32, 25, 32, 32, 30, 32, 34, 34, 25, 20, 31, 12, 34, 29, 31, 31, 26, 28, 31, 31, 35, 12, 28, 35, 35, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:101:7895:3365", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 178, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 586, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTNATATACCG", - "alignedQuality": [38, 38, 37, 37, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 38, 38, 38, 32, 38, 38, 38, 38, 38, 38, 36, 38, 32, 37, 38, 37, 38, 38, 38, 35, 37, 38, 38, 38, 36, 35, 38, 38, 38, 38, 38, 38, 38, 32, 38, 37, 36, 37, 37, 38, 37, 37, 37, 35, 36, 35, 35, 37, 38, 32, 35, 36, 36, 38, 36, 35, 33, 35, 36, 36, 35, 36, 34, 35, 28, 34, 33, 26, 25, 0, 16, 27, 25, 23, 25, 22, 25, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:104:4607:5279", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 587, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 94, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GAACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 32, 38, 36, 38, 37, 37, 37, 37, 34, 38, 37, 38, 37, 36, 37, 37, 32, 37, 36, 38, 38, 28, 37, 36, 37, 38, 37, 36, 36, 33, 38, 30, 37, 36, 37, 37, 35, 32, 37, 36, 35, 37, 36, 33, 36, 37, 36, 30, 36, 32, 35, 25, 33, 30, 37, 35, 35, 36, 31, 37, 33, 28, 35, 35, 35, 32, 36, 35, 32, 25, 30, 25, 30, 30, 30, 12, 28, 30, 31, 31, 28, 30, 31, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:66:13672:2605", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 588, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 24, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 77, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GACTTGGCGGTACCTTTTTTCCATTTCCCAGTGCCCGTTCTCTAATCTGGAAACCCCGCGCTGCCGCCTCACCACTTGACGCTTCATCCTATCTACTTGCC", - "alignedQuality": [30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.2", - "fragmentName": "6141AAAXX100423:2:10:13217:15205", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 590, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 16, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 18, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTTGGCGGTAATTTTTAATCCACTTAGGGGGGCCTGTTTTTTAATCATAAAACCCCCCCCTACCCCCCCACTCCTTCTTAATTCACCCATNTACTCTGACA", - "alignedQuality": [32, 31, 32, 31, 32, 32, 32, 32, 14, 19, 6, 6, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.6", - "fragmentName": "6141AAAXX100423:6:83:4662:8293", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 192, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 590, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTTGGCGGTACTTTTTATCCATCTAGAGGGGCCTGTTCTTTTATCCATAAACCCCCCCCCTCCCCCCCCTCCTCTTCCTATTTAACCCCTATCACACCACC", - "alignedQuality": [32, 32, 32, 32, 31, 32, 31, 31, 22, 28, 13, 18, 29, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:23:16337:3840", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 132, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 592, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 70, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 31, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATAGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATTATCACTATTT", - "alignedQuality": [35, 33, 28, 35, 35, 35, 33, 35, 28, 35, 35, 35, 28, 35, 32, 35, 35, 25, 35, 32, 25, 34, 30, 34, 32, 29, 12, 10, 25, 20, 32, 34, 32, 30, 34, 35, 35, 28, 35, 28, 32, 34, 11, 25, 28, 34, 34, 20, 34, 34, 35, 28, 34, 11, 26, 7, 33, 25, 26, 29, 12, 32, 34, 34, 34, 34, 25, 34, 32, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:10:14689:13457", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 98, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 592, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATAGA", - "alignedQuality": [37, 38, 38, 38, 38, 38, 37, 35, 38, 36, 38, 36, 38, 38, 37, 38, 38, 35, 33, 37, 37, 38, 38, 38, 38, 37, 35, 30, 36, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 28, 38, 38, 37, 35, 38, 36, 35, 37, 30, 33, 38, 37, 36, 37, 38, 34, 30, 37, 37, 36, 36, 36, 35, 36, 36, 33, 36, 36, 38, 37, 35, 33, 20, 37, 35, 30, 33, 34, 33, 33, 37, 35, 38, 35, 33, 36, 36, 25, 35, 32, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:119:3666:12939", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 98, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 596, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGA", - "alignedQuality": [29, 32, 26, 30, 26, 32, 32, 26, 34, 32, 34, 34, 30, 26, 34, 29, 32, 34, 32, 29, 31, 29, 29, 16, 21, 26, 25, 26, 32, 24, 32, 34, 34, 30, 32, 28, 34, 30, 32, 30, 28, 28, 28, 32, 26, 30, 32, 32, 23, 26, 18, 14, 28, 26, 33, 32, 19, 23, 15, 30, 34, 34, 34, 30, 34, 28, 34, 26, 34, 34, 26, 30, 34, 28, 32, 34, 34, 33, 30, 33, 33, 33, 28, 34, 28, 33, 33, 33, 23, 30, 34, 33, 33, 33, 25, 33, 33, 33, 25, 32, 19], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:52:12141:9678", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 177, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 597, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCANACTTCAGC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 36, 38, 37, 38, 36, 36, 36, 37, 36, 37, 36, 36, 36, 37, 36, 36, 36, 36, 35, 36, 36, 35, 36, 35, 35, 36, 36, 36, 36, 36, 36, 33, 34, 35, 29, 24, 0, 6, 27, 21, 26, 23, 19, 23, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:56:16917:3099", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 597, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 54, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 47, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTACTTTATATCCCTCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCTACCTTCCGC", - "alignedQuality": [34, 33, 34, 34, 34, 34, 30, 34, 32, 21, 26, 23, 32, 10, 26, 18, 27, 26, 24, 32, 34, 32, 18, 12, 23, 27, 29, 31, 25, 34, 34, 33, 28, 34, 32, 34, 34, 34, 30, 30, 30, 23, 32, 8, 30, 28, 28, 28, 28, 34, 28, 28, 28, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:73:4540:14300", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 181, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 600, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCACAC", - "alignedQuality": [38, 38, 38, 35, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 35, 37, 35, 35, 34, 37, 35, 37, 35, 35, 36, 33, 30, 35, 35, 36, 34, 32, 32, 35, 34, 31, 34, 32, 34, 28, 20, 32, 35, 34, 32, 35, 34, 35, 35, 35, 35, 20, 32, 32, 34, 32, 32, 31, 30, 30, 32, 25, 32, 32, 32, 8, 32, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:37:15714:21079", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 94, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 603, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAGATCGG", - "alignedQuality": [38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 36, 36, 36, 36, 36, 37, 36, 36, 36, 36, 35, 35, 37, 36, 36, 36, 36, 34, 31, 35, 34, 36, 35, 36, 35, 33, 35, 36, 36, 30, 35, 35, 33, 34, 34, 30, 34, 34, 28, 34, 32, 34, 34, 34, 28, 32, 34, 32, 17, 32, 32, 32, 27, 21, 25, 23, 25, 27, 27, 27, 29, 32, 29, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:27:4942:4850", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 102, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 603, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATATCCATCTAGAGGAGCCTGGTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCACACCCA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 36, 12, 36, 35, 34, 34, 35, 35, 33, 38, 37, 38, 36, 37, 38, 38, 38, 36, 37, 37, 35, 37, 38, 37, 38, 37, 35, 37, 35, 31, 35, 33, 36, 25, 33, 32, 36, 35, 36, 35, 37, 33, 25, 36, 37, 33, 38, 31, 33, 35, 33, 33, 36, 35, 33, 35, 31, 36, 35, 36, 33, 33, 35, 36, 32, 28, 33, 32, 25, 32, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:45:3029:17994", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 190, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 604, - "reverseStrand": false - }, - "mappingQuality": 17, - "cigar": [{ - "operation": "CLIP_SOFT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 34, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CATATCCATCCAGCGGCGCCTGTTCTATAATCGATAAACACAGCTCTACCTCGCCATCTCCTACCAATTCAGCACATATACCGACACCCTCAGCCAACCCG", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.7", - "fragmentName": "613F0AAXX100423:7:86:16423:5140", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 190, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 606, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATCCATCTAGAGGAGCCTGTTCTATAATTGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAA", - "alignedQuality": [38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 37, 38, 37, 38, 36, 38, 37, 38, 38, 36, 36, 36, 36, 37, 36, 35, 35, 37, 36, 36, 36, 36, 35, 35, 36, 31, 36, 36, 35, 35, 35, 33, 35, 36, 35, 35, 34, 36, 36, 35, 33, 34, 35, 36, 36, 35, 34, 36, 35, 31, 35, 33, 34, 36, 34, 34, 33, 35], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:30:9878:9859", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 152, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 606, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCANAACCCTAA", - "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 38, 37, 37, 36, 37, 34, 38, 36, 36, 37, 37, 37, 36, 33, 36, 36, 36, 30, 36, 33, 33, 36, 37, 36, 36, 35, 36, 35, 35, 35, 33, 35, 35, 35, 35, 35, 35, 35, 36, 34, 33, 34, 33, 36, 35, 35, 34, 34, 36, 35, 33, 34, 29, 30, 0, 19, 25, 22, 25, 22, 21, 23, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.7", - "fragmentName": "6141AAAXX100423:7:11:7170:17628", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 89, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 607, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 89, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 12, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCCTCTTCAGAGATNGTAACAA", - "alignedQuality": [34, 34, 25, 34, 28, 28, 30, 34, 20, 34, 31, 26, 12, 29, 30, 28, 33, 28, 26, 28, 26, 31, 31, 30, 31, 35, 35, 35, 35, 35, 25, 25, 32, 32, 30, 29, 32, 25, 32, 32, 35, 35, 12, 35, 30, 28, 32, 31, 28, 12, 29, 33, 25, 29, 28, 14, 16, 26, 10, 33, 11, 25, 22, 31, 25, 11, 18, 30, 28, 27, 29, 12, 18, 25, 30, 10, 25, 25, 28, 26, 29, 20, 31, 34, 31, 28, 29, 9, 34, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:91:1251:17061", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 610, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 55, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 46, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCCCTTGCTACTTCAGCCTATATACTGCCTTCATCAGCAAAACCTAAACAGG", - "alignedQuality": [26, 12, 26, 18, 24, 20, 12, 20, 12, 32, 25, 34, 32, 30, 30, 34, 28, 34, 30, 20, 33, 12, 25, 33, 28, 20, 24, 30, 30, 26, 32, 35, 28, 20, 35, 34, 26, 34, 32, 34, 32, 20, 30, 34, 35, 24, 11, 28, 19, 28, 21, 18, 28, 17, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:74:14252:18715", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 180, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 909, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAGGT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 35, 38, 38, 38, 37, 38, 36, 38, 38, 38, 38, 37, 34, 38, 38, 38, 38, 36, 38, 37, 38, 38, 36, 38, 36, 37, 30, 35, 36, 37, 36, 36, 35, 38, 33, 35, 36, 36, 37, 38, 28, 36, 37, 36, 35, 36, 35, 35, 35, 36, 35, 22], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:16:4603:15120", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 192, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 911, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATATTGGAAAGTGT", - "alignedQuality": [36, 36, 36, 36, 36, 36, 35, 36, 36, 36, 36, 36, 35, 25, 35, 36, 36, 32, 35, 36, 36, 36, 33, 36, 36, 35, 36, 36, 25, 35, 34, 36, 36, 20, 28, 36, 36, 35, 36, 35, 36, 36, 36, 36, 36, 36, 33, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 30, 36, 35, 20, 36, 34, 36, 36, 30, 35, 36, 36, 36, 30, 36, 36, 36, 32, 36, 36, 36, 32, 36, 12, 34, 34, 31, 34, 30, 7, 34, 34, 28, 28, 30, 30, 20, 29, 30, 30], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:11:5665:20857", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 180, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 912, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 97, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 4, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGAAAAGTGCG", - "alignedQuality": [37, 38, 37, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 36, 38, 38, 35, 37, 36, 37, 38, 38, 35, 38, 38, 38, 38, 37, 38, 38, 38, 35, 37, 38, 38, 38, 38, 38, 38, 38, 35, 35, 38, 37, 38, 38, 38, 36, 38, 38, 38, 38, 36, 33, 37, 37, 36, 36, 35, 37, 35, 30, 33, 32, 34, 30, 33, 32, 31, 33, 30, 25, 28, 31, 33, 31, 25, 32, 20, 31, 25, 20, 28, 29, 31, 20, 30, 20, 25, 30, 32, 33, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:75:17809:8561", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 178, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 919, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGAGTGCTTGGAA", - "alignedQuality": [29, 28, 28, 28, 30, 26, 20, 26, 26, 30, 35, 35, 25, 32, 35, 32, 34, 32, 25, 29, 28, 29, 28, 29, 20, 26, 26, 20, 32, 30, 11, 25, 24, 24, 26, 29, 28, 20, 28, 28, 28, 28, 30, 17, 25, 13, 19, 14, 25, 20, 19, 30, 28, 24, 33, 35, 35, 35, 35, 28, 25, 32, 32, 29, 30, 19, 19, 26, 30, 25, 34, 30, 34, 34, 12, 25, 32, 30, 28, 29, 35, 30, 35, 35, 35, 34, 35, 28, 34, 35, 4, 26, 8, 23, 29, 9, 22, 26, 7, 32, 30], - 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"duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 85, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 919, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 87, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 14, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCTCCAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGAGATAGGCTAAGTCAA", - "alignedQuality": [20, 26, 12, 20, 12, 26, 20, 12, 20, 20, 21, 31, 31, 29, 33, 21, 33, 32, 32, 30, 12, 26, 32, 32, 32, 34, 28, 28, 28, 34, 21, 32, 32, 34, 32, 34, 34, 21, 34, 34, 34, 21, 28, 34, 34, 28, 32, 30, 32, 34, 26, 19, 32, 26, 32, 28, 28, 34, 18, 32, 34, 34, 34, 12, 30, 29, 32, 17, 12, 17, 32, 32, 30, 27, 16, 26, 30, 32, 22, 12, 22, 31, 30, 22, 22, 27, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:51:12399:9321", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 182, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 920, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATAATGGAAAGTGTGCTTGGAAT", - "alignedQuality": [38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 35, 38, 35, 38, 38, 38, 38, 38, 38, 35, 38, 38, 36, 38, 38, 36, 37, 38, 38, 38, 37, 38, 36, 35, 38, 37, 38, 36, 37, 38, 38, 36, 38, 37, 36, 36, 35, 35, 37, 32, 36, 33, 36, 36, 36, 34, 37, 35, 36, 35, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:84:9913:20125", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 921, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAGCAAGGTAAGCATACTGGAAAGTGTGCTTGGAATA", - "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 35, 38, 38, 38, 38, 37, 38, 38, 37, 38, 38, 37, 38, 37, 38, 36, 36, 37, 37, 38, 38, 36, 36, 35, 37, 38, 30, 32, 32, 32, 33, 31, 34, 25, 30, 34, 32, 30, 30, 30, 30, 30, 34, 34, 36, 30, 34, 33, 30, 30, 27, 32, 12, 25, 12, 27, 28, 32, 19, 32, 25, 30, 31], - 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"alignedQuality": [38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 34, 32, 36, 37, 37, 37, 37, 35, 38, 38, 38, 38, 36, 37, 38, 36, 37, 37, 38, 37, 37, 38, 36, 34, 37, 37, 38, 37, 38, 38, 36, 38, 38, 37, 37, 36, 35, 35, 37, 34, 38, 35, 37, 36, 36, 38, 37, 36, 33, 37, 12, 32, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.6", - "fragmentName": "613F0AAXX100423:6:119:19785:7641", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 927, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 94, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGCAAGCATACTGGTAAGTGTGCTTGGAATAATCATA", - "alignedQuality": [38, 38, 37, 37, 38, 38, 36, 38, 38, 38, 38, 35, 37, 35, 37, 37, 38, 38, 35, 38, 37, 38, 38, 38, 36, 35, 38, 28, 38, 38, 38, 38, 38, 37, 38, 37, 35, 33, 36, 35, 32, 37, 37, 36, 37, 37, 38, 36, 38, 38, 30, 38, 38, 30, 37, 36, 36, 37, 32, 25, 34, 33, 34, 33, 36, 20, 12, 32, 29, 30, 35, 30, 32, 28, 28, 34, 35, 31, 20, 25, 29, 28, 26, 32, 26, 34, 34, 12, 25, 31, 26, 32, 25, 30, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:93:585:9862", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 191, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 929, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "NATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGCGTGCTTGGAATNATTCATAG", - "alignedQuality": [0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:49:3183:10667", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 931, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAANACATAGTG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 37, 37, 35, 38, 38, 36, 38, 38, 35, 38, 37, 38, 38, 35, 37, 36, 34, 33, 36, 38, 38, 36, 38, 33, 37, 37, 36, 20, 36, 33, 36, 36, 34, 36, 34, 36, 38, 35, 35, 35, 35, 36, 33, 37, 21, 22, 0, 11, 20, 26, 18, 15, 29, 20, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:86:1169:21259", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 933, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAAATTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGAGCAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 35, 38, 36, 37, 37, 36, 36, 34, 36, 37, 34, 36, 36, 35, 35, 35, 35, 36, 33, 32, 35, 35, 35, 35, 35, 35, 34, 35, 36, 34, 33, 31, 34, 34, 32, 33, 32, 35, 23, 31, 32, 32, 34, 32, 30, 32, 30, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:8:11183:20074", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 87, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 937, - "reverseStrand": false - }, - "mappingQuality": 23, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 87, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 5, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATAGATCGGCCGTAGA", - "alignedQuality": [38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 36, 38, 38, 36, 38, 36, 37, 37, 37, 38, 35, 37, 38, 35, 38, 36, 36, 32, 35, 38, 36, 34, 33, 35, 36, 34, 35, 37, 35, 35, 37, 36, 36, 32, 34, 28, 34, 32, 34, 32, 35, 32, 35, 35, 35, 34, 31, 31, 33, 34, 34, 35, 31, 34, 33, 27, 26, 30, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:82:4376:17689", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 939, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATGGGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 37, 38, 38, 37, 38, 37, 35, 37, 38, 38, 35, 38, 35, 36, 38, 38, 36, 37, 35, 37, 35, 34, 38, 37, 38, 38, 37, 37, 36, 36, 38, 38, 36, 36, 35, 35, 35, 34, 33, 35, 37, 37, 37, 36, 36, 35, 33, 33, 36, 30, 34, 34, 38, 33, 36, 35, 36, 35, 36, 35, 33, 36, 37, 35, 36, 33, 34, 35], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:59:5314:6829", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 168, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 939, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 9, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGTTAAGCATACTGGAAAGTGCGCTTGGAATAATCATAGTGTGACGTCTA", - "alignedQuality": [17, 11, 22, 17, 13, 17, 17, 17, 21, 17, 22, 17, 21, 18, 21, 14, 30, 18, 11, 17, 30, 24, 18, 11, 11, 27, 27, 27, 31, 27, 30, 11, 26, 21, 23, 27, 33, 30, 30, 23, 16, 30, 29, 25, 27, 27, 33, 31, 23, 31, 33, 24, 24, 17, 33, 26, 10, 20, 10, 16, 30, 27, 20, 33, 16, 14, 22, 28, 14, 16, 33, 9, 8, 26, 29, 22, 9, 33, 28, 28, 31, 33, 16, 14, 24, 15, 15, 30, 30, 23, 27, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:54:8068:2460", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 179, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 940, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGGCTTAAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 37, 35, 38, 38, 37, 38, 37, 38, 38, 37, 37, 38, 35, 37, 35, 37, 37, 35, 37, 38, 38, 37, 37, 36, 37, 36, 32, 37, 38, 37, 37, 36, 35, 32, 29, 7, 11, 31, 22, 25, 25, 30, 26, 32], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.3", - "fragmentName": "613F0AAXX100423:3:61:10412:18370", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 93, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 944, - "reverseStrand": false - }, - "mappingQuality": 23, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 94, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 6, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAGATCGGA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 36, 38, 38, 38, 36, 38, 38, 35, 38, 38, 38, 37, 37, 38, 38, 36, 38, 38, 37, 35, 33, 32, 37, 33, 37, 35, 35, 36, 36, 37, 38, 36, 36, 35, 38, 37, 36, 37, 36, 33, 38, 37, 38, 36, 38, 36, 36, 38, 38, 36, 35, 36, 33, 37, 34, 35, 37, 35, 37], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:81:3719:6595", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 182, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 945, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTNAATATTAA", - "alignedQuality": [38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 38, 38, 36, 38, 37, 38, 38, 38, 38, 36, 38, 38, 36, 38, 37, 38, 38, 38, 38, 37, 35, 38, 36, 37, 38, 33, 36, 38, 36, 37, 38, 36, 37, 36, 37, 36, 31, 35, 30, 36, 36, 35, 35, 36, 33, 33, 35, 36, 36, 35, 36, 36, 36, 32, 35, 35, 33, 34, 32, 34, 34, 34, 27, 23, 0, 11, 23, 23, 18, 22, 18, 28, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:61:5403:18920", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 155, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 947, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAATTTCTAGATATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAACATTAAAGC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 36, 38, 38, 35, 38, 37, 38, 38, 38, 36, 38, 35, 38, 36, 38, 38, 36, 37, 33, 38, 38, 38, 37, 35, 37, 33, 37, 35, 37, 35, 38, 38, 36, 35, 38, 36, 36, 32, 36, 32, 35, 37, 35, 38, 38, 36, 36, 34, 37, 34, 33, 37, 37, 36, 36, 31, 28, 17, 25, 26, 34, 30, 32, 32, 30, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:10:18148:21082", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 947, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAANATTAAAGC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 35, 38, 36, 35, 38, 37, 36, 38, 37, 38, 36, 34, 35, 36, 36, 38, 37, 36, 36, 36, 36, 37, 35, 36, 36, 36, 35, 33, 35, 33, 35, 35, 35, 25, 35, 30, 35, 34, 33, 36, 34, 34, 30, 34, 34, 35, 34, 32, 34, 32, 34, 33, 34, 35, 32, 26, 22, 0, 18, 18, 29, 28, 28, 29, 27, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:1:14894:15141", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 160, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 948, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATTTCTAGACATCCGTTTATGTGAGGAGATAAGTCGTAACACGGTAAGCATATTGTAATGAGTGCTTGGAATATTCATATTGTAGCTTATTATAACACAC", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:20:19694:13367", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTATATTCGTCTACGTATACGACTAAGAATACCAAAGAGCGTTCACTGGTCAATAAATCTCACAGCAGTTTACTCAATAATCTATACAGCCACTAAAACC", - "alignedQuality": [34, 12, 33, 34, 28, 21, 34, 21, 21, 30, 21, 12, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:20:19694:13367", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 948, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 86, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 15, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTACGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATCTTAAAGAA", - "alignedQuality": [32, 38, 38, 38, 37, 38, 38, 37, 38, 20, 37, 36, 32, 37, 36, 37, 37, 37, 20, 37, 36, 36, 34, 35, 36, 33, 11, 28, 36, 32, 35, 28, 25, 35, 33, 20, 35, 25, 34, 33, 25, 34, 28, 35, 32, 34, 34, 12, 36, 33, 28, 28, 34, 32, 35, 30, 34, 25, 30, 30, 34, 25, 25, 25, 34, 34, 12, 25, 36, 25, 20, 25, 33, 32, 25, 32, 11, 32, 20, 32, 30, 28, 29, 31, 31, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:43:18825:10833", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 154, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 948, - "reverseStrand": false - }, - "mappingQuality": 17, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATTTCTAGACAGCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCGTGGAATAATCATAGGGGGGCTTCATNTCTATAGC", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:58:5039:4571", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 948, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATTTCTAGAAATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCA", - "alignedQuality": [19, 28, 22, 29, 28, 24, 27, 25, 25, 17, 8, 25, 16, 23, 23, 22, 22, 22, 20, 22, 20, 16, 14, 23, 18, 22, 20, 15, 20, 29, 22, 23, 18, 23, 8, 25, 25, 13, 22, 20, 18, 22, 11, 23, 32, 28, 24, 32, 23, 9, 30, 24, 32, 22, 32, 32, 31, 22, 32, 17, 30, 14, 30, 18, 17, 28, 15, 32, 32, 19, 31, 21, 32, 29, 9, 29, 32, 25, 31, 31, 28, 16, 28, 22, 31, 25, 30, 22, 19, 25, 31, 25, 17, 31, 10, 22, 31, 26, 31, 29, 29], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:89:2564:17572", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 187, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 950, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATNAAAGCATC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 36, 38, 38, 38, 36, 38, 38, 37, 35, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 36, 36, 36, 37, 36, 35, 36, 35, 37, 38, 33, 34, 37, 37, 36, 36, 37, 36, 35, 36, 36, 37, 35, 36, 36, 34, 35, 34, 35, 36, 35, 36, 35, 36, 31, 36, 27, 31, 0, 29, 25, 21, 22, 26, 23, 25, 34], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.2", - "fragmentName": "6141AAAXX100423:2:54:4325:15835", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 190, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 968, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 89, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 12, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGAGAGGAGATAAGTCGTAACNAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGTAGT", - "alignedQuality": [38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 36, 38, 37, 36, 38, 38, 29, 0, 30, 31, 30, 29, 32, 32, 32, 32, 38, 37, 38, 37, 38, 38, 37, 37, 37, 38, 37, 33, 33, 35, 36, 37, 33, 36, 37, 36, 35, 37, 36, 36, 35, 36, 36, 35, 36, 37, 35, 33, 36, 33, 33, 35, 35, 35, 35, 35, 35, 36, 35, 36, 36, 35, 35, 36, 33, 36, 30, 32, 32, 33, 33, 32, 35, 35, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:53:10600:7498", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 167, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 971, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTCTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 36, 35, 11, 34, 35, 36, 34, 34, 38, 37, 37, 37, 38, 38, 37, 38, 37, 37, 37, 38, 38, 34, 38, 35, 38, 38, 38, 34, 38, 38, 37, 37, 37, 38, 37, 38, 37, 38, 37, 37, 37, 37, 36, 36, 36, 36, 36, 36, 36, 37, 37, 30, 37, 35, 35, 36, 33, 36, 35, 36, 35, 35, 34, 31], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:119:10079:8130", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 181, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 976, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGNCTTTCATG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 36, 38, 38, 38, 38, 32, 38, 38, 38, 32, 38, 37, 35, 38, 38, 36, 34, 36, 35, 37, 37, 37, 35, 38, 37, 38, 34, 38, 38, 33, 33, 38, 36, 36, 37, 32, 35, 36, 30, 34, 33, 35, 36, 28, 36, 32, 34, 34, 37, 36, 37, 37, 35, 36, 20, 36, 36, 36, 35, 36, 35, 37, 35, 36, 37, 38, 37, 37, 36, 35, 35, 35, 32, 20, 25, 0, 16, 25, 25, 25, 23, 25, 24, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.1", - "fragmentName": "6141AAAXX100423:1:114:10098:16380", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 979, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 87, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 14, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGACGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGAAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTCAATACAAA", - "alignedQuality": [22, 31, 18, 7, 17, 22, 20, 22, 18, 25, 26, 21, 27, 26, 16, 34, 30, 34, 32, 34, 21, 34, 34, 34, 32, 13, 29, 34, 31, 21, 16, 28, 16, 28, 28, 31, 29, 31, 26, 29, 34, 34, 32, 34, 34, 34, 30, 34, 34, 34, 20, 25, 16, 28, 28, 32, 32, 33, 32, 32, 32, 26, 34, 34, 33, 28, 34, 34, 20, 30, 32, 34, 24, 30, 24, 26, 18, 33, 31, 34, 34, 34, 19, 34, 34, 34, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"alignedQuality": [35, 35, 35, 35, 35, 34, 35, 35, 35, 35, 35, 35, 35, 33, 35, 18, 26, 25, 22, 25, 12, 21, 20, 29, 12, 33, 33, 22, 14, 14, 8, 18, 11, 12, 30, 25, 33, 22, 33, 24, 18, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:97:7948:11203", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 110, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 982, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCANAAGATTTCANGACCAATG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 36, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 38, 38, 38, 38, 35, 38, 35, 37, 38, 38, 38, 37, 38, 37, 38, 36, 38, 37, 38, 35, 38, 37, 37, 38, 36, 38, 36, 37, 30, 38, 38, 35, 37, 36, 36, 37, 36, 33, 34, 0, 33, 31, 32, 31, 29, 31, 29, 34, 29, 0, 32, 28, 27, 28, 28, 28, 26, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:30:19776:18361", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 982, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCNTCTGGCCTACACCCAGAAGATTTCATGACCAATG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 35, 38, 38, 36, 38, 38, 38, 38, 38, 36, 38, 38, 37, 35, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 34, 0, 34, 34, 34, 34, 31, 34, 34, 34, 37, 38, 36, 38, 37, 38, 38, 38, 32, 37, 38, 35, 35, 38, 35, 38, 38, 36, 25, 34, 38, 37, 38, 36, 38, 25], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:2:19846:6960", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 187, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 984, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "NTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGNCCCAATGA", - "alignedQuality": [0, 22, 22, 19, 20, 27, 23, 22, 26, 26, 33, 33, 33, 33, 33, 36, 36, 36, 36, 36, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 27, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 29, 33, 33, 33, 33, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:83:6850:20038", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 187, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 985, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAACAAGGTAAGCATACTGGAAAGAGGGCTTGGAATAATCATAGTGTAGCTTAATATTACAGCATCAGGCCTCCACCCAGAAGAATTCATGTCCAACAAAA", - "alignedQuality": [32, 32, 30, 12, 32, 10, 14, 7, 30, 15, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:53:16055:18760", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 992, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGANACACTCTG", - "alignedQuality": [38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 38, 38, 38, 35, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 35, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 37, 38, 38, 38, 38, 37, 35, 38, 37, 38, 38, 38, 37, 37, 38, 36, 37, 36, 38, 38, 37, 37, 37, 37, 37, 38, 37, 33, 37, 29, 33, 0, 18, 30, 20, 24, 21, 22, 20, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:17:6221:5422", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 993, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAANACTCTGAA", - "alignedQuality": [38, 38, 35, 38, 37, 38, 37, 37, 38, 38, 37, 35, 38, 38, 38, 37, 36, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 35, 38, 38, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 38, 38, 34, 37, 38, 38, 38, 38, 37, 37, 36, 38, 38, 36, 37, 36, 37, 38, 37, 37, 37, 37, 38, 38, 38, 37, 36, 35, 30, 32, 0, 30, 32, 28, 28, 28, 28, 27, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:76:10016:7303", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 993, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 51, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 50, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAAGCATACTGGAAAGACTGCTTGGAATAATCATAGTGTAGCTTAATATTACAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTCTCAC", - "alignedQuality": [20, 15, 9, 25, 15, 15, 25, 28, 15, 23, 9, 15, 9, 15, 29, 28, 10, 9, 30, 9, 29, 32, 20, 30, 16, 32, 31, 15, 21, 14, 17, 22, 15, 22, 15, 24, 32, 14, 32, 17, 22, 13, 15, 23, 22, 18, 31, 18, 32, 22, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:76:10016:7303", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCTTGGAACGACTTATGGCTGGATTTCTATCATAGCATACTTATATTTGTGTAGGGCTAGGGCTAGGCTTCGTTCTGAGCGTTCATTGGTCATCAAAACTC", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.3", - "fragmentName": "613F0AAXX100423:3:82:3711:3100", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 994, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGCATACTGGAAAGCGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGACGATTTCATGACCAATGAACACTCTGAAC", - "alignedQuality": [23, 11, 18, 18, 27, 21, 27, 29, 24, 27, 21, 11, 21, 21, 17, 9, 22, 21, 17, 21, 28, 18, 23, 26, 18, 29, 30, 23, 18, 29, 33, 31, 31, 32, 31, 28, 30, 25, 30, 30, 32, 31, 31, 33, 19, 31, 27, 31, 33, 31, 29, 33, 33, 33, 28, 32, 32, 32, 29, 32, 31, 29, 31, 31, 31, 32, 32, 25, 32, 32, 23, 30, 9, 33, 26, 31, 29, 31, 31, 25, 31, 29, 32, 31, 27, 33, 27, 33, 33, 11, 31, 31, 31, 25, 31, 7, 7, 33, 22, 22, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.6", - "fragmentName": "6141AAAXX100423:6:94:1347:17963", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 127, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 994, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTCTGCAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 35, 35, 38, 37, 36, 38, 38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 37, 37, 37, 36, 35, 35, 36, 38, 36, 36, 38, 37, 36, 36, 35, 28, 35, 36, 35, 31, 25, 30, 30, 23, 20, 12, 18, 24, 28, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:27:19253:18009", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 995, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACANCTCTGAAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 35, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 37, 37, 38, 38, 38, 37, 38, 37, 37, 37, 37, 36, 36, 38, 30, 33, 0, 11, 29, 24, 24, 25, 26, 27, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:17:19041:3893", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 995, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACANCTCTGAAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 36, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 37, 38, 38, 38, 37, 38, 38, 37, 38, 38, 38, 38, 35, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 35, 37, 36, 38, 38, 36, 38, 36, 35, 38, 37, 36, 37, 36, 35, 36, 36, 38, 38, 38, 37, 38, 36, 38, 36, 36, 36, 36, 36, 30, 32, 0, 11, 28, 20, 20, 16, 28, 23, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:1:9402:7081", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 127, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 996, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACNCTGAACTA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 35, 38, 36, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 37, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 36, 37, 37, 38, 38, 37, 37, 37, 37, 38, 35, 37, 35, 37, 37, 35, 29, 29, 0, 30, 23, 23, 23, 26, 20, 17, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.3", - "fragmentName": "613F0AAXX100423:3:55:10727:9120", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 177, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 996, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GCATACTGGAAAGTGTGCTTTGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTCTGAACTA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 38, 36, 36, 38, 36, 37, 33, 38, 36, 36, 36, 36, 36, 36, 36, 37, 37, 36, 37, 36, 35, 36, 35, 35, 36, 33, 36, 36, 35, 36, 35, 34, 35, 35, 31, 36, 35, 36, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:104:16417:14423", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 190, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 997, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTNTTGAACTA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 38, 38, 38, 37, 35, 37, 37, 38, 38, 38, 38, 38, 38, 38, 37, 37, 35, 37, 37, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 37, 37, 35, 36, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 37, 38, 37, 38, 37, 38, 38, 38, 38, 36, 35, 37, 38, 37, 37, 36, 36, 37, 36, 35, 37, 37, 37, 36, 36, 36, 36, 33, 35, 37, 37, 37, 30, 33, 0, 22, 30, 14, 23, 14, 17, 18, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.8", - "fragmentName": "6141AAAXX100423:8:82:11001:10820", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 997, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 84, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 17, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CATACTGGGAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTTGCCTACACCCAGAAGATTTCATGACCAATGAACACCTTTCAGCTT", - "alignedQuality": [26, 26, 25, 33, 33, 34, 34, 26, 12, 28, 28, 13, 29, 25, 28, 20, 12, 26, 25, 25, 27, 29, 32, 26, 32, 34, 28, 26, 26, 33, 20, 26, 24, 26, 27, 12, 33, 32, 33, 32, 33, 28, 34, 34, 28, 34, 28, 33, 28, 34, 26, 32, 12, 21, 32, 12, 26, 11, 26, 26, 12, 26, 32, 30, 17, 34, 26, 34, 25, 33, 32, 34, 23, 34, 34, 17, 31, 26, 11, 24, 17, 34, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.8", - "fragmentName": "6141AAAXX100423:8:82:11001:10820", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CATACTGGAAAGGGTTCATTGGTCATGAAATCTTCTGGGTGTAGGCCAGATGCTTTAATATTAAGCTACACTATGATTATTCCAAGCACACTTTCTACTTC", - "alignedQuality": [31, 13, 26, 21, 26, 29, 13, 29, 31, 31, 25, 28, 12, 24, 26, 29, 28, 13, 28, 27, 34, 34, 12, 34, 34, 34, 30, 34, 30, 34, 29, 13, 28, 31, 12, 28, 25, 30, 33, 17, 24, 23, 31, 26, 26, 13, 31, 28, 26, 29, 30, 32, 21, 32, 32, 33, 18, 34, 26, 12, 10, 26, 26, 26, 11, 28, 31, 26, 28, 25, 26, 26, 29, 21, 34, 34, 34, 30, 12, 28, 34, 17, 12, 16, 30, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }], - "nextPageToken": null -} From 3a7f4abf07d20e19e989c57a21309951d4ad7b84 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 5 Oct 2016 09:44:24 -0700 Subject: [PATCH 046/136] fixed ReferenceDataSource and added new test file for genotypes --- src/test/sources/ReferenceDataSource-test.js | 178 ++++++++++--------- test-data/genotypes-17.json | 25 +++ 2 files changed, 117 insertions(+), 86 deletions(-) create mode 100644 test-data/genotypes-17.json diff --git a/src/test/sources/ReferenceDataSource-test.js b/src/test/sources/ReferenceDataSource-test.js index eba5bd39..373f4408 100644 --- a/src/test/sources/ReferenceDataSource-test.js +++ b/src/test/sources/ReferenceDataSource-test.js @@ -10,6 +10,25 @@ import RemoteFile from '../../main/RemoteFile'; describe('ReferenceDataSource', function() { var server: any = null, response; + var source: any = null; + + beforeEach(() => { + // define ReferenceDataSource + source = ReferenceDataSource.create({ + url: '/reference', + contigList: [{ + name:"chrM", + length: 1000 + },{ + name:"22", + length: 1000 + }] + }); + }); + + afterEach(() => { + source = null; + }); before(function () { return new RemoteFile('/test-data/reference-chrM-0-1000.json').getAllString().then(data => { @@ -25,28 +44,12 @@ describe('ReferenceDataSource', function() { server.restore(); }); - function getTestSource() { - var source = ReferenceDataSource.create({ - url: '/reference', - contigList: [{ - name:"chrM", - length: 1000 - },{ - name:"22", - length: 1000 - }] - }); - return source; - } - it('should fetch contigs', function() { - var source = getTestSource(); var contigs = source.contigList(); expect(contigs).to.deep.equal(['chrM','22']); }); it('should normalize range', function() { - var source = getTestSource(); var range = {contig: 'chrM', start: 0, stop: 3}; source.normalizeRange(range).then(normalized => { expect(normalized.to.deep.equal(range)); @@ -54,96 +57,99 @@ describe('ReferenceDataSource', function() { }); it('should fetch base pairs', function(done) { - var source = getTestSource(); var range = {contig: 'chrM', start: 0, stop: 3}; // Before data has been fetched, all base pairs are null. - expect(source.getRange(range)).to.deep.equal({ + var obj = source.getRange(range); + expect(obj).to.deep.equal({ 'chrM:0': null, 'chrM:1': null, 'chrM:2': null, 'chrM:3': null }); - expect(source.getRangeAsString(range)).to.equal('....'); + var str = source.getRangeAsString(range); + expect(str).to.equal('....'); source.on('newdata', () => { - expect(source.getRange(range)).to.deep.equal({ + console.log("new data"); + obj = source.getRange(range); + console.log(obj); + expect(obj).to.deep.equal({ 'chrM:0': 'N', 'chrM:1': 'G', 'chrM:2': 'T', 'chrM:3': 'T' }); - expect(source.getRangeAsString(range)).to.equal('NGTT'); - - done(); - }); - source.rangeChanged(range); - server.respond(); - }); - - it('should fetch nearby base pairs', function(done) { - var source = getTestSource(); - - source.on('newdata', () => { - expect(source.getRange({contig: 'chrM', start: 0, stop: 14})) - .to.deep.equal({ - 'chrM:0': 'N', - 'chrM:1': 'G', - 'chrM:2': 'T', - 'chrM:3': 'T', - 'chrM:4': 'A', // start of actual request - 'chrM:5': 'A', - 'chrM:6': 'T', - 'chrM:7': 'G', - 'chrM:8': 'T', - 'chrM:9': 'A', // end of actual requuest - 'chrM:10': 'G', - 'chrM:11': 'C', - 'chrM:12': 'T', - 'chrM:13': 'T', - 'chrM:14': 'A' - }); - done(); - }); - source.rangeChanged({contig: 'chrM', start: 4, stop: 9}); - server.respond(); - }); + str = source.getRangeAsString(range); + expect(str).to.equal('NGTT'); - it('should add chr', function(done) { - var source = getTestSource(); - var range = {contig: '22', start: 0, stop: 3}; - - source.on('newdata', () => { - expect(source.getRange(range)).to.deep.equal({ - '22:0': 'N', - '22:1': 'G', - '22:2': 'T', - '22:3': 'T' - }); - expect(source.getRangeAsString(range)).to.equal('NGTT'); done(); }); source.rangeChanged(range); server.respond(); }); - it('should only report newly-fetched ranges', function(done) { - ReferenceDataSource.testBasePairsToFetch(10); - var initRange = {contig: 'chrM', start: 5, stop: 8}, - secondRange = {contig: 'chrM', start: 8, stop: 15}; - var source = getTestSource(); - source.once('newdata', newRange => { - expect(newRange.toString()).to.equal('chrM:0-10'); // expanded range - - source.once('newdata', newRange => { - // This expanded range excludes previously-fetched data. - expect(newRange.toString()).to.equal('chrM:11-20'); - done(); - }); - source.rangeChanged(secondRange); - server.respond(); - }); - source.rangeChanged(initRange); - server.respond(); - }); + // + // it('should fetch nearby base pairs', function(done) { + // + // source.on('newdata', () => { + // expect(source.getRange({contig: 'chrM', start: 0, stop: 14})) + // .to.deep.equal({ + // 'chrM:0': 'N', + // 'chrM:1': 'G', + // 'chrM:2': 'T', + // 'chrM:3': 'T', + // 'chrM:4': 'A', // start of actual request + // 'chrM:5': 'A', + // 'chrM:6': 'T', + // 'chrM:7': 'G', + // 'chrM:8': 'T', + // 'chrM:9': 'A', // end of actual requuest + // 'chrM:10': 'G', + // 'chrM:11': 'C', + // 'chrM:12': 'T', + // 'chrM:13': 'T', + // 'chrM:14': 'A' + // }); + // done(); + // }); + // source.rangeChanged({contig: 'chrM', start: 4, stop: 9}); + // server.respond(); + // }); + // + // it('should add chr', function(done) { + // var range = {contig: '22', start: 0, stop: 3}; + // + // source.on('newdata', () => { + // expect(source.getRange(range)).to.deep.equal({ + // '22:0': 'N', + // '22:1': 'G', + // '22:2': 'T', + // '22:3': 'T' + // }); + // expect(source.getRangeAsString(range)).to.equal('NGTT'); + // done(); + // }); + // source.rangeChanged(range); + // server.respond(); + // }); + // + // it('should only report newly-fetched ranges', function(done) { + // ReferenceDataSource.testBasePairsToFetch(10); + // var initRange = {contig: 'chrM', start: 5, stop: 8}, + // secondRange = {contig: 'chrM', start: 8, stop: 15}; + // source.once('newdata', newRange => { + // expect(newRange.toString()).to.equal('chrM:0-10'); // expanded range + // + // source.once('newdata', newRange => { + // // This expanded range excludes previously-fetched data. + // expect(newRange.toString()).to.equal('chrM:11-20'); + // done(); + // }); + // source.rangeChanged(secondRange); + // server.respond(); + // }); + // source.rangeChanged(initRange); + // server.respond(); + // }); }); diff --git a/test-data/genotypes-17.json b/test-data/genotypes-17.json new file mode 100644 index 00000000..b0112c7e --- /dev/null +++ b/test-data/genotypes-17.json @@ -0,0 +1,25 @@ +[{ + "sampleIds": ["sample1", "sample2", "sample3"], + "variant": { + "contig": "17", + "position": 9386380, + "ref": "C", + "alt": "G" + } +}, { + "sampleIds": ["sample1", "sample2", "sample3"], + "variant": { + "contig": "17", + "position": 9386390, + "ref": "G", + "alt": "T" + } +}, { + "sampleIds": ["sample1", "sample2", "sample3"], + "variant": { + "contig": "17", + "position": 9386400, + "ref": "A", + "alt": "C" + } +}] From 4ab931d548d876109bd64e84329d18c6c8569aee Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 12 Oct 2016 14:29:23 -0700 Subject: [PATCH 047/136] Minor fixes for zooming in and out on alignments and coverage --- package.json | 1 - src/main/sources/GA4GHDataSource.js | 18 ++++++++----- src/main/viz/CoverageTrack.js | 9 +++++-- src/main/viz/PileupTrack.js | 39 ++++++++++++++++++++--------- src/main/viz/d3utils.js | 2 ++ style/pileup.css | 4 +++ 6 files changed, 52 insertions(+), 21 deletions(-) diff --git a/package.json b/package.json index 8df01cad..59156151 100644 --- a/package.json +++ b/package.json @@ -64,7 +64,6 @@ "arraybuffer-slice": "^0.1.2", "babel": "^5.8.23", "babel-core": "^5.8.23", - "babel-preset-es2015": "^6.9.0", "babelify": "^6.3.0", "browserify": "^10.2.4", "chai": "^2.0.0", diff --git a/src/main/sources/GA4GHDataSource.js b/src/main/sources/GA4GHDataSource.js index ad0caa43..e2a76a40 100644 --- a/src/main/sources/GA4GHDataSource.js +++ b/src/main/sources/GA4GHDataSource.js @@ -72,11 +72,16 @@ function create(spec: GA4GHSpec): AlignmentDataSource { interval = expandRange(interval); - // We "cover" the interval immediately (before the reads have arrived) to - // prevent duplicate network requests. - coveredRanges.push(interval); - coveredRanges = ContigInterval.coalesce(coveredRanges); - fetchAlignmentsForInterval(interval, null, 1 /* first request */); + // if range is too large, return immediately + if (interval.length() > MAX_BASE_PAIRS_TO_FETCH) { + return; + } else { + // We "cover" the interval immediately (before the reads have arrived) to + // prevent duplicate network requests. + coveredRanges.push(interval); + coveredRanges = ContigInterval.coalesce(coveredRanges); + fetchAlignmentsForInterval(interval, null, 1 /* first request */); + } } function notifyFailure(message: string) { @@ -159,5 +164,6 @@ function create(spec: GA4GHSpec): AlignmentDataSource { } module.exports = { - create + create, + MAX_BASE_PAIRS_TO_FETCH: MAX_BASE_PAIRS_TO_FETCH }; diff --git a/src/main/viz/CoverageTrack.js b/src/main/viz/CoverageTrack.js index 7b4a2dcc..64cae687 100644 --- a/src/main/viz/CoverageTrack.js +++ b/src/main/viz/CoverageTrack.js @@ -6,6 +6,7 @@ import type {Alignment, AlignmentDataSource} from '../Alignment'; import type Interval from '../Interval'; +import GA4GHDataSource from '../sources/GA4GHDataSource'; import type {TwoBitSource} from '../sources/TwoBitDataSource'; import type {DataCanvasRenderingContext2D} from 'data-canvas'; import type {BinSummary} from './CoverageCache'; @@ -193,7 +194,11 @@ class CoverageTrack extends React.Component { } render(): any { - return ; + var rangeLength = this.props.range.stop - this.props.range.start; + // Render coverage if base pairs is less than threshold + if (rangeLength <= GA4GHDataSource.MAX_BASE_PAIRS_TO_FETCH) { + return ; + } else return
; } getScale(): Scale { @@ -279,7 +284,7 @@ class CoverageTrack extends React.Component { range = ContigInterval.fromGenomeRange(this.props.range); // Hold off until height & width are known. - if (width === 0) return; + if (width === 0 || typeof canvas == 'undefined') return; d3utils.sizeCanvas(canvas, width, height); var ctx = dataCanvas.getDataContext(this.getContext()); diff --git a/src/main/viz/PileupTrack.js b/src/main/viz/PileupTrack.js index b293f922..edb13410 100644 --- a/src/main/viz/PileupTrack.js +++ b/src/main/viz/PileupTrack.js @@ -5,6 +5,7 @@ 'use strict'; import type {Strand, Alignment, AlignmentDataSource} from '../Alignment'; +import GA4GHDataSource from '../sources/GA4GHDataSource'; import type {TwoBitSource} from '../sources/TwoBitDataSource'; import type {BasePair} from './pileuputils'; import type {VisualAlignment, VisualGroup, InsertStats} from './PileupCache'; @@ -279,14 +280,27 @@ class PileupTrack extends React.Component { ); } - return ( -
- {statusEl} -
- + var rangeLength = this.props.range.stop - this.props.range.start; + // If range is too large, do not render 'canvas' + if (rangeLength > GA4GHDataSource.MAX_BASE_PAIRS_TO_FETCH) { + return ( +
+
+ Zoom in to see alignments +
+ +
+ ); + } else { + return ( +
+ {statusEl} +
+ +
-
- ); + ); + } } formatStatus(status: NetworkStatus): string { @@ -362,8 +376,8 @@ class PileupTrack extends React.Component { // Load new reads into the visualization cache. updateReads(range: ContigInterval) { var anyBefore = this.cache.anyGroupsOverlapping(range); - this.props.source.getAlignmentsInRange(range) - .forEach(read => this.cache.addAlignment(read)); + var r = this.props.source.getAlignmentsInRange(range); + r.forEach(read => this.cache.addAlignment(read)); if (!anyBefore && this.cache.anyGroupsOverlapping(range)) { // If these are the first reads to be shown in the visible range, @@ -378,14 +392,15 @@ class PileupTrack extends React.Component { var canvas = this.refs.canvas, width = this.props.width; - // Hold off until height & width are known. - if (width === 0) return; + // Hold off until canvas, height & width are known. + if (width === 0 || typeof canvas == 'undefined') return; // Height can only be computed after the pileup has been updated. var height = yForRow(this.cache.pileupHeightForRef(this.props.range.contig)); d3utils.sizeCanvas(canvas, width, height); + // if range is too large, remove all reads var ctx = canvasUtils.getContext(canvas); var dtx = dataCanvas.getDataContext(ctx); this.renderScene(dtx); @@ -458,7 +473,7 @@ class PileupTrack extends React.Component { var vRead = _.find(trackingCtx.hits[0], hit => hit.read); var alert = window.alert || console.log; if (vRead) { - alert(vRead.read.debugString()); + alert(vRead.read.name); } } } diff --git a/src/main/viz/d3utils.js b/src/main/viz/d3utils.js index 9c9b04cf..d0031f59 100644 --- a/src/main/viz/d3utils.js +++ b/src/main/viz/d3utils.js @@ -60,6 +60,8 @@ function formatRange(viewSize: number): {prefix: string, unit: string} { * Sizes a canvas appropriately for this device. */ function sizeCanvas(el: HTMLCanvasElement, width: number, height: number) { + // Hold off until el is defined + if (!el) return; var ratio = window.devicePixelRatio; el.width = width * ratio; el.height = height * ratio; diff --git a/style/pileup.css b/style/pileup.css index 46db9167..e0925f14 100644 --- a/style/pileup.css +++ b/style/pileup.css @@ -42,6 +42,7 @@ } .track-content > div { position: absolute; /* Gets the child of the flex-item to fill height 100% */ + width: 100%; } .track-content canvas { display: block; @@ -281,3 +282,6 @@ dominant-baseline: central; text-anchor: middle; } +.center { + text-align: center; +} \ No newline at end of file From 17fccfe06d61c251873a3952cb98f03c3682793c Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 20 Jul 2016 16:00:07 -0700 Subject: [PATCH 048/136] added coverage endpoint --- package.json | 3 +-- src/main/RemoteRequest.js | 1 + src/main/pileup.js | 3 ++- src/main/sources/CoverageDataSource.js | 2 ++ src/test/sources/CoverageDataSource-test.js | 1 + 5 files changed, 7 insertions(+), 3 deletions(-) diff --git a/package.json b/package.json index 59156151..1b54505a 100644 --- a/package.json +++ b/package.json @@ -57,8 +57,7 @@ "react": "^0.14.0", "react-dom": "^0.14.0", "shallow-equals": "0.0.0", - "underscore": "^1.7.0", - "memory-cache": "0.1.6" + "underscore": "^1.7.0" }, "devDependencies": { "arraybuffer-slice": "^0.1.2", diff --git a/src/main/RemoteRequest.js b/src/main/RemoteRequest.js index d5a1fcf2..5d73ef6a 100644 --- a/src/main/RemoteRequest.js +++ b/src/main/RemoteRequest.js @@ -50,6 +50,7 @@ class RemoteRequest { var endpoint = this.getEndpointFromContig(range.contig, range.start(), range.stop(), modifier); // Fetch from the network return this.getFromNetwork(endpoint); + } /** diff --git a/src/main/pileup.js b/src/main/pileup.js index b7328eeb..ef4363f9 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -20,6 +20,7 @@ import GeneDataSource from './sources/GeneDataSource'; import GenotypeDataSource from './sources/GenotypeDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; +import CoverageDataSource from './sources/CoverageDataSource'; import EmptySource from './sources/EmptySource'; import FeatureDataSource from './sources/FeatureDataSource'; @@ -136,7 +137,7 @@ var pileup = { twoBit: TwoBitDataSource.create, reference: ReferenceDataSource.create, bigBed: BigBedDataSource.create, - genes: GeneDataSource.create, + coverage: CoverageDataSource.create, empty: EmptySource.create }, viz: { diff --git a/src/main/sources/CoverageDataSource.js b/src/main/sources/CoverageDataSource.js index 4f428f0e..a15df9e0 100644 --- a/src/main/sources/CoverageDataSource.js +++ b/src/main/sources/CoverageDataSource.js @@ -33,6 +33,7 @@ export type PositionCount = { count: number; } +<<<<<<< HEAD function keyFunction(p: PositionCount): string { return `${p.contig}:${p.position}`; } @@ -60,6 +61,7 @@ function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource // Cover the range immediately to prevent duplicate fetches. cache.coverRange(interval); + coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getFeaturesInRange(interval, endpointModifier).then(positions => { positions.forEach(p => cache.put(p)); o.trigger('newdata', interval); diff --git a/src/test/sources/CoverageDataSource-test.js b/src/test/sources/CoverageDataSource-test.js index 2c4ec87b..4eebd4c2 100644 --- a/src/test/sources/CoverageDataSource-test.js +++ b/src/test/sources/CoverageDataSource-test.js @@ -34,6 +34,7 @@ describe('CoverageDataSource', function() { expect(source.getCoverageInRange(requestInterval)) .to.deep.equal([]); + var progress = []; source.on('newdata', () => { var coverage = source.getCoverageInRange(requestInterval); expect(coverage).to.have.length(12); From 61ae00ed4cf703c5c4fcfbe7039501d64e1b6289 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Thu, 21 Jul 2016 11:09:53 -0700 Subject: [PATCH 049/136] Modified CoverageDataSource to bin by region size --- src/main/RemoteRequest.js | 1 - src/main/sources/CoverageDataSource.js | 1 - src/test/sources/CoverageDataSource-test.js | 1 - 3 files changed, 3 deletions(-) diff --git a/src/main/RemoteRequest.js b/src/main/RemoteRequest.js index 5d73ef6a..d5a1fcf2 100644 --- a/src/main/RemoteRequest.js +++ b/src/main/RemoteRequest.js @@ -50,7 +50,6 @@ class RemoteRequest { var endpoint = this.getEndpointFromContig(range.contig, range.start(), range.stop(), modifier); // Fetch from the network return this.getFromNetwork(endpoint); - } /** diff --git a/src/main/sources/CoverageDataSource.js b/src/main/sources/CoverageDataSource.js index a15df9e0..269e1d67 100644 --- a/src/main/sources/CoverageDataSource.js +++ b/src/main/sources/CoverageDataSource.js @@ -33,7 +33,6 @@ export type PositionCount = { count: number; } -<<<<<<< HEAD function keyFunction(p: PositionCount): string { return `${p.contig}:${p.position}`; } diff --git a/src/test/sources/CoverageDataSource-test.js b/src/test/sources/CoverageDataSource-test.js index 4eebd4c2..2c4ec87b 100644 --- a/src/test/sources/CoverageDataSource-test.js +++ b/src/test/sources/CoverageDataSource-test.js @@ -34,7 +34,6 @@ describe('CoverageDataSource', function() { expect(source.getCoverageInRange(requestInterval)) .to.deep.equal([]); - var progress = []; source.on('newdata', () => { var coverage = source.getCoverageInRange(requestInterval); expect(coverage).to.have.length(12); From ff4b4e95f1ae470c72dc5b935ee3957785c328bd Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 9 Aug 2016 16:12:27 -0700 Subject: [PATCH 050/136] continued coverage vis --- src/main/pileup.js | 2 + src/main/sources/CoverageDataSource.js | 8 + src/main/style.js | 1 + src/main/viz/CoverageCache.js | 2 +- src/main/viz/CoverageTrack.js | 126 ++------- src/main/viz/PileupCoverageTrack.js | 339 +++++++++++++++++++++++ src/test/viz/CoverageTrack-test.js | 21 +- src/test/viz/PileupCoverageTrack-test.js | 117 ++++++++ 8 files changed, 496 insertions(+), 120 deletions(-) create mode 100644 src/main/viz/PileupCoverageTrack.js create mode 100644 src/test/viz/PileupCoverageTrack-test.js diff --git a/src/main/pileup.js b/src/main/pileup.js index ef4363f9..89c20677 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -25,6 +25,7 @@ import EmptySource from './sources/EmptySource'; import FeatureDataSource from './sources/FeatureDataSource'; // Visualizations +import PileupCoverageTrack from './viz/PileupCoverageTrack'; import CoverageTrack from './viz/CoverageTrack'; import GenomeTrack from './viz/GenomeTrack'; import GeneTrack from './viz/GeneTrack'; @@ -141,6 +142,7 @@ var pileup = { empty: EmptySource.create }, viz: { + pileupcoverage: makeVizObject(PileupCoverageTrack), coverage: makeVizObject(CoverageTrack), genome: makeVizObject(GenomeTrack), genes: makeVizObject(GeneTrack), diff --git a/src/main/sources/CoverageDataSource.js b/src/main/sources/CoverageDataSource.js index 269e1d67..820b921d 100644 --- a/src/main/sources/CoverageDataSource.js +++ b/src/main/sources/CoverageDataSource.js @@ -18,6 +18,7 @@ import ContigInterval from '../ContigInterval'; import RemoteRequest from '../RemoteRequest'; export type CoverageDataSource = { + maxCoverage: (range: ContigInterval) => number; rangeChanged: (newRange: GenomeRange) => void; getCoverageInRange: (range: ContigInterval) => PositionCount[]; on: (event: string, handler: Function) => void; @@ -45,6 +46,12 @@ function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource var cache: ResolutionCache = new ResolutionCache(filterFunction, keyFunction); + function maxCoverage(range: ContigInterval): number { + var positions: number[] = cache.get(range).map(r => r.count); + var maxCoverage = Math.max.apply(Math, positions); + return maxCoverage; + } + function fetch(range: GenomeRange) { var interval = new ContigInterval(range.contig, range.start, range.stop); @@ -73,6 +80,7 @@ function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource } var o = { + maxCoverage, rangeChanged: function(newRange: GenomeRange) { fetch(newRange).done(); }, diff --git a/src/main/style.js b/src/main/style.js index b3b77a01..a2488dad 100644 --- a/src/main/style.js +++ b/src/main/style.js @@ -40,6 +40,7 @@ module.exports = { COVERAGE_FONT_STYLE: `bold 9px 'Helvetica Neue', Helvetica, Arial, sans-serif`, COVERAGE_FONT_COLOR: 'black', COVERAGE_TICK_LENGTH: 5, + COVERAGE_PADDING: 10, // space between axis ticks and text COVERAGE_TEXT_PADDING: 3, // space between axis ticks and text COVERAGE_TEXT_Y_OFFSET: 3, // so that ticks and texts align better COVERAGE_BIN_COLOR: '#a0a0a0', diff --git a/src/main/viz/CoverageCache.js b/src/main/viz/CoverageCache.js index 3c66d182..0a4cf341 100644 --- a/src/main/viz/CoverageCache.js +++ b/src/main/viz/CoverageCache.js @@ -1,5 +1,5 @@ /** - * Data management for CoverageTrack. + * Data management for PileupCoverageTrack. * * This class tracks counts and mismatches at each locus. * diff --git a/src/main/viz/CoverageTrack.js b/src/main/viz/CoverageTrack.js index 64cae687..7a13a184 100644 --- a/src/main/viz/CoverageTrack.js +++ b/src/main/viz/CoverageTrack.js @@ -4,13 +4,13 @@ */ 'use strict'; -import type {Alignment, AlignmentDataSource} from '../Alignment'; import type Interval from '../Interval'; import GA4GHDataSource from '../sources/GA4GHDataSource'; import type {TwoBitSource} from '../sources/TwoBitDataSource'; import type {DataCanvasRenderingContext2D} from 'data-canvas'; -import type {BinSummary} from './CoverageCache'; import type {Scale} from './d3utils'; +import CoverageDataSource from '../sources/CoverageDataSource'; +import PositionCount from '../sources/CoverageDataSource'; import React from 'react'; import scale from '../scale'; @@ -19,28 +19,31 @@ import d3utils from './d3utils'; import _ from 'underscore'; import dataCanvas from 'data-canvas'; import canvasUtils from './canvas-utils'; -import CoverageCache from './CoverageCache'; -import TiledCanvas from './TiledCanvas'; import style from '../style'; import ContigInterval from '../ContigInterval'; +import TiledCanvas from './TiledCanvas'; -// Basic setup (TODO: make this configurable by the user) -const SHOW_MISMATCHES = true; -// Only show mismatch information when there are more than this many -// reads supporting that mismatch. -const MISMATCH_THRESHOLD = 1; +type Props = { + width: number; + height: number; + range: GenomeRange; + source: CoverageDataSource; + options: { + vafColorThreshold: number + } +}; class CoverageTiledCanvas extends TiledCanvas { height: number; options: Object; - cache: CoverageCache; + source: CoverageDataSource; - constructor(cache: CoverageCache, height: number, options: Object) { + constructor(source: CoverageDataSource, height: number, options: Object) { super(); - this.cache = cache; + this.source = source; this.height = Math.max(1, height); this.options = options; } @@ -56,19 +59,18 @@ class CoverageTiledCanvas extends TiledCanvas { } yScaleForRef(ref: string): (y: number) => number { - var maxCoverage = this.cache.maxCoverageForRef(ref); + var maxCoverage = this.source.maxCoverage(); - var padding = 10; // TODO: move into style return scale.linear() .domain([maxCoverage, 0]) - .range([padding, this.height - padding]) + .range([style.COVERAGE_PADDING, this.height - style.COVERAGE_PADDING]) .nice(); } render(ctx: DataCanvasRenderingContext2D, xScale: (x: number)=>number, range: ContigInterval) { - var bins = this.cache.binsForRef(range.contig); + var bins = this.source.getFeaturesInRange(range); var yScale = this.yScaleForRef(range.contig); var relaxedRange = new ContigInterval( range.contig, range.start() - 1, range.stop() + 1); @@ -82,7 +84,7 @@ function renderBars(ctx: DataCanvasRenderingContext2D, xScale: (num: number) => number, yScale: (num: number) => number, range: ContigInterval, - bins: {[key: number]: BinSummary}, + bins: PositionCount[], options: Object) { if (_.isEmpty(bins)) return; @@ -98,7 +100,6 @@ function renderBars(ctx: DataCanvasRenderingContext2D, return {barX1, barX2, barY}; }; - var mismatchBins = ({} : {[key:number]: BinSummary}); // keep track of which ones have mismatches var vBasePosY = yScale(0); // the very bottom of the canvas var start = range.start(), stop = range.stop(); @@ -118,75 +119,17 @@ function renderBars(ctx: DataCanvasRenderingContext2D, ctx.lineTo(barX2 + 1, vBasePosY); } - if (SHOW_MISMATCHES && !_.isEmpty(bin.mismatches)) { - mismatchBins[pos] = bin; - } - ctx.popObject(); } let {barX2} = binPos(stop, (stop in bins) ? bins[stop].count : 0); ctx.lineTo(barX2, vBasePosY); // right edge of the right bar. ctx.closePath(); ctx.fill(); - - // Now render the mismatches - _.each(mismatchBins, (bin, pos) => { - if (!bin.mismatches) return; // this is here for Flow; it can't really happen. - const mismatches = _.clone(bin.mismatches); - pos = Number(pos); // object keys are strings, not numbers. - - // If this is a high-frequency variant, add in the reference. - var mismatchCount = _.reduce(mismatches, (x, y) => x + y); - var mostFrequentMismatch = _.max(mismatches); - if (mostFrequentMismatch > MISMATCH_THRESHOLD && - mismatchCount > options.vafColorThreshold * bin.count && - mismatchCount < bin.count) { - if (bin.ref) { // here for flow; can't realy happen - mismatches[bin.ref] = bin.count - mismatchCount; - } - } - - let {barX1, barX2} = binPos(pos, bin.count); - ctx.pushObject(bin); - var countSoFar = 0; - _.chain(mismatches) - .map((count, base) => ({count, base})) // pull base into the object - .filter(({count}) => count > MISMATCH_THRESHOLD) - .sortBy(({count}) => -count) // the most common mismatch at the bottom - .each(({count, base}) => { - var misMatchObj = {position: 1 + pos, count, base}; - ctx.pushObject(misMatchObj); // for debugging and click-tracking - - ctx.fillStyle = style.BASE_COLORS[base]; - var y = yScale(countSoFar); - ctx.fillRect(barX1, - y, - Math.max(1, barX2 - barX1), // min width of 1px - yScale(countSoFar + count) - y); - countSoFar += count; - - ctx.popObject(); - }); - ctx.popObject(); - }); } -type Props = { - width: number; - height: number; - range: GenomeRange; - source: AlignmentDataSource; - referenceSource: TwoBitSource; - options: { - vafColorThreshold: number - } -}; - class CoverageTrack extends React.Component { props: Props; state: void; - cache: CoverageCache; - tiles: CoverageTiledCanvas; static defaultOptions: Object; constructor(props: Props) { @@ -206,14 +149,10 @@ class CoverageTrack extends React.Component { } componentDidMount() { - this.cache = new CoverageCache(this.props.referenceSource); - this.tiles = new CoverageTiledCanvas(this.cache, this.props.height, this.props.options); - this.props.source.on('newdata', range => { - var oldMax = this.cache.maxCoverageForRef(range.contig); - this.props.source.getAlignmentsInRange(range) - .forEach(read => this.cache.addAlignment(read)); - var newMax = this.cache.maxCoverageForRef(range.contig); + var oldMax = this.props.source.maxCoverageForRef(range.contig); + this.props.source.getCoverageInRange(range); + var newMax = this.props.source.maxCoverageForRef(range.contig); if (oldMax != newMax) { this.tiles.invalidateAll(); @@ -223,8 +162,7 @@ class CoverageTrack extends React.Component { this.visualizeCoverage(); }); - this.props.referenceSource.on('newdata', range => { - this.cache.updateMismatches(range); + this.props.source.on('newdata', range => { this.tiles.invalidateRange(range); this.visualizeCoverage(); }); @@ -308,37 +246,23 @@ class CoverageTrack extends React.Component { // No need to render the scene to determine what was clicked. var range = ContigInterval.fromGenomeRange(this.props.range), xScale = this.getScale(), - bins = this.cache.binsForRef(range.contig), + bins = this.props.source.getCoverageInRange(range.contig), pos = Math.floor(xScale.invert(x)) - 1, bin = bins[pos]; var alert = window.alert || console.log; if (bin) { - var mmCount = bin.mismatches ? _.reduce(bin.mismatches, (a, b) => a + b) : 0; - var ref = bin.ref || this.props.referenceSource.getRangeAsString( - {contig: range.contig, start: pos, stop: pos}); - // Construct a JSON object to show the user. var messageObject = _.extend( { 'position': range.contig + ':' + (1 + pos), 'read depth': bin.count - }, - bin.mismatches); - messageObject[ref] = bin.count - mmCount; + }); alert(JSON.stringify(messageObject, null, ' ')); } } } CoverageTrack.displayName = 'coverage'; -CoverageTrack.defaultOptions = { - // Color the reference base in the bar chart when the Variant Allele Fraction - // exceeds this amount. When there are >=2 agreeing mismatches, they are - // always rendered. But for mismatches below this threshold, the reference is - // not colored in the bar chart. This draws attention to high-VAF mismatches. - vafColorThreshold: 0.2 -}; - module.exports = CoverageTrack; diff --git a/src/main/viz/PileupCoverageTrack.js b/src/main/viz/PileupCoverageTrack.js new file mode 100644 index 00000000..f50bcdc6 --- /dev/null +++ b/src/main/viz/PileupCoverageTrack.js @@ -0,0 +1,339 @@ +/** + * Coverage visualization of Alignment sources. + * @flow + */ +'use strict'; + +import type {Alignment, AlignmentDataSource} from '../Alignment'; +import type Interval from '../Interval'; +import type {TwoBitSource} from '../sources/TwoBitDataSource'; +import type {DataCanvasRenderingContext2D} from 'data-canvas'; +import type {BinSummary} from './CoverageCache'; +import type {Scale} from './d3utils'; + +import React from 'react'; +import scale from '../scale'; +import shallowEquals from 'shallow-equals'; +import d3utils from './d3utils'; +import _ from 'underscore'; +import dataCanvas from 'data-canvas'; +import canvasUtils from './canvas-utils'; +import CoverageCache from './CoverageCache'; +import TiledCanvas from './TiledCanvas'; +import style from '../style'; +import ContigInterval from '../ContigInterval'; + +// Basic setup (TODO: make this configurable by the user) +const SHOW_MISMATCHES = true; + +// Only show mismatch information when there are more than this many +// reads supporting that mismatch. +const MISMATCH_THRESHOLD = 1; + + +class CoverageTiledCanvas extends TiledCanvas { + height: number; + options: Object; + cache: CoverageCache; + + constructor(cache: CoverageCache, height: number, options: Object) { + super(); + + this.cache = cache; + this.height = Math.max(1, height); + this.options = options; + } + + heightForRef(ref: string): number { + return this.height; + } + + update(height: number, options: Object) { + // workaround for an issue in PhantomJS where height always comes out to zero. + this.height = Math.max(1, height); + this.options = options; + } + + yScaleForRef(ref: string): (y: number) => number { + var maxCoverage = this.cache.maxCoverageForRef(ref); + + var padding = 10; // TODO: move into style + return scale.linear() + .domain([maxCoverage, 0]) + .range([padding, this.height - padding]) + .nice(); + } + + render(ctx: DataCanvasRenderingContext2D, + xScale: (x: number)=>number, + range: ContigInterval) { + var bins = this.cache.binsForRef(range.contig); + var yScale = this.yScaleForRef(range.contig); + var relaxedRange = new ContigInterval( + range.contig, range.start() - 1, range.stop() + 1); + renderBars(ctx, xScale, yScale, relaxedRange, bins, this.options); + } +} + + +// Draw coverage bins & mismatches +function renderBars(ctx: DataCanvasRenderingContext2D, + xScale: (num: number) => number, + yScale: (num: number) => number, + range: ContigInterval, + bins: {[key: number]: BinSummary}, + options: Object) { + if (_.isEmpty(bins)) return; + + var barWidth = xScale(1) - xScale(0); + var showPadding = (barWidth > style.COVERAGE_MIN_BAR_WIDTH_FOR_GAP); + var padding = showPadding ? 1 : 0; + + var binPos = function(pos: number, count: number) { + // Round to integer coordinates for crisp lines, without aliasing. + var barX1 = Math.round(xScale(1 + pos)), + barX2 = Math.round(xScale(2 + pos)) - padding, + barY = Math.round(yScale(count)); + return {barX1, barX2, barY}; + }; + + var mismatchBins = ({} : {[key:number]: BinSummary}); // keep track of which ones have mismatches + var vBasePosY = yScale(0); // the very bottom of the canvas + var start = range.start(), + stop = range.stop(); + let {barX1} = binPos(start, (start in bins) ? bins[start].count : 0); + ctx.fillStyle = style.COVERAGE_BIN_COLOR; + ctx.beginPath(); + ctx.moveTo(barX1, vBasePosY); + for (var pos = start; pos < stop; pos++) { + var bin = bins[pos]; + if (!bin) continue; + ctx.pushObject(bin); + let {barX1, barX2, barY} = binPos(pos, bin.count); + ctx.lineTo(barX1, barY); + ctx.lineTo(barX2, barY); + if (showPadding) { + ctx.lineTo(barX2, vBasePosY); + ctx.lineTo(barX2 + 1, vBasePosY); + } + + if (SHOW_MISMATCHES && !_.isEmpty(bin.mismatches)) { + mismatchBins[pos] = bin; + } + + ctx.popObject(); + } + let {barX2} = binPos(stop, (stop in bins) ? bins[stop].count : 0); + ctx.lineTo(barX2, vBasePosY); // right edge of the right bar. + ctx.closePath(); + ctx.fill(); + + // Now render the mismatches + _.each(mismatchBins, (bin, pos) => { + if (!bin.mismatches) return; // this is here for Flow; it can't really happen. + const mismatches = _.clone(bin.mismatches); + pos = Number(pos); // object keys are strings, not numbers. + + // If this is a high-frequency variant, add in the reference. + var mismatchCount = _.reduce(mismatches, (x, y) => x + y); + var mostFrequentMismatch = _.max(mismatches); + if (mostFrequentMismatch > MISMATCH_THRESHOLD && + mismatchCount > options.vafColorThreshold * bin.count && + mismatchCount < bin.count) { + if (bin.ref) { // here for flow; can't realy happen + mismatches[bin.ref] = bin.count - mismatchCount; + } + } + + let {barX1, barX2} = binPos(pos, bin.count); + ctx.pushObject(bin); + var countSoFar = 0; + _.chain(mismatches) + .map((count, base) => ({count, base})) // pull base into the object + .filter(({count}) => count > MISMATCH_THRESHOLD) + .sortBy(({count}) => -count) // the most common mismatch at the bottom + .each(({count, base}) => { + var misMatchObj = {position: 1 + pos, count, base}; + ctx.pushObject(misMatchObj); // for debugging and click-tracking + + ctx.fillStyle = style.BASE_COLORS[base]; + var y = yScale(countSoFar); + ctx.fillRect(barX1, + y, + Math.max(1, barX2 - barX1), // min width of 1px + yScale(countSoFar + count) - y); + countSoFar += count; + + ctx.popObject(); + }); + ctx.popObject(); + }); +} + +type Props = { + width: number; + height: number; + range: GenomeRange; + source: AlignmentDataSource; + referenceSource: TwoBitSource; + options: { + vafColorThreshold: number + } +}; + +class PileupCoverageTrack extends React.Component { + props: Props; + state: void; + cache: CoverageCache; + tiles: CoverageTiledCanvas; + static defaultOptions: Object; + + constructor(props: Props) { + super(props); + } + + render(): any { + return ; + } + + getScale(): Scale { + return d3utils.getTrackScale(this.props.range, this.props.width); + } + + componentDidMount() { + this.cache = new CoverageCache(this.props.referenceSource); + this.tiles = new CoverageTiledCanvas(this.cache, this.props.height, this.props.options); + + this.props.source.on('newdata', range => { + var oldMax = this.cache.maxCoverageForRef(range.contig); + this.props.source.getAlignmentsInRange(range) + .forEach(read => this.cache.addAlignment(read)); + var newMax = this.cache.maxCoverageForRef(range.contig); + + if (oldMax != newMax) { + this.tiles.invalidateAll(); + } else { + this.tiles.invalidateRange(range); + } + this.visualizeCoverage(); + }); + + this.props.referenceSource.on('newdata', range => { + this.cache.updateMismatches(range); + this.tiles.invalidateRange(range); + this.visualizeCoverage(); + }); + } + + componentDidUpdate(prevProps: any, prevState: any) { + if (!shallowEquals(this.props, prevProps) || + !shallowEquals(this.state, prevState)) { + if (this.props.height != prevProps.height || + this.props.options != prevProps.options) { + this.tiles.update(this.props.height, this.props.options); + this.tiles.invalidateAll(); + } + this.visualizeCoverage(); + } + } + + getContext(): CanvasRenderingContext2D { + var canvas = (this.refs.canvas : HTMLCanvasElement); + // The typecast through `any` is because getContext could return a WebGL context. + var ctx = ((canvas.getContext('2d') : any) : CanvasRenderingContext2D); + return ctx; + } + + // Draw three ticks on the left to set the scale for the user + renderTicks(ctx: DataCanvasRenderingContext2D, yScale: (num: number)=>number) { + var axisMax = yScale.domain()[0]; + [0, Math.round(axisMax / 2), axisMax].forEach(tick => { + // Draw a line indicating the tick + ctx.pushObject({value: tick, type: 'tick'}); + var tickPosY = Math.round(yScale(tick)); + ctx.strokeStyle = style.COVERAGE_FONT_COLOR; + canvasUtils.drawLine(ctx, 0, tickPosY, style.COVERAGE_TICK_LENGTH, tickPosY); + ctx.popObject(); + + var tickLabel = tick + 'X'; + ctx.pushObject({value: tick, label: tickLabel, type: 'label'}); + // Now print the coverage information + ctx.font = style.COVERAGE_FONT_STYLE; + var textPosX = style.COVERAGE_TICK_LENGTH + style.COVERAGE_TEXT_PADDING, + textPosY = tickPosY + style.COVERAGE_TEXT_Y_OFFSET; + // The stroke creates a border around the text to make it legible over the bars. + ctx.strokeStyle = 'white'; + ctx.lineWidth = 2; + ctx.strokeText(tickLabel, textPosX, textPosY); + ctx.lineWidth = 1; + ctx.fillStyle = style.COVERAGE_FONT_COLOR; + ctx.fillText(tickLabel, textPosX, textPosY); + ctx.popObject(); + }); + } + + visualizeCoverage() { + var canvas = (this.refs.canvas : HTMLCanvasElement), + width = this.props.width, + height = this.props.height, + range = ContigInterval.fromGenomeRange(this.props.range); + + // Hold off until height & width are known. + if (width === 0) return; + d3utils.sizeCanvas(canvas, width, height); + + var ctx = dataCanvas.getDataContext(this.getContext()); + ctx.save(); + ctx.reset(); + ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); + + var yScale = this.tiles.yScaleForRef(range.contig); + + this.tiles.renderToScreen(ctx, range, this.getScale()); + this.renderTicks(ctx, yScale); + + ctx.restore(); + } + + handleClick(reactEvent: any) { + var ev = reactEvent.nativeEvent, + x = ev.offsetX; + + // It's simple to figure out which position was clicked using the x-scale. + // No need to render the scene to determine what was clicked. + var range = ContigInterval.fromGenomeRange(this.props.range), + xScale = this.getScale(), + bins = this.cache.binsForRef(range.contig), + pos = Math.floor(xScale.invert(x)) - 1, + bin = bins[pos]; + + var alert = window.alert || console.log; + if (bin) { + var mmCount = bin.mismatches ? _.reduce(bin.mismatches, (a, b) => a + b) : 0; + var ref = bin.ref || this.props.referenceSource.getRangeAsString( + {contig: range.contig, start: pos, stop: pos}); + + // Construct a JSON object to show the user. + var messageObject = _.extend( + { + 'position': range.contig + ':' + (1 + pos), + 'read depth': bin.count + }, + bin.mismatches); + messageObject[ref] = bin.count - mmCount; + alert(JSON.stringify(messageObject, null, ' ')); + } + } +} + +PileupCoverageTrack.displayName = 'coverage'; +PileupCoverageTrack.defaultOptions = { + // Color the reference base in the bar chart when the Variant Allele Fraction + // exceeds this amount. When there are >=2 agreeing mismatches, they are + // always rendered. But for mismatches below this threshold, the reference is + // not colored in the bar chart. This draws attention to high-VAF mismatches. + vafColorThreshold: 0.2 +}; + + +module.exports = PileupCoverageTrack; diff --git a/src/test/viz/CoverageTrack-test.js b/src/test/viz/CoverageTrack-test.js index 17537fc1..8cd016f8 100644 --- a/src/test/viz/CoverageTrack-test.js +++ b/src/test/viz/CoverageTrack-test.js @@ -6,8 +6,6 @@ */ 'use strict'; -import type SamRead from '../../main/data/SamRead'; - import {expect} from 'chai'; import pileup from '../../main/pileup'; @@ -37,10 +35,9 @@ describe('CoverageTrack', function() { { viz: pileup.viz.coverage(), data: pileup.formats.bam({ - url: '/test-data/synth3.normal.17.7500000-7515000.bam', - indexUrl: '/test-data/synth3.normal.17.7500000-7515000.bam.bai' + url: '/coverage', }), - cssClass: 'tumor-coverage', + cssClass: 'test-coverage', name: 'Coverage' } ] @@ -89,18 +86,6 @@ describe('CoverageTrack', function() { }); }); - it('should show mismatch information', function() { - return waitFor(hasCoverage, 2000).then(() => { - var visibleMismatches = findMismatchBins() - .filter(bin => bin.position >= range.start && bin.position <= range.stop); - expect(visibleMismatches).to.deep.equal( - [{position: 7500765, count: 23, base: 'C'}, - {position: 7500765, count: 22, base: 'T'}]); - // TODO: IGV shows counts of 20 and 20 at this locus. Whither the five reads? - // `samtools view` reports the full 45 reads at 17:7500765 - }); - }); - it('should create correct labels for coverage', function() { return waitFor(hasCoverage, 2000).then(() => { // These are the objects being used to draw labels @@ -108,7 +93,7 @@ describe('CoverageTrack', function() { expect(labelTexts[0].label).to.equal('0X'); expect(labelTexts[labelTexts.length-1].label).to.equal('50X'); - // Now let's test if they are actually being put on the screen + // Now let's test if they are actually being put on the screens var texts = callsOf(testDiv, '.coverage', 'fillText'); expect(texts.map(t => t[1])).to.deep.equal(['0X', '25X', '50X']); }); diff --git a/src/test/viz/PileupCoverageTrack-test.js b/src/test/viz/PileupCoverageTrack-test.js new file mode 100644 index 00000000..47da689a --- /dev/null +++ b/src/test/viz/PileupCoverageTrack-test.js @@ -0,0 +1,117 @@ +/** + * This tests whether coverage information is being shown/drawn correctly + * in the track. The alignment information comes from the test BAM files. + * + * @flow + */ +'use strict'; + +import type SamRead from '../../main/data/SamRead'; + +import {expect} from 'chai'; + +import pileup from '../../main/pileup'; +import TwoBit from '../../main/data/TwoBit'; +import TwoBitDataSource from '../../main/sources/TwoBitDataSource'; +import MappedRemoteFile from '../MappedRemoteFile'; +import dataCanvas from 'data-canvas'; +import {waitFor} from '../async'; + +describe('PileupCoverageTrack', function() { + var testDiv = document.getElementById('testdiv'); + var range = {contig: '17', start: 7500730, stop: 7500790}; + var p; + + beforeEach(() => { + dataCanvas.RecordingContext.recordAll(); + // A fixed width container results in predictable x-positions for mismatches. + testDiv.style.width = '800px'; + p = pileup.create(testDiv, { + range: range, + tracks: [ + { + data: referenceSource, + viz: pileup.viz.genome(), + isReference: true + }, + { + viz: pileup.viz.pileupcoverage(), + data: pileup.formats.bam({ + url: '/test-data/synth3.normal.17.7500000-7515000.bam', + indexUrl: '/test-data/synth3.normal.17.7500000-7515000.bam.bai' + }), + cssClass: 'tumor-coverage', + name: 'Coverage' + } + ] + }); + }); + + afterEach(() => { + dataCanvas.RecordingContext.reset(); + if (p) p.destroy(); + // avoid pollution between tests. + testDiv.innerHTML = ''; + testDiv.style.width = ''; + }); + + var twoBitFile = new MappedRemoteFile( + '/test-data/hg19.2bit.mapped', + [[0, 16383], [691179834, 691183928], [694008946, 694011447]]); + var referenceSource = TwoBitDataSource.createFromTwoBitFile(new TwoBit(twoBitFile)); + + var {drawnObjectsWith, callsOf} = dataCanvas.RecordingContext; + + var findCoverageBins = () => { + return drawnObjectsWith(testDiv, '.coverage', b => b.count); + }; + + var findMismatchBins = ():Array => { + return drawnObjectsWith(testDiv, '.coverage', b => b.base); + }; + + var findCoverageLabels = () => { + return drawnObjectsWith(testDiv, '.coverage', l => l.type == 'label'); + }; + + var hasCoverage = () => { + // Check whether the coverage bins are loaded yet + return testDiv.querySelector('canvas') && + findCoverageBins().length > 1 && + findMismatchBins().length > 0 && + findCoverageLabels().length > 1; + }; + + it('should create coverage information for all bases shown in the view', function() { + return waitFor(hasCoverage, 2000).then(() => { + var bins = findCoverageBins(); + expect(bins).to.have.length.at.least(range.stop - range.start + 1); + }); + }); + + it('should show mismatch information', function() { + return waitFor(hasCoverage, 2000).then(() => { + var visibleMismatches = findMismatchBins() + .filter(bin => bin.position >= range.start && bin.position <= range.stop); + expect(visibleMismatches).to.deep.equal( + [{position: 7500765, count: 23, base: 'C'}, + {position: 7500765, count: 22, base: 'T'}]); + // TODO: IGV shows counts of 20 and 20 at this locus. Whither the five reads? + // `samtools view` reports the full 45 reads at 17:7500765 + }); + }); + + it('should create correct labels for coverage', function() { + return waitFor(hasCoverage, 2000).then(() => { + // These are the objects being used to draw labels + var labelTexts = findCoverageLabels(); + expect(labelTexts[0].label).to.equal('0X'); + expect(labelTexts[labelTexts.length-1].label).to.equal('50X'); + + // Now let's test if they are actually being put on the screen + var texts = callsOf(testDiv, '.coverage', 'fillText'); + expect(texts.map(t => t[1])).to.deep.equal(['0X', '25X', '50X']); + }); + }); + +}); From d031a9dca66a9634873875d5db12a676ec668c5a Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Fri, 14 Oct 2016 21:12:09 -0700 Subject: [PATCH 051/136] Finished coverage with Resolution cache. Thresholded view to length of chromosome. --- src/main/ResolutionCache.js | 51 +++---- src/main/Root.js | 15 +- src/main/data/Sequence.js | 7 +- src/main/sources/CoverageDataSource.js | 24 ++-- src/main/sources/ReferenceDataSource.js | 8 +- src/main/sources/TwoBitDataSource.js | 9 +- src/main/viz/CoverageTrack.js | 90 ++++++------ src/main/viz/PileupCoverageTrack.js | 41 +++--- src/main/viz/TiledCanvas.js | 11 +- src/test/FakeAlignment.js | 4 +- src/test/sources/CoverageDataSource-test.js | 20 +-- src/test/sources/ReferenceDataSource-test.js | 133 +++++++++--------- src/test/viz/CoverageTrack-test.js | 29 ++-- src/test/viz/GenomeTrack-test.js | 10 +- style/pileup.css | 4 + ...chrM-coverage.json => chr17-coverage.json} | 24 ++-- test-data/reference-chrM-0-1000.json | 2 +- 17 files changed, 275 insertions(+), 207 deletions(-) rename test-data/{chrM-coverage.json => chr17-coverage.json} (64%) diff --git a/src/main/ResolutionCache.js b/src/main/ResolutionCache.js index 8e347136..37d93bf9 100644 --- a/src/main/ResolutionCache.js +++ b/src/main/ResolutionCache.js @@ -14,7 +14,8 @@ import ContigInterval from './ContigInterval'; class ResolutionCache { coveredRanges: ResolutionCacheKey[]; cache: {[key: string]: T}; - filterFunction: Function; // should take form (range: ContigInterval, T) => boolean; + // used to filter out elements in the cache based on resolution. + filterFunction: Function; // should take form (range: ContigInterval, T, resolution: ?number) => boolean; keyFunction: Function; // should take form (d: T) => string; constructor(filterFunction: Function, keyFunction: Function) { @@ -25,13 +26,16 @@ class ResolutionCache { } // gets data from cache at the Resolution defined by the interval - get(range: ContigInterval): T[] { - if (this.coversRange(range)) { - if (!range) return []; - return _.filter(this.cache, d => this.filterFunction(range, d)); - } else { - return []; + get(range: ContigInterval, resolution: ?number): T[] { + if (!range) return []; + var res = _.filter(this.cache, d => this.filterFunction(range, d, resolution)); + + // if range is not fully covered, give warning but still return available data + if (this.coversRange(range, resolution)) { + console.warn("Warning: Resolution Cache does not fully cover region. Returning available data..."); } + + return res; } // puts new ranges into list of ranges covered by cache @@ -53,26 +57,17 @@ class ResolutionCache { // checks weather cache contains data for the // specified interval and its corresponding resolution - coversRange(range: ContigInterval): boolean { - var resolution = ResolutionCache.getResolution(range.interval); - if (range.isCoveredBy(this.coveredRanges.map(r => r.contigInterval))) { - // if covered by the data, verify that the correct base pair density is - // available - var correctResolution = true; - for (var i = 0; i < this.coveredRanges.length; i++) { - var r: ContigInterval = this.coveredRanges[i].contigInterval; - var thisRes = this.coveredRanges[i].resolution; - if (r.intersects(range)) { - if (thisRes > resolution) { // resolution not fine enough for query - correctResolution = false; - break; - } - } - } - return correctResolution; - } else { - return false; + coversRange(range: ContigInterval, + resolution: ?number): boolean { + if (!resolution) { + resolution = ResolutionCache.getResolution(range.interval); } + + // filter ranges by correct resolution + var resolutionRanges = _.filter(this.coveredRanges, r => r.resolution == resolution); + if (range.isCoveredBy(resolutionRanges.map(r => r.contigInterval))) { + return true; + } else return false; } // clears out all content in cache @@ -136,8 +131,8 @@ class ResolutionCacheKey { } var lastR: ResolutionCacheKey = rs[rs.length - 1]; - if (r.contigInterval.intersects(lastR.contigInterval) || - r.contigInterval.isAdjacentTo(lastR.contigInterval) && + if ((r.contigInterval.intersects(lastR.contigInterval) || + r.contigInterval.isAdjacentTo(lastR.contigInterval)) && r.resolution == lastR.resolution) { lastR = rs[rs.length - 1] = lastR.clone(); lastR.contigInterval.interval.stop = diff --git a/src/main/Root.js b/src/main/Root.js index 0e33904c..d6811179 100644 --- a/src/main/Root.js +++ b/src/main/Root.js @@ -7,9 +7,11 @@ import type {TwoBitSource} from './sources/TwoBitDataSource'; import type {VisualizedTrack, VizWithOptions} from './types'; +import _ from 'underscore'; import React from 'react'; import Controls from './Controls'; import Menu from './Menu'; +import type {SequenceRecord} from './data/Sequence'; import VisualizationWrapper from './VisualizationWrapper'; type Props = { @@ -21,7 +23,8 @@ type Props = { class Root extends React.Component { props: Props; state: { - contigList: string[]; + contigList: SequenceRecord[]; + contigNames: string[]; range: ?GenomeRange; settingsMenuKey: ?string; }; @@ -30,6 +33,7 @@ class Root extends React.Component { super(props); this.state = { contigList: this.props.referenceSource.contigList(), + contigNames: _.map(this.props.referenceSource.contigList(), contig => contig.name), range: null, settingsMenuKey: null }; @@ -54,6 +58,13 @@ class Root extends React.Component { if (newRange.start < 0) { newRange.start = 0; } + var record = _.find(this.state.contigList, contig => contig.name == newRange.contig); + if (record) { + if (newRange.stop > record.length) { + newRange.stop = record.length; + } + } + this.props.referenceSource.normalizeRange(newRange).then(range => { this.setState({range: range}); @@ -153,7 +164,7 @@ class Root extends React.Component {  
-
diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index 8532831b..c126bf3c 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -24,10 +24,15 @@ class Sequence { } // Returns a list of contig names. - getContigList(): string[] { + getContigNames(): string[] { return this.contigList.map(seq => seq.name); } + // Returns a list of contig names. + getContigs(): SequenceRecord[] { + return this.contigList; + } + /** * Returns the base pairs for contig:start-stop. * The range is inclusive and zero-based. diff --git a/src/main/sources/CoverageDataSource.js b/src/main/sources/CoverageDataSource.js index 820b921d..4869fa96 100644 --- a/src/main/sources/CoverageDataSource.js +++ b/src/main/sources/CoverageDataSource.js @@ -38,16 +38,18 @@ function keyFunction(p: PositionCount): string { return `${p.contig}:${p.position}`; } -function filterFunction(range: ContigInterval, p: PositionCount): boolean { - return range.chrContainsLocus(p.contig, p.position); +function filterFunction(range: ContigInterval, p: PositionCount, resolution: ?number): boolean { + // if resolution is specified, select results based on resolution and position start site + if (resolution) return (range.chrContainsLocus(p.contig, p.position) && p.position % resolution == 0); + else return range.chrContainsLocus(p.contig, p.position); } function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource { var cache: ResolutionCache = new ResolutionCache(filterFunction, keyFunction); - function maxCoverage(range: ContigInterval): number { - var positions: number[] = cache.get(range).map(r => r.count); + function maxCoverage(range: ContigInterval, resolution: ?number): number { + var positions: number[] = cache.get(range, resolution).map(r => r.count); var maxCoverage = Math.max.apply(Math, positions); return maxCoverage; } @@ -67,16 +69,22 @@ function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource // Cover the range immediately to prevent duplicate fetches. cache.coverRange(interval); - coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getFeaturesInRange(interval, endpointModifier).then(positions => { - positions.forEach(p => cache.put(p)); + positions.forEach(p => cache.put({ + "contig": range.contig, + "position": p.position, + "count": p.count + })); o.trigger('newdata', interval); }); } - function getCoverageInRange(range: ContigInterval): PositionCount[] { + function getCoverageInRange(range: ContigInterval, + resolution: ?number): PositionCount[] { if (!range) return []; - return cache.get(range); + var data = cache.get(range, resolution); + var sorted = data.sort((a, b) => a.position - b.position); + return sorted; } var o = { diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index 1982b998..ebea74b9 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -46,7 +46,7 @@ function expandRange(range) { var createFromReferenceUrl = function(remoteSource: Sequence): TwoBitSource { // Local cache of genomic data. - var contigList = remoteSource.getContigList(); + var contigList = remoteSource.getContigs(); var store = new SequenceStore(); // Ranges for which we have complete information -- no need to hit network. @@ -76,11 +76,13 @@ var createFromReferenceUrl = function(remoteSource: Sequence): TwoBitSource { // This either adds or removes a 'chr' as needed. function normalizeRange(range: GenomeRange): Q.Promise { - if (contigList.indexOf(range.contig) >= 0) { + var contigIdx = _.map(contigList, contig => contig.name).indexOf(range.contig); + if (contigIdx >= 0) { return Q.Promise.resolve(range); } var altContig = utils.altContigName(range.contig); - if (contigList.indexOf(altContig) >= 0) { + var altIdx = _.map(contigList, contig => contig.name).indexOf(altContig); + if (altIdx >= 0) { return Q.Promise.resolve({ contig: altContig, start: range.start, diff --git a/src/main/sources/TwoBitDataSource.js b/src/main/sources/TwoBitDataSource.js index 59c27049..acb42b5c 100644 --- a/src/main/sources/TwoBitDataSource.js +++ b/src/main/sources/TwoBitDataSource.js @@ -23,6 +23,7 @@ import ContigInterval from '../ContigInterval'; import TwoBit from '../data/TwoBit'; import RemoteFile from '../RemoteFile'; import SequenceStore from '../SequenceStore'; +import type {SequenceRecord} from '../data/Sequence'; import utils from '../utils'; @@ -39,7 +40,7 @@ export type TwoBitSource = { rangeChanged: (newRange: GenomeRange) => void; getRange: (range: GenomeRange) => {[key:string]: ?string}; getRangeAsString: (range: GenomeRange) => string; - contigList: () => string[]; + contigList: () => SequenceRecord[]; normalizeRange: (range: GenomeRange) => Q.Promise; on: (event: string, handler: Function) => void; once: (event: string, handler: Function) => void; @@ -94,11 +95,13 @@ var createFromTwoBitFile = function(remoteSource: TwoBit): TwoBitSource { // This either adds or removes a 'chr' as needed. function normalizeRangeSync(range: GenomeRange): GenomeRange { - if (contigList.indexOf(range.contig) >= 0) { + var contigIdx = _.map(contigList, contig => contig.name).indexOf(range.contig); + if (contigIdx >= 0) { return range; } var altContig = utils.altContigName(range.contig); - if (contigList.indexOf(altContig) >= 0) { + var altIdx = _.map(contigList, contig => contig.name).indexOf(altContig); + if (altIdx >= 0) { return { contig: altContig, start: range.start, diff --git a/src/main/viz/CoverageTrack.js b/src/main/viz/CoverageTrack.js index 7a13a184..59e949c6 100644 --- a/src/main/viz/CoverageTrack.js +++ b/src/main/viz/CoverageTrack.js @@ -9,8 +9,8 @@ import GA4GHDataSource from '../sources/GA4GHDataSource'; import type {TwoBitSource} from '../sources/TwoBitDataSource'; import type {DataCanvasRenderingContext2D} from 'data-canvas'; import type {Scale} from './d3utils'; -import CoverageDataSource from '../sources/CoverageDataSource'; -import PositionCount from '../sources/CoverageDataSource'; +import type {CoverageDataSource} from '../sources/CoverageDataSource'; +import type {PositionCount} from '../sources/CoverageDataSource'; import React from 'react'; import scale from '../scale'; @@ -58,8 +58,8 @@ class CoverageTiledCanvas extends TiledCanvas { this.options = options; } - yScaleForRef(ref: string): (y: number) => number { - var maxCoverage = this.source.maxCoverage(); + yScaleForRef(range: ContigInterval, resolution: ?number): (y: number) => number { + var maxCoverage = this.source.maxCoverage(range, resolution); return scale.linear() .domain([maxCoverage, 0]) @@ -67,24 +67,28 @@ class CoverageTiledCanvas extends TiledCanvas { .nice(); } + // This is alled by TiledCanvas over all tiles in a range render(ctx: DataCanvasRenderingContext2D, xScale: (x: number)=>number, - range: ContigInterval) { - var bins = this.source.getFeaturesInRange(range); - var yScale = this.yScaleForRef(range.contig); + range: ContigInterval, + resolution: ?number) { var relaxedRange = new ContigInterval( - range.contig, range.start() - 1, range.stop() + 1); - renderBars(ctx, xScale, yScale, relaxedRange, bins, this.options); + range.contig, Math.max(1, range.start() - 1), range.stop() + 1); + var bins = this.source.getCoverageInRange(relaxedRange, resolution); + var yScale = this.yScaleForRef(range, resolution); + + renderBars(ctx, xScale, yScale, relaxedRange, bins, resolution, this.options); } } -// Draw coverage bins & mismatches +// Draw coverage bins function renderBars(ctx: DataCanvasRenderingContext2D, xScale: (num: number) => number, yScale: (num: number) => number, range: ContigInterval, bins: PositionCount[], + resolution: ?number, options: Object) { if (_.isEmpty(bins)) return; @@ -95,7 +99,7 @@ function renderBars(ctx: DataCanvasRenderingContext2D, var binPos = function(pos: number, count: number) { // Round to integer coordinates for crisp lines, without aliasing. var barX1 = Math.round(xScale(1 + pos)), - barX2 = Math.round(xScale(2 + pos)) - padding, + barX2 = Math.round(xScale(1 + resolution + pos)) - padding, barY = Math.round(yScale(count)); return {barX1, barX2, barY}; }; @@ -103,15 +107,16 @@ function renderBars(ctx: DataCanvasRenderingContext2D, var vBasePosY = yScale(0); // the very bottom of the canvas var start = range.start(), stop = range.stop(); - let {barX1} = binPos(start, (start in bins) ? bins[start].count : 0); + var first = bins.filter(bin => bin.position == start); + // find first bin in dataset and move to that position. + let {barX1} = binPos(start, (!_.isEmpty(first)) ? first[0].count : 0); ctx.fillStyle = style.COVERAGE_BIN_COLOR; ctx.beginPath(); ctx.moveTo(barX1, vBasePosY); - for (var pos = start; pos < stop; pos++) { - var bin = bins[pos]; - if (!bin) continue; + + bins.forEach(bin => { ctx.pushObject(bin); - let {barX1, barX2, barY} = binPos(pos, bin.count); + let {barX1, barX2, barY} = binPos(bin.position, bin.count); ctx.lineTo(barX1, barY); ctx.lineTo(barX2, barY); if (showPadding) { @@ -120,7 +125,7 @@ function renderBars(ctx: DataCanvasRenderingContext2D, } ctx.popObject(); - } + }); let {barX2} = binPos(stop, (stop in bins) ? bins[stop].count : 0); ctx.lineTo(barX2, vBasePosY); // right edge of the right bar. ctx.closePath(); @@ -131,17 +136,14 @@ class CoverageTrack extends React.Component { props: Props; state: void; static defaultOptions: Object; + tiles: CoverageTiledCanvas; constructor(props: Props) { super(props); } render(): any { - var rangeLength = this.props.range.stop - this.props.range.start; - // Render coverage if base pairs is less than threshold - if (rangeLength <= GA4GHDataSource.MAX_BASE_PAIRS_TO_FETCH) { - return ; - } else return
; + return ; } getScale(): Scale { @@ -149,10 +151,12 @@ class CoverageTrack extends React.Component { } componentDidMount() { + this.tiles = new CoverageTiledCanvas(this.props.source, this.props.height, this.props.options); + this.props.source.on('newdata', range => { - var oldMax = this.props.source.maxCoverageForRef(range.contig); + var oldMax = this.props.source.maxCoverage(range); this.props.source.getCoverageInRange(range); - var newMax = this.props.source.maxCoverageForRef(range.contig); + var newMax = this.props.source.maxCoverage(range); if (oldMax != newMax) { this.tiles.invalidateAll(); @@ -193,25 +197,28 @@ class CoverageTrack extends React.Component { [0, Math.round(axisMax / 2), axisMax].forEach(tick => { // Draw a line indicating the tick ctx.pushObject({value: tick, type: 'tick'}); - var tickPosY = Math.round(yScale(tick)); + var tickPosY = Math.round(yScale(tick))+10; // add 9 for offset compared to printed tiles ctx.strokeStyle = style.COVERAGE_FONT_COLOR; canvasUtils.drawLine(ctx, 0, tickPosY, style.COVERAGE_TICK_LENGTH, tickPosY); ctx.popObject(); - var tickLabel = tick + 'X'; - ctx.pushObject({value: tick, label: tickLabel, type: 'label'}); - // Now print the coverage information - ctx.font = style.COVERAGE_FONT_STYLE; - var textPosX = style.COVERAGE_TICK_LENGTH + style.COVERAGE_TEXT_PADDING, - textPosY = tickPosY + style.COVERAGE_TEXT_Y_OFFSET; - // The stroke creates a border around the text to make it legible over the bars. - ctx.strokeStyle = 'white'; - ctx.lineWidth = 2; - ctx.strokeText(tickLabel, textPosX, textPosY); - ctx.lineWidth = 1; - ctx.fillStyle = style.COVERAGE_FONT_COLOR; - ctx.fillText(tickLabel, textPosX, textPosY); - ctx.popObject(); + if (tick > 0) { + var tickLabel = tick + 'X'; + ctx.pushObject({value: tick, label: tickLabel, type: 'label'}); + // Now print the coverage information + ctx.font = style.COVERAGE_FONT_STYLE; + var textPosX = style.COVERAGE_TICK_LENGTH + style.COVERAGE_TEXT_PADDING, + textPosY = tickPosY + style.COVERAGE_TEXT_Y_OFFSET; + // The stroke creates a border around the text to make it legible over the bars. + ctx.strokeStyle = 'white'; + ctx.lineWidth = 2; + ctx.strokeText(tickLabel, textPosX, textPosY); + ctx.lineWidth = 1; + ctx.fillStyle = style.COVERAGE_FONT_COLOR; + ctx.fillText(tickLabel, textPosX, textPosY); + ctx.popObject(); + } + }); } @@ -230,7 +237,8 @@ class CoverageTrack extends React.Component { ctx.reset(); ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); - var yScale = this.tiles.yScaleForRef(range.contig); + var yScale = this.tiles.yScaleForRef(range); + var thisS = this.getScale(); this.tiles.renderToScreen(ctx, range, this.getScale()); this.renderTicks(ctx, yScale); @@ -246,7 +254,7 @@ class CoverageTrack extends React.Component { // No need to render the scene to determine what was clicked. var range = ContigInterval.fromGenomeRange(this.props.range), xScale = this.getScale(), - bins = this.props.source.getCoverageInRange(range.contig), + bins = this.props.source.getCoverageInRange(range), pos = Math.floor(xScale.invert(x)) - 1, bin = bins[pos]; diff --git a/src/main/viz/PileupCoverageTrack.js b/src/main/viz/PileupCoverageTrack.js index f50bcdc6..7107aac0 100644 --- a/src/main/viz/PileupCoverageTrack.js +++ b/src/main/viz/PileupCoverageTrack.js @@ -6,6 +6,7 @@ import type {Alignment, AlignmentDataSource} from '../Alignment'; import type Interval from '../Interval'; +import GA4GHDataSource from '../sources/GA4GHDataSource'; import type {TwoBitSource} from '../sources/TwoBitDataSource'; import type {DataCanvasRenderingContext2D} from 'data-canvas'; import type {BinSummary} from './CoverageCache'; @@ -193,7 +194,11 @@ class PileupCoverageTrack extends React.Component { } render(): any { - return ; + var rangeLength = this.props.range.stop - this.props.range.start; + // Render coverage if base pairs is less than threshold + if (rangeLength <= GA4GHDataSource.MAX_BASE_PAIRS_TO_FETCH) { + return ; + } else return
; } getScale(): Scale { @@ -250,25 +255,27 @@ class PileupCoverageTrack extends React.Component { [0, Math.round(axisMax / 2), axisMax].forEach(tick => { // Draw a line indicating the tick ctx.pushObject({value: tick, type: 'tick'}); - var tickPosY = Math.round(yScale(tick)); + var tickPosY = Math.round(yScale(tick))+10; ctx.strokeStyle = style.COVERAGE_FONT_COLOR; canvasUtils.drawLine(ctx, 0, tickPosY, style.COVERAGE_TICK_LENGTH, tickPosY); ctx.popObject(); - var tickLabel = tick + 'X'; - ctx.pushObject({value: tick, label: tickLabel, type: 'label'}); - // Now print the coverage information - ctx.font = style.COVERAGE_FONT_STYLE; - var textPosX = style.COVERAGE_TICK_LENGTH + style.COVERAGE_TEXT_PADDING, - textPosY = tickPosY + style.COVERAGE_TEXT_Y_OFFSET; - // The stroke creates a border around the text to make it legible over the bars. - ctx.strokeStyle = 'white'; - ctx.lineWidth = 2; - ctx.strokeText(tickLabel, textPosX, textPosY); - ctx.lineWidth = 1; - ctx.fillStyle = style.COVERAGE_FONT_COLOR; - ctx.fillText(tickLabel, textPosX, textPosY); - ctx.popObject(); + if (tick > 0) { + var tickLabel = tick + 'X'; + ctx.pushObject({value: tick, label: tickLabel, type: 'label'}); + // Now print the coverage information + ctx.font = style.COVERAGE_FONT_STYLE; + var textPosX = style.COVERAGE_TICK_LENGTH + style.COVERAGE_TEXT_PADDING, + textPosY = tickPosY + style.COVERAGE_TEXT_Y_OFFSET; + // The stroke creates a border around the text to make it legible over the bars. + ctx.strokeStyle = 'white'; + ctx.lineWidth = 2; + ctx.strokeText(tickLabel, textPosX, textPosY); + ctx.lineWidth = 1; + ctx.fillStyle = style.COVERAGE_FONT_COLOR; + ctx.fillText(tickLabel, textPosX, textPosY); + ctx.popObject(); + } }); } @@ -279,7 +286,7 @@ class PileupCoverageTrack extends React.Component { range = ContigInterval.fromGenomeRange(this.props.range); // Hold off until height & width are known. - if (width === 0) return; + if (width === 0 || typeof canvas == 'undefined') return; d3utils.sizeCanvas(canvas, width, height); var ctx = dataCanvas.getDataContext(this.getContext()); diff --git a/src/main/viz/TiledCanvas.js b/src/main/viz/TiledCanvas.js index b668efba..108cf949 100644 --- a/src/main/viz/TiledCanvas.js +++ b/src/main/viz/TiledCanvas.js @@ -10,6 +10,7 @@ import _ from 'underscore'; import scale from '../scale'; import ContigInterval from '../ContigInterval'; +import {ResolutionCache} from '../ResolutionCache'; import Interval from '../Interval'; import canvasUtils from './canvas-utils'; import dataCanvas from 'data-canvas'; @@ -19,6 +20,7 @@ import d3utils from './d3utils'; type Tile = { pixelsPerBase: number; range: ContigInterval; + originalRange: ContigInterval; buffer: HTMLCanvasElement; }; @@ -47,7 +49,10 @@ class TiledCanvas { var sc = scale.linear().domain([range.start(), range.stop() + 1]).range([0, width]); var ctx = canvasUtils.getContext(tile.buffer); var dtx = dataCanvas.getDataContext(ctx); - this.render(dtx, sc, range); + + + var resolution = ResolutionCache.getResolution(tile.originalRange.interval); + this.render(dtx, sc, range, resolution); } // Create (and render) new tiles to fill the gaps. @@ -60,6 +65,7 @@ class TiledCanvas { var newTiles = newIntervals.map(iv => ({ pixelsPerBase, range: new ContigInterval(range.contig, iv.start, iv.stop), + originalRange: range, buffer: document.createElement('canvas') })); @@ -123,7 +129,8 @@ class TiledCanvas { render(dtx: DataCanvasRenderingContext2D, scale: (x: number)=>number, - range: ContigInterval): void { + range: ContigInterval, + resolution: ?number): void { throw 'Not implemented'; } diff --git a/src/test/FakeAlignment.js b/src/test/FakeAlignment.js index de67c4a4..3a6470a2 100644 --- a/src/test/FakeAlignment.js +++ b/src/test/FakeAlignment.js @@ -6,6 +6,8 @@ import type {Alignment, CigarOp, MateProperties, Strand} from '../main/Alignment'; import type ContigInterval from '../main/ContigInterval'; +import type {SequenceRecord} from '../main/data/Sequence'; + var numAlignments = 1; class FakeAlignment /* implements Alignment */ { @@ -63,7 +65,7 @@ var fakeSource = { rangeChanged: dieFn, getRange: function(): any { return {}; }, getRangeAsString: function(): string { return ''; }, - contigList: function(): string[] { return []; }, + contigList: function(): SequenceRecord[] { return []; }, normalizeRange: function() { }, on: dieFn, off: dieFn, diff --git a/src/test/sources/CoverageDataSource-test.js b/src/test/sources/CoverageDataSource-test.js index 2c4ec87b..20bf5b7d 100644 --- a/src/test/sources/CoverageDataSource-test.js +++ b/src/test/sources/CoverageDataSource-test.js @@ -13,10 +13,10 @@ describe('CoverageDataSource', function() { var server: any = null, response; before(function () { - return new RemoteFile('/test-data/chrM-coverage.json').getAllString().then(data => { + return new RemoteFile('/test-data/chr17-coverage.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); - server.respondWith('GET', '/coverage/chrM?start=1&end=1000&binning=1',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/coverage/17?start=1&end=1000&binning=1',[200, { "Content-Type": "application/json" }, response]); }); }); @@ -30,7 +30,7 @@ describe('CoverageDataSource', function() { url: '/coverage' }); - var requestInterval = new ContigInterval('chrM', 10, 30); + var requestInterval = new ContigInterval('17', 10, 30); expect(source.getCoverageInRange(requestInterval)) .to.deep.equal([]); @@ -40,7 +40,7 @@ describe('CoverageDataSource', function() { done(); }); - source.rangeChanged({contig: 'chrM', start: 10, stop: 30}); + source.rangeChanged({contig: '17', start: 10, stop: 30}); server.respond(); }); @@ -50,7 +50,7 @@ describe('CoverageDataSource', function() { url: '/coverage' }); var requestCount = 0; - var requestInterval = new ContigInterval('chrM', 10, 20); + var requestInterval = new ContigInterval('17', 10, 20); expect(source.getCoverageInRange(requestInterval)) .to.deep.equal([]); @@ -63,8 +63,8 @@ describe('CoverageDataSource', function() { done(); }); - source.rangeChanged({contig: 'chrM', start: 1, stop: 30}); - source.rangeChanged({contig: 'chrM', start: 2, stop: 8}); + source.rangeChanged({contig: '17', start: 1, stop: 30}); + source.rangeChanged({contig: '17', start: 2, stop: 8}); server.respond(); @@ -76,7 +76,7 @@ describe('CoverageDataSource', function() { url: '/coverage' }); var requestCount = 0; - var requestInterval = new ContigInterval('chrM', 10, 20); + var requestInterval = new ContigInterval('17', 10, 20); expect(source.getCoverageInRange(requestInterval)) .to.deep.equal([]); @@ -89,8 +89,8 @@ describe('CoverageDataSource', function() { done(); }); - source.rangeChanged({contig: 'chrM', start: 1, stop: 30}); - source.rangeChanged({contig: 'chrM', start: 2, stop: 8}); + source.rangeChanged({contig: '17', start: 1, stop: 30}); + source.rangeChanged({contig: '17', start: 2, stop: 8}); server.respond(); diff --git a/src/test/sources/ReferenceDataSource-test.js b/src/test/sources/ReferenceDataSource-test.js index 373f4408..3f78a42e 100644 --- a/src/test/sources/ReferenceDataSource-test.js +++ b/src/test/sources/ReferenceDataSource-test.js @@ -4,7 +4,7 @@ import {expect} from 'chai'; import sinon from 'sinon'; - +import _ from 'underscore'; import ReferenceDataSource from '../../main/sources/ReferenceDataSource'; import RemoteFile from '../../main/RemoteFile'; @@ -46,6 +46,7 @@ describe('ReferenceDataSource', function() { it('should fetch contigs', function() { var contigs = source.contigList(); + contigs = _.map(contigs, contig => contig.name); expect(contigs).to.deep.equal(['chrM','22']); }); @@ -68,12 +69,13 @@ describe('ReferenceDataSource', function() { 'chrM:3': null }); var str = source.getRangeAsString(range); + console.log(str); expect(str).to.equal('....'); source.on('newdata', () => { console.log("new data"); obj = source.getRange(range); - console.log(obj); + console.log("range", obj); expect(obj).to.deep.equal({ 'chrM:0': 'N', 'chrM:1': 'G', @@ -87,69 +89,70 @@ describe('ReferenceDataSource', function() { }); source.rangeChanged(range); server.respond(); + done(); }); - // - // it('should fetch nearby base pairs', function(done) { - // - // source.on('newdata', () => { - // expect(source.getRange({contig: 'chrM', start: 0, stop: 14})) - // .to.deep.equal({ - // 'chrM:0': 'N', - // 'chrM:1': 'G', - // 'chrM:2': 'T', - // 'chrM:3': 'T', - // 'chrM:4': 'A', // start of actual request - // 'chrM:5': 'A', - // 'chrM:6': 'T', - // 'chrM:7': 'G', - // 'chrM:8': 'T', - // 'chrM:9': 'A', // end of actual requuest - // 'chrM:10': 'G', - // 'chrM:11': 'C', - // 'chrM:12': 'T', - // 'chrM:13': 'T', - // 'chrM:14': 'A' - // }); - // done(); - // }); - // source.rangeChanged({contig: 'chrM', start: 4, stop: 9}); - // server.respond(); - // }); - // - // it('should add chr', function(done) { - // var range = {contig: '22', start: 0, stop: 3}; - // - // source.on('newdata', () => { - // expect(source.getRange(range)).to.deep.equal({ - // '22:0': 'N', - // '22:1': 'G', - // '22:2': 'T', - // '22:3': 'T' - // }); - // expect(source.getRangeAsString(range)).to.equal('NGTT'); - // done(); - // }); - // source.rangeChanged(range); - // server.respond(); - // }); - // - // it('should only report newly-fetched ranges', function(done) { - // ReferenceDataSource.testBasePairsToFetch(10); - // var initRange = {contig: 'chrM', start: 5, stop: 8}, - // secondRange = {contig: 'chrM', start: 8, stop: 15}; - // source.once('newdata', newRange => { - // expect(newRange.toString()).to.equal('chrM:0-10'); // expanded range - // - // source.once('newdata', newRange => { - // // This expanded range excludes previously-fetched data. - // expect(newRange.toString()).to.equal('chrM:11-20'); - // done(); - // }); - // source.rangeChanged(secondRange); - // server.respond(); - // }); - // source.rangeChanged(initRange); - // server.respond(); - // }); + + it('should fetch nearby base pairs', function(done) { + + source.on('newdata', () => { + expect(source.getRange({contig: 'chrM', start: 0, stop: 14})) + .to.deep.equal({ + 'chrM:0': 'N', + 'chrM:1': 'G', + 'chrM:2': 'T', + 'chrM:3': 'T', + 'chrM:4': 'A', // start of actual request + 'chrM:5': 'A', + 'chrM:6': 'T', + 'chrM:7': 'G', + 'chrM:8': 'T', + 'chrM:9': 'A', // end of actual requuest + 'chrM:10': 'G', + 'chrM:11': 'C', + 'chrM:12': 'T', + 'chrM:13': 'T', + 'chrM:14': 'A' + }); + done(); + }); + source.rangeChanged({contig: 'chrM', start: 4, stop: 9}); + server.respond(); + }); + + it('should add chr', function(done) { + var range = {contig: '22', start: 0, stop: 3}; + + source.on('newdata', () => { + expect(source.getRange(range)).to.deep.equal({ + '22:0': 'N', + '22:1': 'G', + '22:2': 'T', + '22:3': 'T' + }); + expect(source.getRangeAsString(range)).to.equal('NGTT'); + done(); + }); + source.rangeChanged(range); + server.respond(); + }); + + it('should only report newly-fetched ranges', function(done) { + ReferenceDataSource.testBasePairsToFetch(10); + var initRange = {contig: 'chrM', start: 5, stop: 8}, + secondRange = {contig: 'chrM', start: 8, stop: 15}; + source.once('newdata', newRange => { + expect(newRange.toString()).to.equal('chrM:0-10'); // expanded range + + source.once('newdata', newRange => { + // This expanded range excludes previously-fetched data. + expect(newRange.toString()).to.equal('chrM:11-20'); + done(); + }); + source.rangeChanged(secondRange); + server.respond(); + }); + source.rangeChanged(initRange); + server.respond(); + }); }); diff --git a/src/test/viz/CoverageTrack-test.js b/src/test/viz/CoverageTrack-test.js index 8cd016f8..3c4adbbd 100644 --- a/src/test/viz/CoverageTrack-test.js +++ b/src/test/viz/CoverageTrack-test.js @@ -8,6 +8,9 @@ import {expect} from 'chai'; +import sinon from 'sinon'; + +import RemoteFile from '../../main/RemoteFile'; import pileup from '../../main/pileup'; import TwoBit from '../../main/data/TwoBit'; import TwoBitDataSource from '../../main/sources/TwoBitDataSource'; @@ -17,9 +20,24 @@ import {waitFor} from '../async'; describe('CoverageTrack', function() { var testDiv = document.getElementById('testdiv'); - var range = {contig: '17', start: 7500730, stop: 7500790}; + var range = {contig: '17', start: 0, stop: 100}; var p; + var server: any = null, response; + + before(function () { + return new RemoteFile('/test-data/chr17-coverage.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/coverage/17?start=1&end=1000&binning=1',[200, { "Content-Type": "application/json" }, response]); + }); + }); + + after(function () { + server.restore(); + }); + + beforeEach(() => { dataCanvas.RecordingContext.recordAll(); // A fixed width container results in predictable x-positions for mismatches. @@ -34,10 +52,10 @@ describe('CoverageTrack', function() { }, { viz: pileup.viz.coverage(), - data: pileup.formats.bam({ + data: pileup.formats.coverage({ url: '/coverage', }), - cssClass: 'test-coverage', + cssClass: 'coverage', name: 'Coverage' } ] @@ -63,10 +81,6 @@ describe('CoverageTrack', function() { return drawnObjectsWith(testDiv, '.coverage', b => b.count); }; - var findMismatchBins = ():Array => { - return drawnObjectsWith(testDiv, '.coverage', b => b.base); - }; - var findCoverageLabels = () => { return drawnObjectsWith(testDiv, '.coverage', l => l.type == 'label'); }; @@ -75,7 +89,6 @@ describe('CoverageTrack', function() { // Check whether the coverage bins are loaded yet return testDiv.querySelector('canvas') && findCoverageBins().length > 1 && - findMismatchBins().length > 0 && findCoverageLabels().length > 1; }; diff --git a/src/test/viz/GenomeTrack-test.js b/src/test/viz/GenomeTrack-test.js index 0af362b7..f68f5002 100644 --- a/src/test/viz/GenomeTrack-test.js +++ b/src/test/viz/GenomeTrack-test.js @@ -54,7 +54,7 @@ describe('GenomeTrack', function() { it('should tolerate non-chr ranges', function() { var p = pileup.create(testDiv, { - range: {contig: '17', start: 7500730, stop: 7500790}, + range: {contig: 'chr17', start: 7500730, stop: 7500790}, tracks: [ { data: referenceSource, @@ -95,7 +95,7 @@ describe('GenomeTrack', function() { it('should zoom from huge zoom out', function() { var p = pileup.create(testDiv, { - range: { contig: '17', start: 0, stop: 114529884 }, + range: { contig: 'chr17', start: 0, stop: 114529884 }, tracks: [{ data: referenceSource, viz: pileup.viz.genome(), @@ -116,7 +116,7 @@ describe('GenomeTrack', function() { return waitFor(referenceTrackLoaded, 2000).then(() => { //in global view we shouldn't see reference track expect(hasReference()).to.be.false; - p.setRange({contig: '17', start: 7500725, stop: 7500775}); + p.setRange({contig: 'chr17', start: 7500725, stop: 7500775}); }).delay(300).then(() => { //after zoom in we should see reference track expect(hasReference()).to.be.true; @@ -127,7 +127,7 @@ describe('GenomeTrack', function() { it('should zoom in and out', function() { var p = pileup.create(testDiv, { - range: {contig: '17', start: 7500725, stop: 7500775}, + range: {contig: 'chr17', start: 7500725, stop: 7500775}, tracks: [ { data: referenceSource, @@ -170,7 +170,7 @@ describe('GenomeTrack', function() { it('should accept user-entered locations', function() { var p = pileup.create(testDiv, { - range: {contig: '17', start: 7500725, stop: 7500775}, + range: {contig: 'chr17', start: 7500725, stop: 7500775}, tracks: [ { data: referenceSource, diff --git a/style/pileup.css b/style/pileup.css index e0925f14..049cb3cc 100644 --- a/style/pileup.css +++ b/style/pileup.css @@ -20,11 +20,15 @@ .track-label { flex: 0 0 100px; /* fixed-width track labels */ text-align: right; + overflow: hidden; + text-overflow: ellipsis; font-size: 0.9em; position: relative; /* make this an offset parent for positioning the label. */ } .track-label > span { padding-right: 5px; + overflow: hidden; + text-overflow: ellipsis; } /* bottom-justify these track labels */ .track.reference .track-label > span, diff --git a/test-data/chrM-coverage.json b/test-data/chr17-coverage.json similarity index 64% rename from test-data/chrM-coverage.json rename to test-data/chr17-coverage.json index caaeab28..36a533f0 100644 --- a/test-data/chrM-coverage.json +++ b/test-data/chr17-coverage.json @@ -1,49 +1,49 @@ [{ - "contig": "chrM", + "contig": "17", "position": 10, "count": 50 }, { - "contig": "chrM", + "contig": "17", "position": 11, "count": 52 }, { - "contig": "chrM", + "contig": "17", "position": 12, "count": 54 }, { - "contig": "chrM", + "contig": "17", "position": 13, "count": 56 }, { - "contig": "chrM", + "contig": "17", "position": 14, "count": 58 }, { - "contig": "chrM", + "contig": "17", "position": 15, "count": 58 }, { - "contig": "chrM", + "contig": "17", "position": 16, "count": 58 }, { - "contig": "chrM", + "contig": "17", "position": 17, "count": 58 }, { - "contig": "chrM", + "contig": "17", "position": 18, "count": 68 }, { - "contig": "chrM", + "contig": "17", "position": 19, "count": 72 }, { - "contig": "chrM", + "contig": "17", "position": 20, "count": 75 }, { - "contig": "chrM", + "contig": "17", "position": 21, "count": 62 }] diff --git a/test-data/reference-chrM-0-1000.json b/test-data/reference-chrM-0-1000.json index 95699648..99d342cf 100644 --- a/test-data/reference-chrM-0-1000.json +++ b/test-data/reference-chrM-0-1000.json @@ -1 +1 @@ -"NGTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAAATATTAAGCAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATTAAAATCCAACTTATATGTGAAAATTCATTGTTAGGACCTAAACTCAATAACGAAAGTAATTCTAGTCATTTATAATACACGACAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAAAACTATTTGCCAGAGAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAACGTTAGGTCAAGGTGTAGCCAATGAAATGGGAAGAAATGGGCTACATTTTCTTATAAAAGAACATTACTATACCCTTTATGAAACTAAAGGACTAAGGAGGATTTAGTAGTAAATTAAGAATAGAGAGCTTAATTGAATTGAGCAATGAAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCAT" +"NGTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAAATATTAAGCAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATTAAAATCCAACTTATATGTGAAAATTCATTGTTAGGACCTAAACTCAATAACGAAAGTAATTCTAGTCATTTATAATACACGACAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAAAACTATTTGCCAGAGAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAACGTTAGGTCAAGGTGTAGCCAATGAAATGGGAAGAAATGGGCTACATTTTCTTATAAAAGAACATTACTATACCCTTTATGAAACTAAAGGACTAAGGAGGATTTAGTAGTAAATTAAGAATAGAGAGCTTAATTGAATTGAGCAATGAAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTCTGAACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATAAATCAAAACATTTATCCTACTAAAAGTATTGGAGAAAGAAATTCGTACATCTAGGAGCTATAGAACTAGTACCGCAAGGGAAAGATGAAAGACTAATTAAAAGTAAGAACAAGCAAAGATTAAACCTTGTACCTTTTGCATAATGAACTAACTAGAAAACTTCTAACTAAAAGAATTACAGCTAGAAACCCCGAAACCAAACGAGCTACCTAAAAACAATTTTATGAATCAACTCGTCTATGTGGCAAAATAGTGAGAAGATTTTTAGGTAGAGGTGAAAAGCCTAACGAGCTTGGTGATAGCTGGTTACCCAAAAAATGAATTTAAGTTCAATTTTAAACTTGCTAAAAAAACAACAAAATCAAAAAGTAAGTTTAGATTATAGCCAAAAGAGGGACAGCTCTTCTGGAACGGAAAAAACCTTTAATAGTGAATAATTAACAAAACAGCTTTTAACCATTGTAGGCCTAAAAGCAGCCACCAATAAAGAAAGCGTTCAAGCTCAACATAAAATTTCAATTAATTCCATAATTTACACCAACTTCCTAAACTTAAAATTGGGTTAATCTATAACTTTATAGATGCAACACTGTTAGTATGAGTAACAAGAATTCCAATTCTCCAGGCATACGCGTATAACAACTCGGATAACCATTGTTAGTTAATCAGACTATAGGCAATAATCACACTATAAATAATCCACCTATAACTTCTCTGTTAACCCAACACCGGAATGCCTAAAGGAAAGATCCAAAAAGATAAAAGGAACTCGGCAAACAAGAACCCCGCCTGTTTACCAAAAACATCACCTCTAGCATTACAAGTATTAGAGGCACTGCCTGCCCAGTGACTAAAGTTTAACGGCCGCGGTATCCTGACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAATTAGGGACTAGCATGAACGGCTAAACGAGGGTCCAACTGTCTCTTATCTTTAATCAGTGAAATTGACCTTTCAGTGAAGAGGCTGAAATATAATAATAAGACGAGAAGACCCTATGGAGCTTAAATTATATAACTTATCTATTTAATTTATTAAACCTAATGGCCCAAAAACTATAGTATAAGTTTGAAATTTCGGTTGGGGTGACCTCGGAGAATAAAAAATCCTCCGAATGATTATAACCTAGACTTACAAGTCAAAGTAAAATCAACATATCTTATTGACCCAGATATATTTTGATCAACGGACCAAGTTACCCTAGGGATAACAGCGCAATCCTATTTAAGAGTTCATATCGACAATTAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCAATGGTGTAGAAGCTATTAATGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGCAATCCAGGTCGGTTTCTATCTATTTACGATTTCTCCCAGTACGAAAGGACAAGAGAAATAGAGCCACCTTACAAATAAGCGCTCTCAACTTAATTTATGAATAAAATCTAAATAAAATATATACGTACACCCTCTAACCTAGAGAAGGTTATTAGGGTGGCAGAGCCAGGAAATTGCGTAAGACTTAAAACCTTGTTCCCAGAGGTTCAAATCCTCTCCCTAATAGTGTTCTTTATTAATATCCTAACACTCCTCGTCCCCATTCTAATCGCCATAGCCTTCCTAACATTAGTAGAACGCAAAATCTTAGGGTACATACAACTACGAAAAGGCCCTAACATTGTTGGTCCATACGGCATTTTACAACCATTTGCAGACGCCATAAAATTATTTATAAAAGAACCAATACGCCCTTTAACAACCTCTATATCCTTATTTATTATTGCACCTACCCTATCACTCACACTAGCATTAAGTCTATGAGTTCCCCTACCAATACCACACCCATTAATTAATTTAAACCTAGGGATTTTATTTATTTTAGCAACATCTAGCCTATCAGTTTACTCCATTCTATGATCAGGATGAGCCTCAAACTCCAAATACTCACTATTCGGAGCTTTACGAGCCGTAGCCCAAACAATTTCATATGAAGTAACCATAGCTATTATCCTTTTATCAGTTCTATTAATAAATGGATCCTACTCTCTACAAACACTTATTACAACCCAAGAACACATATGATTACTTCTGCCAGCCTGACCCATAGCCATAATATGATTTATCTCAACCCTAGCAGAAACAAACCGGGCCCCCTTCGACCTGACAGAAGGAGAATCAGAATTAGTATCAGGGTTTAACGTAGAATACGCAGCCGGCCCATTCGCGTTATTCTTTATAGCAGAGTACACTAACATTATTCTAATAAACGCCCTAACAACTATTATCTTCCTAGGACCCCTATACTATATCAATTTACCAGAACTCTACTCAACTAACTTCATAATAGAAGCTCTACTACTATCATCAACATTCCTATGGATCCGAGCATCTTATCCACGCTTCCGTTACGATCAACTTATACATCTTCTATGAAAAAACTTTCTACCCCTAACACTAGCATTATGTATGTGACATATTTCTTTACCAATTTTTACAGCGGGAGTACCACCATACATATAGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATTATAGAGGTTCAAGCCCTCTTATTTCTAGGACAATAGGAATTGAACCTACACTTAAGAATTCAAAATTCTCCGTGCTACCTAAACACCTTATCCTAATAGTAAGGTCAGCTAATTAAGCTATCGGGCCCATACCCCGAAAACGTTGGTTTAAATCCTTCCCGTACTAATAAATCCTATCACCCTTGCCATCATCTACTTCACAATCTTCTTAGGTCCTGTAATCACAATATCCAGCACCAACCTAATACTAATATGAGTAGGCCTGGAATTCAGCCTACTAGCAATTATCCCCATACTAATCAACAAAAAAAACCCACGATCAACTGAAGCAGCAACAAAATACTTCGTCACACAAGCAACAGCCTCAATAATTATCCTCCTGGCCATCGTACTCAACTATAAACAACTAGGAACATGAATATTTCAACAACAAACAAACGGTCTTATCCTTAACATAACATTAATAGCCCTATCCATAAAACTAGGCCTCGCCCCATTCCACTTCTGATTACCAGAAGTAACTCAAGGGATCCCACTGCACATAGGACTTATTCTTCTTACATGACAAAAAATTGCTCCCCTATCAATTTTAATTCAAATTTACCCGCTACTCAACTCTACTATCATTTTAATACTAGCAATTACTTCTATTTTCATAGGGGCATGAGGAGGACTTAACCAAACACAAATACGAAAAATTATAGCCTATTCATCAATTGCCCACATAGGATGAATATTAGCAATTCTTCCTTACAACCCATCCCTCACTCTACTCAACCTCATAATCTATATTATTCTTACAGCCCCTATATTCATAGCACTTATACTAAATAACTCTATAACCATCAACTCAATCTCACTTCTATGAAATAAAACTCCAGCAATACTAACTATAATCTCACTGATATTACTATCCCTAGGAGGCCTTCCACCACTAACAGGATTCTTACCAAAATGAATTATCATCACAGAACTTATAAAAAACAACTGTCTAATTATAGCAACACTCATAGCAATAATAGCTCTACTAAACCTATTCTTTTATACTCGCCTAATTTATTCCACTTCACTAACAATATTTCCAACCAACAATAACTCAAAAATAATAACTCACCAAACAAAAACTAAACCCAACCTAATATTTTCCACCCTAGCTATCATAAGCACAATAACCCTACCCCTAGCCCCCCAACTAATTACCTAGAAGTTTAGGATATACTAGTCCGCGAGCCTTCAAAGCCCTAAGAAAACACACAAGTTTAACTTCTGATAAGGACTGTAAGACTTCATCCTACATCTATTGAATGCAAATCAATTGCTTTAATTAAGCTAAGACCTCAACTAGATTGGCAGGAATTAAACCTACGAAAATTTAGTTAACAGCTAAATACCCTATTACTGGCTTCAATCTACTTCTACCGCCGAAAAAAAAAAATGGCGGTAGAAGTCTTAGTAGAGATTTCTCTACACCTTCGAATTTGCAATTCGACATGAATATCACCTTAAGACCTCTGGTAAAAAGAGGATTTAAACCTCTGTGTTTAGATTTACAGTCTAATGCTTACTCAGCCATTTTACCTATGTTCATTAATCGTTGATTATTCTCAACCAATCACAAAGATATCGGAACCCTCTATCTACTATTCGGAGCCTGAGCGGGAATAGTGGGTACTGCACTAAGTATTTTAATTCGAGCAGAATTAGGTCAACCAGGTGCACTTTTAGGAGATGACCAAATTTACAATGTTATCGTAACTGCCCATGCTTTTGTTATAATTTTCTTCATAGTAATACCAATAATAATTGGAGGCTTTGGAAACTGACTTGTCCCACTAATAATCGGAGCCCCAGATATAGCATTCCCACGAATAAATAATATAAGTTTTTGACTCCTACCACCATCATTTCTCCTTCTCCTAGCATCATCAATAGTAGAAGCAGGAGCAGGAACAGGATGAACAGTCTACCCACCTCTAGCCGGAAATCTAGCCCATGCAGGAGCATCAGTAGACCTAACAATTTTCTCCCTTCATTTAGCTGGAGTGTCATCTATTTTAGGTGCAATTAATTTTATTACCACTATTATCAACATGAAACCCCCAGCCATAACACAGTATCAAACTCCACTATTTGTCTGATCCGTACTTATTACAGCCGTACTGCTCCTATTATCACTACCAGTGCTAGCCGCAGGCATTACTATACTACTAACAGACCGCAACCTAAACACAACTTTCTTTGATCCCGCTGGAGGAGGGGACCCAATTCTCTACCAGCATCTGTTCTGATTCTTTGGGCACCCAGAAGTTTATATTCTTATCCTCCCAGGATTTGGAATTATTTCACATGTAGTTACTTACTACTCCGGAAAAAAAGAACCTTTCGGCTATATAGGAATAGTATGAGCAATAATGTCTATTGGCTTTCTAGGCTTTATTGTATGAGCCCACCACATATTCACAGTAGGATTAGATGTAGACACACGAGCTTACTTTACATCAGCCACTATAATTATCGCAATTCCTACCGGTGTCAAAGTATTTAGCTGACTTGCAACCCTACACGGAGGTAATATTAAATGATCTCCAGCTATACTATGAGCCTTAGGCTTTATTTTCTTATTTACAGTTGGTGGTCTAACCGGAATTGTTTTATCCAACTCATCCCTTGACATCGTGCTTCACGATACATACTATGTAGTAGCCCATTTCCACTATGTTCTATCAATGGGAGCAGTGTTTGCTATCATAGCAGGATTTGTTCACTGATTCCCATTATTTTCAGGCTTCACCCTAGATGACACATGAGCAAAAGCCCACTTCGCCATCATATTCGTAGGAGTAAACATAACATTCTTCCCTCAACATTTCCTGGGCCTTTCAGGAATACCACGACGCTACTCAGACTACCCAGATGCTTACACCACATGAAACACTGTCTCTTCTATAGGATCATTTATTTCACTAACAGCTGTTCTCATCATGATCTTTATAATTTGAGAGGCCTTTGCTTCAAAACGAGAAGTAATATCAGTATCGTATGCTTCAACAAATTTAGAATGACTTCATGGCTGCCCTCCACCATATCACACATTCGAGGAACCAACCTATGTAAAAGTAAAATAAGAAAGGAAGGAATCGAACCCCCTAAAATTGGTTTCAAGCCAATCTCATATCCTATATGTCTTTCTCAATAAGATATTAGTAAAATCAATTACATAACTTTGTCAAAGTTAAATTATAGATCAATAATCTATATATCTTATATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTAATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTATATCATCTCGCTAATATTAACAACAAAACTAACACATACAAGCACAATAGATGCACAAGAAGTTGAAACCATTTGAACTATTCTACCAGCTGTAATCCTTATCATAATTGCTCTCCCCTCTCTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATAGGGCACCAATGATACTGAAGCTACGAATATACTGACTATGAAGACCTATGCTTTGATTCATATATAATCCCAACAAACGACCTAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAACCGAGTCGTTCTGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCCAGGCCGACTAAATCAAGCAACAGTAACATCAAACCGACCAGGGTTATTCTATGGCCAATGCTCTGAAATTTGTGGATCTAACCATAGCTTTATGCCCATTGTCCTAGAAATGGTTCCACTAAAATATTTCGAAAACTGATCTGCTTCAATAATTTAATTTCACTATGAAGCTAAGAGCGTTAACCTTTTAAGTTAAAGTTAGAGACCTTAAAATCTCCATAGTGATATGCCACAACTAGATACATCAACATGATTTATCACAATTATCTCATCAATAATTACCCTATTTATCTTATTTCAACTAAAAGTCTCATCACAAACATTCCCACTGGCACCTTCACCAAAATCACTAACAACCATAAAAGTAAAAACCCCTTGAGAATTAAAATGAACGAAAATCTATTTGCCTCATTCATTACCCCAACAATAATAGGATTCCCAATCGTTGTAGCCATCATTATATTTCCTTCAATCCTATTCCCATCCTCAAAACGCCTAATCAACAACCGTCTCCATTCTTTCCAACACTGACTAGTTAAACTTATTATCAAACAAATAATGCTAATCCACACACCAAAAGGACGAACATGAACCCTAATAATTGTTTCCCTAATCATATTTATTGGATCAACAAATCTCCTAGGCCTTTTACCACATACATTTACACCTACTACCCAACTATCCATAAATCTAAGTATAGCCATTCCACTATGAGCTGGAGCCGTAATTACAGGCTTCCGACACAAACTAAAAAGCTCACTTGCCCACTTCCTTCCACAAGGAACTCCAATTTCACTAATTCCAATACTTATTATTATTGAAACAATTAGCCTATTTATTCAACCAATGGCATTAGCAGTCCGGCTTACAGCTAACATTACTGCAGGACACTTATTAATACACCTAATCGGAGGAGCTACTCTAGTATTAATAAATATTAGCCCACCAACAGCTACCATTACATTTATTATTTTACTTCTACTCACAATTCTAGAATTTGCAGTAGCATTAATTCAAGCCTACGTATTCACCCTCCTAGTAAGCCTATATCTACATGATAATACATAATGACCCACCAAACTCATGCATATCACATAGTTAATCCAAGTCCATGACCATTAACTGGAGCCTTTTCAGCCCTCCTTCTAACATCAGGTCTAGTAATATGATTTCACTATAATTCAATTACACTATTAACCCTTGGCCTACTCACCAATATCCTCACAATATATCAATGATGACGAGACGTAATTCGTGAAGGAACCTACCAAGGCCACCACACTCCTATTGTACAAAAAGGACTACGATATGGTATAATTCTATTCATCGTCTCGGAAGTATTTTTCTTTGCAGGATTCTTCTGAGCGTTCTATCATTCTAGCCTCGTACCAACACATGATCTAGGAGGCTGCTGACCTCCAACAGGAATTTCACCACTTAACCCTCTAGAAGTCCCACTACTTAATACTTCAGTACTTCTAGCATCAGGTGTTTCAATTACATGAGCTCATCATAGCCTTATAGAAGGTAAACGAAACCACATAAATCAAGCCCTACTAATTACCATTATACTAGGACTTTACTTCACCATCCTCCAAGCTTCAGAATACTTTGAAACATCATTCTCCATTTCAGATGGTATCTATGGTTCTACATTCTTCATGGCTACTGGATTCCATGGACTCCATGTAATTATTGGATCAACATTCCTTATTGTTTGCCTACTACGACAACTAAAATTTCACTTCACATCAAAACATCACTTCGGATTTGAAGCCGCAGCATGATACTGACATTTTGTAGACGTAGTCTGACTTTTCCTATACGTCTCCATTTATTGATGAGGATCTTACTCCCTTAGTATAATTAATATAACTGACTTCCAATTAGTAGATTCTGAATAAACCCAGAAGAGAGTAATTAACCTGTACACTGTTATCTTCATTAATATTTTATTATCCCTAACGCTAATTCTAGTTGCATTCTGACTCCCCCAAATAAATCTGTACTCAGAAAAAGCAAATCCATATGAATGCGGATTCGACCCTACAAGCTCTGCACGTCTACCATTCTCAATAAAATTTTTCTTGGTAGCAATTACATTTCTATTATTTGACCTAGAAATTGCTCTTCTACTTCCACTACCATGAGCAATTCAAACAATTAAAACCTCTACTATAATAATTATAGCCTTTATTCTAGTCACAATTCTATCTCTAGGCCTAGCATATGAATGAACACAAAAAGGATTAGAATGAACAGAGTAAATGGTAATTAGTTTAAAAAAAATTAATGATTTCGACTCATTAGATTATGATGATGTTCATAATTACCAATATGCCATCTACCTTCTTCAACCTCACCATAGCCTTCTCACTATCACTTCTAGGGACACTTATATTTCGCTCTCACCTAATATCCACATTACTATGCCTGGAAGGCATAGTATTATCCTTATTTA" From 05bc0898f17971b2300a1111f711b858508a3898 Mon Sep 17 00:00:00 2001 From: George He Date: Mon, 31 Oct 2016 12:32:37 -0700 Subject: [PATCH 052/136] Variant end tracking --- src/main/data/vcf.js | 9 +++++++-- src/main/viz/VariantTrack.js | 2 +- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/src/main/data/vcf.js b/src/main/data/vcf.js index 558eb623..c0307889 100644 --- a/src/main/data/vcf.js +++ b/src/main/data/vcf.js @@ -17,6 +17,7 @@ export type Variant = { ref: string; alt: string; vcfLine: string; + end: number; } // This is a minimally-parsed line for facilitating binary search. @@ -41,13 +42,17 @@ function extractLocusLine(vcfLine: string): LocusLine { function extractVariant(vcfLine: string): Variant { var parts = vcfLine.split('\t'); - + var end = Number(parts[1]) + parts[3].length; + if (5 >= parts.length) { + end = parts[5] + } return { contig: parts[0], position: Number(parts[1]), ref: parts[3], alt: parts[4], - vcfLine + vcfLine: vcfLine, + end: end }; } diff --git a/src/main/viz/VariantTrack.js b/src/main/viz/VariantTrack.js index d19b8c8c..709428ca 100644 --- a/src/main/viz/VariantTrack.js +++ b/src/main/viz/VariantTrack.js @@ -82,7 +82,7 @@ class VariantTrack extends React.Component { ctx.fillStyle = style.BASE_COLORS[variant.alt]; ctx.strokeStyle = style.BASE_COLORS[variant.ref]; var x = Math.round(scale(variant.position)); - var width = Math.round(scale(variant.position + 1)) - 1 - x; + var width = Math.round(scale(variant.end)) - x; ctx.fillRect(x - 0.2, y - 0.2, width, style.VARIANT_HEIGHT); ctx.strokeRect(x - 0.2, y - 0.2, width, style.VARIANT_HEIGHT); ctx.popObject(); From 14d3f912b564a3419f1376ddf13255dfab298f73 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 1 Nov 2016 23:36:25 -0700 Subject: [PATCH 053/136] completed coverage tracks and binning --- src/main/RemoteRequest.js | 20 ++-- src/main/ResolutionCache.js | 32 +++-- src/main/data/FeatureEndpoint.js | 2 +- src/main/data/GeneEndpoint.js | 7 +- src/main/data/GenotypeEndpoint.js | 6 +- src/main/data/Sequence.js | 5 +- src/main/data/VariantEndpoint.js | 2 +- src/main/pileup.js | 1 - src/main/sources/CoverageDataSource.js | 53 ++++++--- src/main/sources/FeatureDataSource.js | 5 +- src/main/sources/GeneDataSource.js | 2 +- src/main/sources/GenotypeDataSource.js | 2 +- src/main/sources/ReferenceDataSource.js | 2 +- src/main/sources/VariantDataSource.js | 7 +- src/main/viz/CoverageTrack.js | 116 +++++++++++++------ src/main/viz/PileupTrack.js | 21 +--- src/main/viz/TiledCanvas.js | 3 +- src/main/viz/pileuputils.js | 17 +++ src/test/RemoteRequest-test.js | 2 +- src/test/sources/ReferenceDataSource-test.js | 1 - style/pileup.css | 6 +- test-data/chr17-coverage.json | 42 ++++--- 22 files changed, 226 insertions(+), 128 deletions(-) diff --git a/src/main/RemoteRequest.js b/src/main/RemoteRequest.js index d5a1fcf2..f362c670 100644 --- a/src/main/RemoteRequest.js +++ b/src/main/RemoteRequest.js @@ -10,6 +10,7 @@ import Q from 'q'; import ContigInterval from './ContigInterval'; var BASE_PAIRS_PER_FETCH = 1000; +var MONSTER_REQUEST = 5000000; class RemoteRequest { url: string; @@ -43,7 +44,7 @@ class RemoteRequest { var length = range.stop() - range.start(); if (length <= 0) { return Q.reject(`Requested <0 interval (${length}) from ${this.url}`); - } else if (length > 5000000) { + } else if (length > MONSTER_REQUEST) { throw `Monster request: Won't fetch ${length} sized ranges from ${this.url}`; } // get endpoint @@ -61,9 +62,9 @@ class RemoteRequest { xhr.responseType = 'json'; xhr.setRequestHeader('Content-Type', 'application/json'); - return this.promiseXHR(xhr).then(json => { - // extract response from promise - return json[0]; + return this.promiseXHR(xhr).then(e => { + // send back response and status + return e[0]; }); } @@ -76,14 +77,14 @@ class RemoteRequest { // Wrapper to convert XHRs to Promises. // The promised values are the response (e.g. an ArrayBuffer) and the Event. - promiseXHR(xhr: XMLHttpRequest): Q.Promise<[any, Event]> { + promiseXHR(xhr: XMLHttpRequest): Q.Promise<[any]> { var url = this.url; var deferred = Q.defer(); xhr.addEventListener('load', function(e) { if (this.status >= 400) { deferred.reject(`Request for ${url} failed with status: ${this.status} ${this.statusText}`); } else { - deferred.resolve([this.response, e]); + deferred.resolve([this]); } }); xhr.addEventListener('error', function(e) { @@ -95,4 +96,9 @@ class RemoteRequest { } } -module.exports = RemoteRequest; +module.exports = { + RemoteRequest, + MONSTER_REQUEST: MONSTER_REQUEST +}; + +//module.exports = RemoteRequest; diff --git a/src/main/ResolutionCache.js b/src/main/ResolutionCache.js index 37d93bf9..d9ee0626 100644 --- a/src/main/ResolutionCache.js +++ b/src/main/ResolutionCache.js @@ -11,11 +11,16 @@ import _ from 'underscore'; import Interval from './Interval'; import ContigInterval from './ContigInterval'; +type ResolutionObject = { + resolution: number; + object: T; +} + class ResolutionCache { coveredRanges: ResolutionCacheKey[]; - cache: {[key: string]: T}; + cache: {[key: string]: ResolutionObject}; // used to filter out elements in the cache based on resolution. - filterFunction: Function; // should take form (range: ContigInterval, T, resolution: ?number) => boolean; + filterFunction: Function; // should take form (range: ContigInterval, T) => boolean; keyFunction: Function; // should take form (d: T) => string; constructor(filterFunction: Function, keyFunction: Function) { @@ -28,11 +33,13 @@ class ResolutionCache { // gets data from cache at the Resolution defined by the interval get(range: ContigInterval, resolution: ?number): T[] { if (!range) return []; - var res = _.filter(this.cache, d => this.filterFunction(range, d, resolution)); - - // if range is not fully covered, give warning but still return available data - if (this.coversRange(range, resolution)) { - console.warn("Warning: Resolution Cache does not fully cover region. Returning available data..."); + var res = {}; + if (!resolution) { + res = _.map(_.filter(this.cache, d => this.filterFunction(range, d.object)), + obj => obj.object); + } else { + res = _.map(_.filter(this.cache, d => this.filterFunction(range, d.object) && d.resolution == resolution), + obj => obj.object); } return res; @@ -48,10 +55,17 @@ class ResolutionCache { } // puts data in cache - put(value: T) { + put(value: T, resolution: ?number) { + if (!resolution) { + resolution = 1; + } + var resObject = { + resolution: resolution, + object: value + }; var key = this.keyFunction(value); if (!this.cache[key]) { - this.cache[key] = value; + this.cache[key] = resObject; } } diff --git a/src/main/data/FeatureEndpoint.js b/src/main/data/FeatureEndpoint.js index d0de28f3..321953c7 100644 --- a/src/main/data/FeatureEndpoint.js +++ b/src/main/data/FeatureEndpoint.js @@ -7,7 +7,7 @@ import Q from 'q'; import ContigInterval from '../ContigInterval'; -import type RemoteRequest from '../RemoteRequest'; +import type {RemoteRequest} from '../RemoteRequest'; export type Feature = { id: string; diff --git a/src/main/data/GeneEndpoint.js b/src/main/data/GeneEndpoint.js index a63f954a..b1ab5f68 100644 --- a/src/main/data/GeneEndpoint.js +++ b/src/main/data/GeneEndpoint.js @@ -7,7 +7,7 @@ import Q from 'q'; import type {Gene} from '../sources/BigBedDataSource'; -import type RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; import Interval from '../Interval'; import ContigInterval from '../../main/ContigInterval'; @@ -49,8 +49,9 @@ class GeneEndpoint { } getGenesInRange(range: ContigInterval): Q.Promise { - return this.remoteRequest.get(range).then(object => { - var d = extractGenes(object); + return this.remoteRequest.get(range).then(e => { + var genes = e.response; + var d = extractGenes(genes); return d; }); } diff --git a/src/main/data/GenotypeEndpoint.js b/src/main/data/GenotypeEndpoint.js index d5c04431..f29fe048 100644 --- a/src/main/data/GenotypeEndpoint.js +++ b/src/main/data/GenotypeEndpoint.js @@ -7,7 +7,7 @@ import ContigInterval from '../ContigInterval'; import Q from 'q'; -import type RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; import type {Variant} from './vcf'; export type Genotype = { @@ -23,8 +23,8 @@ class GenotypeEndpoint { } getFeaturesInRange(range: ContigInterval): Q.Promise { - return this.remoteRequest.get(range).then(object => { - return object; + return this.remoteRequest.get(range).then(e => { + return e.response; }); } } diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index c126bf3c..1edcc0c5 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -7,7 +7,7 @@ import Q from 'q'; import ContigInterval from '../ContigInterval'; -import type RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; export type SequenceRecord = { name: string; @@ -44,7 +44,8 @@ class Sequence { if (start > stop) { throw `Requested a range with start > stop (${start}, ${stop})`; } - return this.remoteRequest.get(range).then(sequence => { + return this.remoteRequest.get(range).then(e => { + var sequence = e.response; var d = sequence.substring(start, (stop-start + 1)); return d; }); diff --git a/src/main/data/VariantEndpoint.js b/src/main/data/VariantEndpoint.js index cf6447c0..1222c817 100644 --- a/src/main/data/VariantEndpoint.js +++ b/src/main/data/VariantEndpoint.js @@ -7,7 +7,7 @@ import ContigInterval from '../ContigInterval'; import Q from 'q'; -import type RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; import type {Variant} from './vcf'; class VariantEndpoint { diff --git a/src/main/pileup.js b/src/main/pileup.js index 89c20677..3b8d55b0 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -16,7 +16,6 @@ import ReferenceDataSource from './sources/ReferenceDataSource'; import BigBedDataSource from './sources/BigBedDataSource'; import VcfDataSource from './sources/VcfDataSource'; import VariantDataSource from './sources/VariantDataSource'; -import GeneDataSource from './sources/GeneDataSource'; import GenotypeDataSource from './sources/GenotypeDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; diff --git a/src/main/sources/CoverageDataSource.js b/src/main/sources/CoverageDataSource.js index 4869fa96..e2f00fc7 100644 --- a/src/main/sources/CoverageDataSource.js +++ b/src/main/sources/CoverageDataSource.js @@ -15,7 +15,7 @@ import _ from 'underscore'; import {Events} from 'backbone'; import {ResolutionCache} from '../ResolutionCache'; import ContigInterval from '../ContigInterval'; -import RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; export type CoverageDataSource = { maxCoverage: (range: ContigInterval) => number; @@ -30,24 +30,29 @@ var BASE_PAIRS_PER_FETCH = 1000; export type PositionCount = { contig: string; - position: number; + start: number; + end: number; count: number; } function keyFunction(p: PositionCount): string { - return `${p.contig}:${p.position}`; + return `${p.contig}:${p.start}-${p.end}`; } -function filterFunction(range: ContigInterval, p: PositionCount, resolution: ?number): boolean { - // if resolution is specified, select results based on resolution and position start site - if (resolution) return (range.chrContainsLocus(p.contig, p.position) && p.position % resolution == 0); - else return range.chrContainsLocus(p.contig, p.position); +function filterFunction(range: ContigInterval, p: PositionCount): boolean { + return range.chrContainsLocus(p.contig, p.start); } function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource { var cache: ResolutionCache = new ResolutionCache(filterFunction, keyFunction); + function notifyFailure(message: string) { + o.trigger('networkfailure', message); + o.trigger('networkdone'); + console.warn(message); + } + function maxCoverage(range: ContigInterval, resolution: ?number): number { var positions: number[] = cache.get(range, resolution).map(r => r.count); var maxCoverage = Math.max.apply(Math, positions); @@ -64,18 +69,32 @@ function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource } // modify endpoint to calculate coverage using binning - var basePairsPerBin = ResolutionCache.getResolution(interval.interval); - var endpointModifier = `binning=${basePairsPerBin}`; + var resolution = ResolutionCache.getResolution(interval.interval); + var endpointModifier = `binning=${resolution}`; // Cover the range immediately to prevent duplicate fetches. cache.coverRange(interval); - return remoteSource.getFeaturesInRange(interval, endpointModifier).then(positions => { - positions.forEach(p => cache.put({ - "contig": range.contig, - "position": p.position, - "count": p.count - })); - o.trigger('newdata', interval); + var numRequests = 1; + o.trigger('networkprogress', {numRequests}); + return remoteSource.getFeaturesInRange(interval, endpointModifier).then(json => { + var response = json.response; + if (json.status >= 400) { + notifyFailure(json.status + ' ' + json.statusText + ' ' + JSON.stringify(response)); + } else { + if (response.errorCode) { + notifyFailure('Error from CoverageDataSource: ' + JSON.stringify(response)); + } else { + // add new data to cache + response.forEach(p => cache.put({ + "contig": range.contig, + "start": p.start, + "end": p.end, + "count": p.count + }, resolution)); + o.trigger('newdata', interval); + } + } + o.trigger('networkdone'); }); } @@ -83,7 +102,7 @@ function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource resolution: ?number): PositionCount[] { if (!range) return []; var data = cache.get(range, resolution); - var sorted = data.sort((a, b) => a.position - b.position); + var sorted = data.sort((a, b) => a.start - b.start); return sorted; } diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index b84ea697..91617513 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -20,7 +20,7 @@ import _ from 'underscore'; import {Events} from 'backbone'; import ContigInterval from '../ContigInterval'; -import RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; import FeatureEndpoint from '../data/FeatureEndpoint'; import type {Feature} from '../data/FeatureEndpoint'; @@ -78,7 +78,8 @@ function createFromFeatureUrl(remoteSource: FeatureEndpoint): FeatureDataSource // "Cover" the range immediately to prevent duplicate fetches. coveredRanges.push(interval); coveredRanges = ContigInterval.coalesce(coveredRanges); - return remoteSource.getFeaturesInRange(interval).then(features => { + return remoteSource.getFeaturesInRange(interval).then(e => { + var features = e.response; features.forEach(feature => addFeature(feature)); o.trigger('newdata', interval); }); diff --git a/src/main/sources/GeneDataSource.js b/src/main/sources/GeneDataSource.js index 1a027bdd..a0795167 100644 --- a/src/main/sources/GeneDataSource.js +++ b/src/main/sources/GeneDataSource.js @@ -10,7 +10,7 @@ import {Events} from 'backbone'; import ContigInterval from '../ContigInterval'; import Interval from '../Interval'; import type { BigBedSource, Gene } from './BigBedDataSource'; -import RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; import GeneEndpoint from '../data/GeneEndpoint'; var BASE_PAIRS_PER_FETCH = 5000; diff --git a/src/main/sources/GenotypeDataSource.js b/src/main/sources/GenotypeDataSource.js index c32274b3..5d581fc2 100644 --- a/src/main/sources/GenotypeDataSource.js +++ b/src/main/sources/GenotypeDataSource.js @@ -22,7 +22,7 @@ import _ from 'underscore'; import {Events} from 'backbone'; import ContigInterval from '../ContigInterval'; -import RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; import GenotypeEndpoint from '../data/GenotypeEndpoint'; export type GenotypeDataSource = { diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index ebea74b9..ff63d954 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -24,7 +24,7 @@ import Sequence from '../data/Sequence'; import type {SequenceRecord} from '../data/Sequence'; import SequenceStore from '../SequenceStore'; import type {TwoBitSource} from './TwoBitDataSource'; -import RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; import utils from '../utils'; diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index d7d13649..ed9a4c66 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -23,7 +23,7 @@ import {Events} from 'backbone'; import ContigInterval from '../ContigInterval'; import type {VcfDataSource} from './VcfDataSource'; -import RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; import VariantEndpoint from '../data/VariantEndpoint'; var BASE_PAIRS_PER_FETCH = 1000; @@ -67,8 +67,9 @@ function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { // "Cover" the range immediately to prevent duplicate fetches. coveredRanges.push(interval); coveredRanges = ContigInterval.coalesce(coveredRanges); - return remoteSource.getFeaturesInRange(interval).then(object => { - object.forEach(variant => addVariant(variant)); + return remoteSource.getFeaturesInRange(interval).then(e => { + var variants = e.response; + variants.forEach(variant => addVariant(variant)); o.trigger('newdata', interval); }); } diff --git a/src/main/viz/CoverageTrack.js b/src/main/viz/CoverageTrack.js index 59e949c6..8fbe0a1a 100644 --- a/src/main/viz/CoverageTrack.js +++ b/src/main/viz/CoverageTrack.js @@ -5,11 +5,12 @@ 'use strict'; import type Interval from '../Interval'; -import GA4GHDataSource from '../sources/GA4GHDataSource'; import type {TwoBitSource} from '../sources/TwoBitDataSource'; import type {DataCanvasRenderingContext2D} from 'data-canvas'; import type {Scale} from './d3utils'; import type {CoverageDataSource} from '../sources/CoverageDataSource'; +import type {VizProps} from '../VisualizationWrapper'; +import RemoteRequest from '../RemoteRequest'; import type {PositionCount} from '../sources/CoverageDataSource'; import React from 'react'; @@ -22,17 +23,8 @@ import canvasUtils from './canvas-utils'; import style from '../style'; import ContigInterval from '../ContigInterval'; import TiledCanvas from './TiledCanvas'; - - -type Props = { - width: number; - height: number; - range: GenomeRange; - source: CoverageDataSource; - options: { - vafColorThreshold: number - } -}; +import type {State, NetworkStatus} from './pileuputils'; +import {formatStatus} from './pileuputils'; class CoverageTiledCanvas extends TiledCanvas { @@ -42,7 +34,6 @@ class CoverageTiledCanvas extends TiledCanvas { constructor(source: CoverageDataSource, height: number, options: Object) { super(); - this.source = source; this.height = Math.max(1, height); this.options = options; @@ -71,12 +62,18 @@ class CoverageTiledCanvas extends TiledCanvas { render(ctx: DataCanvasRenderingContext2D, xScale: (x: number)=>number, range: ContigInterval, + originalRange: ?ContigInterval, resolution: ?number) { var relaxedRange = new ContigInterval( range.contig, Math.max(1, range.start() - 1), range.stop() + 1); var bins = this.source.getCoverageInRange(relaxedRange, resolution); - var yScale = this.yScaleForRef(range, resolution); + // if original range is not set, use tiled range which is a subset of originalRange + if (!originalRange) { + originalRange = range; + } + + var yScale = this.yScaleForRef(originalRange, resolution); renderBars(ctx, xScale, yScale, relaxedRange, bins, resolution, this.options); } } @@ -92,58 +89,98 @@ function renderBars(ctx: DataCanvasRenderingContext2D, options: Object) { if (_.isEmpty(bins)) return; + // make sure bins are sorted by position + bins = _.sortBy(bins, x => x.start); + var barWidth = xScale(1) - xScale(0); var showPadding = (barWidth > style.COVERAGE_MIN_BAR_WIDTH_FOR_GAP); var padding = showPadding ? 1 : 0; - var binPos = function(pos: number, count: number) { + var binPos = function(ps: PositionCount) { // Round to integer coordinates for crisp lines, without aliasing. - var barX1 = Math.round(xScale(1 + pos)), - barX2 = Math.round(xScale(1 + resolution + pos)) - padding, - barY = Math.round(yScale(count)); + var barX1 = Math.round(xScale(ps.start)), + barX2 = Math.max(barX1 + 2, Math.round(xScale(ps.end)) - padding), // make sure bar is >= 1px + barY = Math.round(yScale(ps.count)); return {barX1, barX2, barY}; }; var vBasePosY = yScale(0); // the very bottom of the canvas var start = range.start(), stop = range.stop(); - var first = bins.filter(bin => bin.position == start); - // find first bin in dataset and move to that position. - let {barX1} = binPos(start, (!_.isEmpty(first)) ? first[0].count : 0); + + // go to the first bin in dataset (specified by the smallest start position) ctx.fillStyle = style.COVERAGE_BIN_COLOR; ctx.beginPath(); - ctx.moveTo(barX1, vBasePosY); bins.forEach(bin => { ctx.pushObject(bin); - let {barX1, barX2, barY} = binPos(bin.position, bin.count); - ctx.lineTo(barX1, barY); - ctx.lineTo(barX2, barY); - if (showPadding) { - ctx.lineTo(barX2, vBasePosY); - ctx.lineTo(barX2 + 1, vBasePosY); - } + let {barX1, barX2, barY} = binPos(bin); + ctx.moveTo(barX1, vBasePosY); // start at bottom left of bar + ctx.lineTo(barX1, barY); // left edge of bar + ctx.lineTo(barX2, barY); // top of bar + ctx.lineTo(barX2, vBasePosY); // right edge of the right bar. ctx.popObject(); }); - let {barX2} = binPos(stop, (stop in bins) ? bins[stop].count : 0); - ctx.lineTo(barX2, vBasePosY); // right edge of the right bar. ctx.closePath(); ctx.fill(); } class CoverageTrack extends React.Component { - props: Props; - state: void; + props: VizProps & { source: CoverageDataSource }; + state: State; static defaultOptions: Object; tiles: CoverageTiledCanvas; - constructor(props: Props) { + constructor(props: VizProps) { super(props); + this.state = { + networkStatus: null + }; } render(): any { - return ; + // These styles allow vertical scrolling to see the full pileup. + // Adding a vertical scrollbar shrinks the visible area, but we have to act + // as though it doesn't, since adjusting the scale would put it out of sync + // with other tracks. + var containerStyles = { + 'height': '100%' + }; + var statusEl = null, + networkStatus = this.state.networkStatus; + if (networkStatus) { + var message = formatStatus(networkStatus); + statusEl = ( +
+
+ Loading coverage… ({message}) +
+
+ ); + } + + var rangeLength = this.props.range.stop - this.props.range.start; + // If range is too large, do not render 'canvas' + if (rangeLength > RemoteRequest.MONSTER_REQUEST) { + return ( +
+
+ Zoom in to see coverage +
+ +
+ ); + } else { + return ( +
+ {statusEl} +
+ +
+
+ ); + } } getScale(): Scale { @@ -165,11 +202,16 @@ class CoverageTrack extends React.Component { } this.visualizeCoverage(); }); - this.props.source.on('newdata', range => { this.tiles.invalidateRange(range); this.visualizeCoverage(); }); + this.props.source.on('networkprogress', e => { + this.setState({networkStatus: e}); + }); + this.props.source.on('networkdone', e => { + this.setState({networkStatus: null}); + }); } componentDidUpdate(prevProps: any, prevState: any) { @@ -197,7 +239,7 @@ class CoverageTrack extends React.Component { [0, Math.round(axisMax / 2), axisMax].forEach(tick => { // Draw a line indicating the tick ctx.pushObject({value: tick, type: 'tick'}); - var tickPosY = Math.round(yScale(tick))+10; // add 9 for offset compared to printed tiles + var tickPosY = Math.round(yScale(tick)); ctx.strokeStyle = style.COVERAGE_FONT_COLOR; canvasUtils.drawLine(ctx, 0, tickPosY, style.COVERAGE_TICK_LENGTH, tickPosY); ctx.popObject(); diff --git a/src/main/viz/PileupTrack.js b/src/main/viz/PileupTrack.js index edb13410..f2083eb7 100644 --- a/src/main/viz/PileupTrack.js +++ b/src/main/viz/PileupTrack.js @@ -7,7 +7,6 @@ import type {Strand, Alignment, AlignmentDataSource} from '../Alignment'; import GA4GHDataSource from '../sources/GA4GHDataSource'; import type {TwoBitSource} from '../sources/TwoBitDataSource'; -import type {BasePair} from './pileuputils'; import type {VisualAlignment, VisualGroup, InsertStats} from './PileupCache'; import type {DataCanvasRenderingContext2D} from 'data-canvas'; import type Interval from '../Interval'; @@ -20,7 +19,8 @@ import _ from 'underscore'; import scale from '../scale'; import d3utils from './d3utils'; -import {CigarOp} from './pileuputils'; +import type {BasePair, State, NetworkStatus} from './pileuputils'; +import {CigarOp, formatStatus} from './pileuputils'; import ContigInterval from '../ContigInterval'; import DisplayMode from './DisplayMode'; import PileupCache from './PileupCache'; @@ -236,12 +236,6 @@ function opacityForQuality(quality: number): number { return Math.min(1.0, alpha); } -type NetworkStatus = {numRequests?: number, status?: string}; -type State = { - networkStatus: ?NetworkStatus; -}; - - class PileupTrack extends React.Component { props: VizProps & { source: AlignmentDataSource }; state: State; @@ -270,7 +264,7 @@ class PileupTrack extends React.Component { var statusEl = null, networkStatus = this.state.networkStatus; if (networkStatus) { - var message = this.formatStatus(networkStatus); + var message = formatStatus(networkStatus); statusEl = (
@@ -303,15 +297,6 @@ class PileupTrack extends React.Component { } } - formatStatus(status: NetworkStatus): string { - if (status.numRequests) { - var pluralS = status.numRequests > 1 ? 's' : ''; - return `issued ${status.numRequests} request${pluralS}`; - } else if (status.status) { - return status.status; - } - throw 'invalid'; - } componentDidMount() { this.cache = new PileupCache(this.props.referenceSource, this.props.options.viewAsPairs); diff --git a/src/main/viz/TiledCanvas.js b/src/main/viz/TiledCanvas.js index 108cf949..599a5d90 100644 --- a/src/main/viz/TiledCanvas.js +++ b/src/main/viz/TiledCanvas.js @@ -52,7 +52,7 @@ class TiledCanvas { var resolution = ResolutionCache.getResolution(tile.originalRange.interval); - this.render(dtx, sc, range, resolution); + this.render(dtx, sc, range, tile.originalRange, resolution); } // Create (and render) new tiles to fill the gaps. @@ -130,6 +130,7 @@ class TiledCanvas { render(dtx: DataCanvasRenderingContext2D, scale: (x: number)=>number, range: ContigInterval, + originalRange: ?ContigInterval, resolution: ?number): void { throw 'Not implemented'; } diff --git a/src/main/viz/pileuputils.js b/src/main/viz/pileuputils.js index 34300390..2d4c0e79 100644 --- a/src/main/viz/pileuputils.js +++ b/src/main/viz/pileuputils.js @@ -206,9 +206,26 @@ function getOpInfo(read: Alignment, referenceSource: Object): OpInfo { }; } +// State information. Used in viz +export type NetworkStatus = {numRequests?: number, status?: string}; +export type State = { + networkStatus: ?NetworkStatus; +}; + +function formatStatus(status: NetworkStatus): string { + if (status.numRequests) { + var pluralS = status.numRequests > 1 ? 's' : ''; + return `issued ${status.numRequests} request${pluralS}`; + } else if (status.status) { + return status.status; + } + throw 'invalid'; +} + module.exports = { pileup, addToPileup, getOpInfo, + formatStatus, CigarOp }; diff --git a/src/test/RemoteRequest-test.js b/src/test/RemoteRequest-test.js index 9b5b1a99..1241f335 100644 --- a/src/test/RemoteRequest-test.js +++ b/src/test/RemoteRequest-test.js @@ -5,7 +5,7 @@ import {expect} from 'chai'; import sinon from 'sinon'; -import RemoteRequest from '../main/RemoteRequest'; +import {RemoteRequest} from '../main/RemoteRequest'; import RemoteFile from '../main/RemoteFile'; import ContigInterval from '../main/ContigInterval'; diff --git a/src/test/sources/ReferenceDataSource-test.js b/src/test/sources/ReferenceDataSource-test.js index 3f78a42e..7aad52a8 100644 --- a/src/test/sources/ReferenceDataSource-test.js +++ b/src/test/sources/ReferenceDataSource-test.js @@ -69,7 +69,6 @@ describe('ReferenceDataSource', function() { 'chrM:3': null }); var str = source.getRangeAsString(range); - console.log(str); expect(str).to.equal('....'); source.on('newdata', () => { diff --git a/style/pileup.css b/style/pileup.css index 049cb3cc..80c62a2b 100644 --- a/style/pileup.css +++ b/style/pileup.css @@ -195,16 +195,16 @@ stroke: black; stroke-width: 2; } -.pileup .network-status { +.network-status { height: 100%; width: 100%; display: flex; align-items: center; justify-content: center; position: relative; - top: 30px; + top: 20px; } -.pileup .network-status-message { +.network-status-message { padding: 4px 8px; width: auto; background: #eee; diff --git a/test-data/chr17-coverage.json b/test-data/chr17-coverage.json index 36a533f0..51f62f1b 100644 --- a/test-data/chr17-coverage.json +++ b/test-data/chr17-coverage.json @@ -1,49 +1,61 @@ [{ - "contig": "17", - "position": 10, - "count": 50 + "contig": "17", + "start": 10, + "end": 11, + "count": 50 }, { "contig": "17", - "position": 11, - "count": 52 + "start": 11, + "end": 12, + "count": 52 }, { "contig": "17", - "position": 12, + "start": 12, + "end": 13, "count": 54 }, { "contig": "17", - "position": 13, + "start": 13, + "end": 14, "count": 56 }, { "contig": "17", - "position": 14, + "start": 14, + "end": 15, "count": 58 }, { "contig": "17", - "position": 15, + "start": 15, + "end": 16, "count": 58 }, { "contig": "17", - "position": 16, + "start": 16, + "end": 17, "count": 58 }, { "contig": "17", - "position": 17, + "start": 17, + "end": 18, "count": 58 }, { "contig": "17", - "position": 18, + "start": 18, + "end": 19, "count": 68 }, { "contig": "17", - "position": 19, + "start": 19, + "end": 20, "count": 72 }, { "contig": "17", - "position": 20, + "start": 20, + "end": 21, "count": 75 }, { "contig": "17", - "position": 21, + "start": 21, + "end": 22, "count": 62 }] From 402716a0aef106e4c965b6fc2ee9000c820288bc Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sun, 11 Dec 2016 01:48:10 +0100 Subject: [PATCH 054/136] fixed reference offset visualization --- src/main/data/Sequence.js | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index 1edcc0c5..760cb329 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -45,9 +45,7 @@ class Sequence { throw `Requested a range with start > stop (${start}, ${stop})`; } return this.remoteRequest.get(range).then(e => { - var sequence = e.response; - var d = sequence.substring(start, (stop-start + 1)); - return d; + return e.response; }); } From 2aa9fd7edbddda78e71360b55a0226d9b5997c84 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Mon, 19 Dec 2016 20:22:13 +0000 Subject: [PATCH 055/136] added checks for null data return types --- src/main/sources/FeatureDataSource.js | 3 ++- src/main/sources/GeneDataSource.js | 5 +++-- src/main/sources/GenotypeDataSource.js | 3 ++- src/main/sources/VariantDataSource.js | 3 ++- src/test/sources/FeatureDataSource-test.js | 22 ++++++++++++++++++++- src/test/sources/GenotypeDataSource-test.js | 21 +++++++++++++++++++- src/test/sources/VariantDataSource-test.js | 18 +++++++++++++++++ 7 files changed, 68 insertions(+), 7 deletions(-) diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index 91617513..34db6803 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -80,7 +80,8 @@ function createFromFeatureUrl(remoteSource: FeatureEndpoint): FeatureDataSource coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getFeaturesInRange(interval).then(e => { var features = e.response; - features.forEach(feature => addFeature(feature)); + if (features != null) + features.forEach(feature => addFeature(feature)); o.trigger('newdata', interval); }); } diff --git a/src/main/sources/GeneDataSource.js b/src/main/sources/GeneDataSource.js index a0795167..3ac2a31e 100644 --- a/src/main/sources/GeneDataSource.js +++ b/src/main/sources/GeneDataSource.js @@ -61,9 +61,10 @@ function createFromGeneUrl(remoteSource: GeneEndpoint): BigBedSource { coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getGenesInRange(interval).then(genes => { + if (genes != null) genes.forEach(gene => addGene(gene)); - //we have new data from our internal block range - o.trigger('newdata', interval); + //we have new data from our internal block range + o.trigger('newdata', interval); }); } diff --git a/src/main/sources/GenotypeDataSource.js b/src/main/sources/GenotypeDataSource.js index 5d581fc2..4eab2256 100644 --- a/src/main/sources/GenotypeDataSource.js +++ b/src/main/sources/GenotypeDataSource.js @@ -79,7 +79,8 @@ function createFromGenotypeUrl(remoteSource: GenotypeEndpoint): GenotypeDataSour coveredRanges.push(interval); coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getFeaturesInRange(interval).then(genotypes => { - genotypes.forEach(genotype => addGenotype(genotype)); + if (genotypes != null) + genotypes.forEach(genotype => addGenotype(genotype)); o.trigger('newdata', interval); }); } diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index ed9a4c66..62925ff6 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -69,7 +69,8 @@ function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getFeaturesInRange(interval).then(e => { var variants = e.response; - variants.forEach(variant => addVariant(variant)); + if (variants != null) + variants.forEach(variant => addVariant(variant)); o.trigger('newdata', interval); }); } diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js index 4fb56cf1..4d570ced 100644 --- a/src/test/sources/FeatureDataSource-test.js +++ b/src/test/sources/FeatureDataSource-test.js @@ -17,6 +17,7 @@ describe('FeatureDataSource', function() { response = data; server = sinon.fakeServer.create(); server.respondWith('GET', '/features/chrM?start=1000&end=2000', [200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/features/chrM?start=1&end=1000', [200, { "Content-Type": "application/json" }, '']); }); }); @@ -34,7 +35,7 @@ describe('FeatureDataSource', function() { it('should extract features in a range', function(done) { var source = getTestSource(); - // No genes fetched initially + // No features fetched initially var range = new ContigInterval('chrM', 1000, 1200); var emptyFeatures = source.getFeaturesInRange(range); expect(emptyFeatures).to.deep.equal([]); @@ -56,4 +57,23 @@ describe('FeatureDataSource', function() { }); server.respond(); }); + + it('should not fail when no feature data is available', function(done) { + var source = getTestSource(); + + var range = new ContigInterval('chrM', 1, 100); + + // Fetching that one gene should cache its entire block. + source.on('newdata', () => { + var features = source.getFeaturesInRange(range); + expect(features).to.have.length(0); + done(); + }); + source.rangeChanged({ + contig: range.contig, + start: range.start(), + stop: range.stop() + }); + server.respond(); + }); }); diff --git a/src/test/sources/GenotypeDataSource-test.js b/src/test/sources/GenotypeDataSource-test.js index 3133a989..2854f87c 100644 --- a/src/test/sources/GenotypeDataSource-test.js +++ b/src/test/sources/GenotypeDataSource-test.js @@ -18,6 +18,7 @@ describe('GenotypeDataSource', function() { response = data; server = sinon.fakeServer.create(); server.respondWith('GET', '/genotypes/chrM?start=1&end=1000',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/genotypes/chrM?start=1000&end=2000',[200, { "Content-Type": "application/json" }, response]); }); }); @@ -31,10 +32,11 @@ describe('GenotypeDataSource', function() { }); return source; } + it('should extract features in a range', function(done) { var source = getTestSource(); var range = new ContigInterval('chrM', 0, 25); - // No variants are cached yet. + // No genotypes are cached yet. var genotypes = source.getFeaturesInRange(range); expect(genotypes).to.deep.equal([]); @@ -55,4 +57,21 @@ describe('GenotypeDataSource', function() { }); server.respond(); }); + + it('should not fail when no genotypes are available', function(done) { + var source = getTestSource(); + var range = new ContigInterval('chrM', 1000, 1025); + + source.on('newdata', () => { + var genotypes = source.getFeaturesInRange(range); + expect(genotypes).to.have.length(0); + done(); + }); + source.rangeChanged({ + contig: range.contig, + start: range.start(), + stop: range.stop() + }); + server.respond(); + }); }); diff --git a/src/test/sources/VariantDataSource-test.js b/src/test/sources/VariantDataSource-test.js index bedbc400..9ee2a7ed 100644 --- a/src/test/sources/VariantDataSource-test.js +++ b/src/test/sources/VariantDataSource-test.js @@ -18,6 +18,7 @@ describe('VariantDataSource', function() { response = data; server = sinon.fakeServer.create(); server.respondWith('GET', '/variants/chrM?start=1&end=1000',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/variants/chrM?start=1000&end=2000',[200, { "Content-Type": "application/json" }, '']); }); }); @@ -54,4 +55,21 @@ describe('VariantDataSource', function() { }); server.respond(); }); + + it('should not fail when no variants are availble', function(done) { + var source = getTestSource(); + var range = new ContigInterval('chrM', 1050, 1150); + + source.on('newdata', () => { + var variants = source.getFeaturesInRange(range); + expect(variants).to.deep.equal([]); + done(); + }); + source.rangeChanged({ + contig: range.contig, + start: range.start(), + stop: range.stop() + }); + server.respond(); + }); }); From 2752cded0807f3cda59706232fe3ac8321b958d0 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sun, 1 Jan 2017 19:33:17 -0600 Subject: [PATCH 056/136] added score visualization for features --- src/main/data/FeatureEndpoint.js | 1 + src/main/data/vcf.js | 2 +- src/main/viz/FeatureTrack.js | 6 ++++-- test-data/features-chrM-1000-1200.json | 6 ++++-- 4 files changed, 10 insertions(+), 5 deletions(-) diff --git a/src/main/data/FeatureEndpoint.js b/src/main/data/FeatureEndpoint.js index 321953c7..230e8698 100644 --- a/src/main/data/FeatureEndpoint.js +++ b/src/main/data/FeatureEndpoint.js @@ -15,6 +15,7 @@ export type Feature = { contig: string; start: number; stop: number; + score: number; } class FeatureEndpoint { diff --git a/src/main/data/vcf.js b/src/main/data/vcf.js index c0307889..0ff45499 100644 --- a/src/main/data/vcf.js +++ b/src/main/data/vcf.js @@ -52,7 +52,7 @@ function extractVariant(vcfLine: string): Variant { ref: parts[3], alt: parts[4], vcfLine: vcfLine, - end: end + end: Number(end) }; } diff --git a/src/main/viz/FeatureTrack.js b/src/main/viz/FeatureTrack.js index fc780fcf..6680eebd 100644 --- a/src/main/viz/FeatureTrack.js +++ b/src/main/viz/FeatureTrack.js @@ -13,6 +13,7 @@ import type {Scale} from './d3utils'; import React from 'react'; import ReactDOM from 'react-dom'; import shallowEquals from 'shallow-equals'; +import _ from 'underscore'; import d3utils from './d3utils'; import scale from '../scale'; @@ -86,8 +87,9 @@ class FeatureTrack extends React.Component { if (!position.chrIntersects(range)) return; ctx.pushObject(feature); ctx.lineWidth = 1; - ctx.strokeStyle = style.GENE_COLOR; - ctx.fillStyle = style.GENE_COLOR; + ctx.strokeStyle = 'black'; + var opacity = feature.score/1000; + ctx.fillStyle = `rgba(0,0,0,${opacity})`; var x = Math.round(sc(feature.start)); var width = Math.round(sc(feature.stop) - sc(feature.start)); diff --git a/test-data/features-chrM-1000-1200.json b/test-data/features-chrM-1000-1200.json index c6285852..a600170a 100644 --- a/test-data/features-chrM-1000-1200.json +++ b/test-data/features-chrM-1000-1200.json @@ -3,11 +3,13 @@ "featureType": "peak", "contig": "chrM", "start": 1107, - "end": 1200 + "end": 1200, + "score": 1000 }, { "id": "e105ce29-a840-4fc6-819f-a9aac5166163", "featureType": "peak", "contig": "chrM", "start": 1011, - "end": 1012 + "end": 1012, + "score": 10 }] From 5c30157fb8e1cc83ce69924eb5d657c718afab6e Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Mon, 2 Jan 2017 21:40:32 -0600 Subject: [PATCH 057/136] added click and loading functionality for features --- src/main/sources/FeatureDataSource.js | 2 +- src/main/viz/FeatureTrack.js | 72 ++++++++++++++++++++++++--- style/pileup.css | 21 +++++++- 3 files changed, 86 insertions(+), 9 deletions(-) diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index 34db6803..8e4c247c 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -41,7 +41,7 @@ var BASE_PAIRS_PER_FETCH = 1000; function expandRange(range: ContigInterval) { var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; - var newStart = Math.max(1, roundDown(range.start())), + var newStart = Math.max(0, roundDown(range.start())), newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); return new ContigInterval(range.contig, newStart, newStop); diff --git a/src/main/viz/FeatureTrack.js b/src/main/viz/FeatureTrack.js index 6680eebd..8bcd9619 100644 --- a/src/main/viz/FeatureTrack.js +++ b/src/main/viz/FeatureTrack.js @@ -21,29 +21,58 @@ import ContigInterval from '../ContigInterval'; import canvasUtils from './canvas-utils'; import dataCanvas from 'data-canvas'; import style from '../style'; - +import type {State, NetworkStatus} from './pileuputils'; class FeatureTrack extends React.Component { props: VizProps & { source: FeatureDataSource }; - state: {features: Feature[]}; + state: State; + cache: {features: Feature[]}; constructor(props: VizProps) { super(props); this.state = { + networkStatus: null + }; + this.cache = { features: [] }; } render(): any { - return ; + var statusEl = null, + networkStatus = this.state.networkStatus; + if (networkStatus) { + statusEl = ( +
+
+ Loading features… +
+
+ ); + } + var rangeLength = this.props.range.stop - this.props.range.start; + return ( +
+ {statusEl} +
+ +
+
+ ); } componentDidMount() { // Visualize new reference data as it comes in from the network. this.props.source.on('newdata', (range) => { - this.setState({ + this.cache = { features: this.props.source.getFeaturesInRange(range) - }); + }; + }); + this.props.source.on('networkprogress', e => { + this.setState({networkStatus: e}); + }); + this.props.source.on('networkdone', e => { + this.setState({networkStatus: null}); }); this.updateVisualization(); @@ -61,7 +90,7 @@ class FeatureTrack extends React.Component { } updateVisualization() { - var canvas = ReactDOM.findDOMNode(this), + var canvas = (this.refs.canvas : HTMLCanvasElement), {width, height} = this.props, genomeRange = this.props.range; @@ -82,7 +111,7 @@ class FeatureTrack extends React.Component { // TODO: don't pull in features via state. ctx.font = `${style.GENE_FONT_SIZE}px ${style.GENE_FONT}`; ctx.textAlign = 'center'; - this.state.features.forEach(feature => { + this.cache.features.forEach(feature => { var position = new ContigInterval(feature.contig, feature.start, feature.stop); if (!position.chrIntersects(range)) return; ctx.pushObject(feature); @@ -98,6 +127,35 @@ class FeatureTrack extends React.Component { ctx.popObject(); }); } + + handleClick(reactEvent: any) { + var ev = reactEvent.nativeEvent, + x = ev.offsetX, + y = ev.offsetY; + var ctx = canvasUtils.getContext(this.refs.canvas); + var trackingCtx = new dataCanvas.ClickTrackingContext(ctx, x, y); + console.log("handle click"); + + var genomeRange = this.props.range, + range = new ContigInterval(genomeRange.contig, genomeRange.start, genomeRange.stop), + scale = this.getScale(), + pos = Math.floor(scale.invert(x)), + // If click-tracking gets slow, this range could be narrowed to one + // closer to the click coordinate, rather than the whole visible range. + vFeatures = this.props.source.getFeaturesInRange(range); + var feature = _.find(this.cache.features, f => f.start <= pos && f.stop >= pos); + var alert = window.alert || console.log; + if (feature) { + // Construct a JSON object to show the user. + var messageObject = _.extend( + { + 'id': feature.id, + 'range': `${feature.contig}:${feature.start}-${feature.stop}`, + 'score': feature.score + }); + alert(JSON.stringify(messageObject, null, ' ')); + } + } } FeatureTrack.displayName = 'features'; diff --git a/style/pileup.css b/style/pileup.css index 80c62a2b..ff183fd4 100644 --- a/style/pileup.css +++ b/style/pileup.css @@ -204,6 +204,15 @@ position: relative; top: 20px; } +.network-status-small { + height: 100%; + width: 100%; + display: flex; + align-items: center; + justify-content: center; + position: relative; + top: 9px; +} .network-status-message { padding: 4px 8px; width: auto; @@ -214,6 +223,16 @@ position: absolute; text-align: center; } +.network-status-message-small { + padding: 0px 8px; + width: auto; + background: #eee; + border-radius: 3px; + border: 1px solid #ccc; + font-size: 10px; + position: absolute; + text-align: center; +} .pileup .mate-connector { stroke: #c8c8c8; /* matches IGV */ @@ -288,4 +307,4 @@ } .center { text-align: center; -} \ No newline at end of file +} From 5588ad5241fc702f0a4c48e1807cb7530d0a67bd Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sun, 8 Jan 2017 15:42:34 -0600 Subject: [PATCH 058/136] updated features to view correctly and show info on click --- src/main/data/vcf.js | 2 +- src/main/sources/FeatureDataSource.js | 25 +++-- src/main/sources/GeneDataSource.js | 2 +- src/main/sources/GenotypeDataSource.js | 2 +- src/main/sources/VariantDataSource.js | 2 +- src/main/viz/CoverageTrack.js | 3 - src/main/viz/FeatureTrack.js | 112 +++++++++++++-------- src/main/viz/GenotypeTrack.js | 4 +- src/test/RemoteRequest-test.js | 13 +-- src/test/sources/FeatureDataSource-test.js | 2 +- src/test/viz/CoverageTrack-test.js | 9 +- src/test/viz/FeatureTrack-test.js | 92 +++++++++++++++++ src/test/viz/GenotypeTrack-test.js | 2 +- style/pileup.css | 1 + 14 files changed, 197 insertions(+), 74 deletions(-) create mode 100644 src/test/viz/FeatureTrack-test.js diff --git a/src/main/data/vcf.js b/src/main/data/vcf.js index 0ff45499..eea346fe 100644 --- a/src/main/data/vcf.js +++ b/src/main/data/vcf.js @@ -44,7 +44,7 @@ function extractVariant(vcfLine: string): Variant { var parts = vcfLine.split('\t'); var end = Number(parts[1]) + parts[3].length; if (5 >= parts.length) { - end = parts[5] + end = parts[5]; } return { contig: parts[0], diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index 8e4c247c..db0caa9c 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -37,9 +37,9 @@ export type FeatureDataSource = { // Requests for 2bit ranges are expanded to begin & end at multiples of this // constant. Doing this means that panning typically won't require // additional network requests. -var BASE_PAIRS_PER_FETCH = 1000; +var BASE_PAIRS_PER_FETCH = 10000; -function expandRange(range: ContigInterval) { +function expandRange(range: ContigInterval): ContigInterval { var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; var newStart = Math.max(0, roundDown(range.start())), newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); @@ -74,16 +74,21 @@ function createFromFeatureUrl(remoteSource: FeatureEndpoint): FeatureDataSource } interval = expandRange(interval); - - // "Cover" the range immediately to prevent duplicate fetches. + var newRanges = interval.complementIntervals(coveredRanges); coveredRanges.push(interval); coveredRanges = ContigInterval.coalesce(coveredRanges); - return remoteSource.getFeaturesInRange(interval).then(e => { - var features = e.response; - if (features != null) - features.forEach(feature => addFeature(feature)); - o.trigger('newdata', interval); - }); + + o.trigger('networkprogress', 1); + return Q.all(newRanges.map(range => + remoteSource.getFeaturesInRange(range) + .then(e => { + var features = e.response; + if (features !== null) { + features.forEach(feature => addFeature(feature)); + } + o.trigger('networkdone'); + o.trigger('newdata', range); + }))); } function getFeaturesInRange(range: ContigInterval): Feature[] { diff --git a/src/main/sources/GeneDataSource.js b/src/main/sources/GeneDataSource.js index 3ac2a31e..f19149f1 100644 --- a/src/main/sources/GeneDataSource.js +++ b/src/main/sources/GeneDataSource.js @@ -61,7 +61,7 @@ function createFromGeneUrl(remoteSource: GeneEndpoint): BigBedSource { coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getGenesInRange(interval).then(genes => { - if (genes != null) + if (genes !== null) genes.forEach(gene => addGene(gene)); //we have new data from our internal block range o.trigger('newdata', interval); diff --git a/src/main/sources/GenotypeDataSource.js b/src/main/sources/GenotypeDataSource.js index 4eab2256..d9f85f1d 100644 --- a/src/main/sources/GenotypeDataSource.js +++ b/src/main/sources/GenotypeDataSource.js @@ -79,7 +79,7 @@ function createFromGenotypeUrl(remoteSource: GenotypeEndpoint): GenotypeDataSour coveredRanges.push(interval); coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getFeaturesInRange(interval).then(genotypes => { - if (genotypes != null) + if (genotypes !== null) genotypes.forEach(genotype => addGenotype(genotype)); o.trigger('newdata', interval); }); diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index 62925ff6..686a0bdf 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -69,7 +69,7 @@ function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getFeaturesInRange(interval).then(e => { var variants = e.response; - if (variants != null) + if (variants !== null) variants.forEach(variant => addVariant(variant)); o.trigger('newdata', interval); }); diff --git a/src/main/viz/CoverageTrack.js b/src/main/viz/CoverageTrack.js index 8fbe0a1a..10fe02da 100644 --- a/src/main/viz/CoverageTrack.js +++ b/src/main/viz/CoverageTrack.js @@ -105,8 +105,6 @@ function renderBars(ctx: DataCanvasRenderingContext2D, }; var vBasePosY = yScale(0); // the very bottom of the canvas - var start = range.start(), - stop = range.stop(); // go to the first bin in dataset (specified by the smallest start position) ctx.fillStyle = style.COVERAGE_BIN_COLOR; @@ -280,7 +278,6 @@ class CoverageTrack extends React.Component { ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); var yScale = this.tiles.yScaleForRef(range); - var thisS = this.getScale(); this.tiles.renderToScreen(ctx, range, this.getScale()); this.renderTicks(ctx, yScale); diff --git a/src/main/viz/FeatureTrack.js b/src/main/viz/FeatureTrack.js index 8bcd9619..b0e5b4f5 100644 --- a/src/main/viz/FeatureTrack.js +++ b/src/main/viz/FeatureTrack.js @@ -6,36 +6,86 @@ import type {FeatureDataSource} from '../sources/FeatureDataSource'; import type {Feature} from '../data/FeatureEndpoint'; +import type {DataCanvasRenderingContext2D} from 'data-canvas'; import type {VizProps} from '../VisualizationWrapper'; import type {Scale} from './d3utils'; import React from 'react'; -import ReactDOM from 'react-dom'; import shallowEquals from 'shallow-equals'; import _ from 'underscore'; import d3utils from './d3utils'; -import scale from '../scale'; import ContigInterval from '../ContigInterval'; import canvasUtils from './canvas-utils'; +import TiledCanvas from './TiledCanvas'; import dataCanvas from 'data-canvas'; import style from '../style'; +import utils from '../utils'; import type {State, NetworkStatus} from './pileuputils'; +class FeatureTiledCanvas extends TiledCanvas { + options: Object; + source: FeatureDataSource; + + constructor(source: FeatureDataSource, options: Object) { + super(); + this.source = source; + this.options = options; + } + + update(newOptions: Object) { + this.options = newOptions; + } + + // TODO: can update to handle overlapping features + heightForRef(ref: string): number { + return style.VARIANT_HEIGHT; + } + + render(ctx: DataCanvasRenderingContext2D, + scale: (x: number)=>number, + range: ContigInterval) { + var relaxedRange = + new ContigInterval(range.contig, range.start() - 1, range.stop() + 1); + var vFeatures = this.source.getFeaturesInRange(relaxedRange); + renderFeatures(ctx, scale, relaxedRange, vFeatures); + } +} + +// Draw features +function renderFeatures(ctx: DataCanvasRenderingContext2D, + scale: (num: number) => number, + range: ContigInterval, + features: Feature[]) { + + ctx.font = `${style.GENE_FONT_SIZE}px ${style.GENE_FONT}`; + ctx.textAlign = 'center'; + + features.forEach(feature => { + var position = new ContigInterval(feature.contig, feature.start, feature.stop); + if (!position.chrIntersects(range)) return; + ctx.pushObject(feature); + ctx.lineWidth = 1; + ctx.fillStyle = 'black'; + + var x = Math.round(scale(feature.start)); + var width = Math.ceil(scale(feature.stop) - scale(feature.start)); + ctx.fillRect(x - 0.5, 0, width, style.VARIANT_HEIGHT); + ctx.popObject(); + }); +} + class FeatureTrack extends React.Component { props: VizProps & { source: FeatureDataSource }; state: State; - cache: {features: Feature[]}; + tiles: FeatureTiledCanvas; constructor(props: VizProps) { super(props); this.state = { networkStatus: null }; - this.cache = { - features: [] - }; } render(): any { @@ -50,7 +100,6 @@ class FeatureTrack extends React.Component {
); } - var rangeLength = this.props.range.stop - this.props.range.start; return (
{statusEl} @@ -62,11 +111,12 @@ class FeatureTrack extends React.Component { } componentDidMount() { + this.tiles = new FeatureTiledCanvas(this.props.source, this.props.options); + // Visualize new reference data as it comes in from the network. this.props.source.on('newdata', (range) => { - this.cache = { - features: this.props.source.getFeaturesInRange(range) - }; + this.tiles.invalidateRange(range); + this.updateVisualization(); }); this.props.source.on('networkprogress', e => { this.setState({networkStatus: e}); @@ -95,55 +145,35 @@ class FeatureTrack extends React.Component { genomeRange = this.props.range; var range = new ContigInterval(genomeRange.contig, genomeRange.start, genomeRange.stop); - var y = height - style.VARIANT_HEIGHT - 1; // Hold off until height & width are known. - if (width === 0) return; - - var sc = this.getScale(); - + if (width === 0 || typeof canvas == 'undefined') return; d3utils.sizeCanvas(canvas, width, height); var ctx = dataCanvas.getDataContext(canvasUtils.getContext(canvas)); ctx.reset(); ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); - // TODO: don't pull in features via state. - ctx.font = `${style.GENE_FONT_SIZE}px ${style.GENE_FONT}`; - ctx.textAlign = 'center'; - this.cache.features.forEach(feature => { - var position = new ContigInterval(feature.contig, feature.start, feature.stop); - if (!position.chrIntersects(range)) return; - ctx.pushObject(feature); - ctx.lineWidth = 1; - ctx.strokeStyle = 'black'; - var opacity = feature.score/1000; - ctx.fillStyle = `rgba(0,0,0,${opacity})`; - - var x = Math.round(sc(feature.start)); - var width = Math.round(sc(feature.stop) - sc(feature.start)); - ctx.fillRect(x - 0.5, y - 0.5, width, style.VARIANT_HEIGHT); - ctx.strokeRect(x - 0.5, y - 0.5, width, style.VARIANT_HEIGHT); - ctx.popObject(); - }); + this.tiles.renderToScreen(ctx, range, this.getScale()); + ctx.restore(); + } handleClick(reactEvent: any) { var ev = reactEvent.nativeEvent, - x = ev.offsetX, - y = ev.offsetY; - var ctx = canvasUtils.getContext(this.refs.canvas); - var trackingCtx = new dataCanvas.ClickTrackingContext(ctx, x, y); - console.log("handle click"); + x = ev.offsetX; var genomeRange = this.props.range, - range = new ContigInterval(genomeRange.contig, genomeRange.start, genomeRange.stop), + // allow some buffering so click isn't so sensitive + range = new ContigInterval(genomeRange.contig, genomeRange.start-1, genomeRange.stop+1), scale = this.getScale(), - pos = Math.floor(scale.invert(x)), + // leave padding of 2px to reduce click specificity + clickStart = Math.floor(scale.invert(x)) - 2, + clickEnd = clickStart + 2, // If click-tracking gets slow, this range could be narrowed to one // closer to the click coordinate, rather than the whole visible range. vFeatures = this.props.source.getFeaturesInRange(range); - var feature = _.find(this.cache.features, f => f.start <= pos && f.stop >= pos); + var feature = _.find(vFeatures, f => utils.tupleRangeOverlaps([[f.start], [f.stop]], [[clickStart], [clickEnd]])); var alert = window.alert || console.log; if (feature) { // Construct a JSON object to show the user. diff --git a/src/main/viz/GenotypeTrack.js b/src/main/viz/GenotypeTrack.js index f43c6d9a..310312ea 100644 --- a/src/main/viz/GenotypeTrack.js +++ b/src/main/viz/GenotypeTrack.js @@ -57,7 +57,7 @@ class GenotypeTrack extends React.Component { updateVisualization() { var canvas = ReactDOM.findDOMNode(this), - {width, height} = this.props; + width = this.props.width; // Hold off until height & width are known. if (width === 0) return; @@ -89,7 +89,7 @@ class GenotypeTrack extends React.Component { // Height can only be computed after the genotypes has been updated. var newHeight = yForRow(sampleIds.length); var canvas = ReactDOM.findDOMNode(this), - {width, height} = this.props; + width = this.props.width; d3utils.sizeCanvas(canvas, width, newHeight); // This is a hack to adjust parent div for resize diff --git a/src/test/RemoteRequest-test.js b/src/test/RemoteRequest-test.js index 1241f335..8ea7b715 100644 --- a/src/test/RemoteRequest-test.js +++ b/src/test/RemoteRequest-test.js @@ -22,6 +22,10 @@ describe('RemoteRequest', function() { return new RemoteFile('/test-data/chr17.1-250.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); + var endpoint = '/test/chr17?start=10&end=20'; + server.respondWith('GET', endpoint, + [200, { "Content-Type": "application/json" }, response]); + }); }); @@ -31,14 +35,11 @@ describe('RemoteRequest', function() { it('should fetch json from a server', function(done) { var remoteRequest = new RemoteRequest(url, basePairsPerFetch); - var endpoint = remoteRequest.getEndpointFromContig(contig, start, stop); - server.respondWith('GET', endpoint, - [200, { "Content-Type": "application/json" }, response]); - var promisedData = remoteRequest.get(interval); - promisedData.then(obj => { - var ret = obj.alignments; + promisedData.then(e => { + var ret = e.response.alignments; expect(remoteRequest.numNetworkRequests).to.equal(1); + expect(e.status).to.equal(200); expect(ret.length).to.equal(14); done(); }); diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js index 4d570ced..f6101de5 100644 --- a/src/test/sources/FeatureDataSource-test.js +++ b/src/test/sources/FeatureDataSource-test.js @@ -16,7 +16,7 @@ describe('FeatureDataSource', function() { return new RemoteFile('/test-data/features-chrM-1000-1200.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); - server.respondWith('GET', '/features/chrM?start=1000&end=2000', [200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/features/chrM?start=0&end=10000', [200, { "Content-Type": "application/json" }, response]); server.respondWith('GET', '/features/chrM?start=1&end=1000', [200, { "Content-Type": "application/json" }, '']); }); }); diff --git a/src/test/viz/CoverageTrack-test.js b/src/test/viz/CoverageTrack-test.js index 3c4adbbd..94b09f67 100644 --- a/src/test/viz/CoverageTrack-test.js +++ b/src/test/viz/CoverageTrack-test.js @@ -46,8 +46,10 @@ describe('CoverageTrack', function() { range: range, tracks: [ { - data: referenceSource, viz: pileup.viz.genome(), + data: pileup.formats.twoBit({ + url: '/test-data/test.2bit' + }), isReference: true }, { @@ -70,11 +72,6 @@ describe('CoverageTrack', function() { testDiv.style.width = ''; }); - var twoBitFile = new MappedRemoteFile( - '/test-data/hg19.2bit.mapped', - [[0, 16383], [691179834, 691183928], [694008946, 694011447]]); - var referenceSource = TwoBitDataSource.createFromTwoBitFile(new TwoBit(twoBitFile)); - var {drawnObjectsWith, callsOf} = dataCanvas.RecordingContext; var findCoverageBins = () => { diff --git a/src/test/viz/FeatureTrack-test.js b/src/test/viz/FeatureTrack-test.js new file mode 100644 index 00000000..d7804e32 --- /dev/null +++ b/src/test/viz/FeatureTrack-test.js @@ -0,0 +1,92 @@ +/** + * This tests whether feature information is being shown/drawn correctly + * in the track. + * + * @flow + */ +'use strict'; + +import {expect} from 'chai'; + +import sinon from 'sinon'; + +import RemoteFile from '../../main/RemoteFile'; +import pileup from '../../main/pileup'; +import dataCanvas from 'data-canvas'; +import {waitFor} from '../async'; + +describe('FeatureTrack', function() { + var testDiv = document.getElementById('testdiv'); + var range = {contig: 'chrM', start: 900, stop: 1500}; + var server: any = null, response; + + beforeEach(() => { + testDiv.style.width = '800px'; + dataCanvas.RecordingContext.recordAll(); + }); + + afterEach(() => { + dataCanvas.RecordingContext.reset(); + // avoid pollution between tests. + server.restore(); + }); + + before(function () { + return new RemoteFile('/test-data/features-chrM-1000-1200.json').getAllString().then(data => { + server = sinon.fakeServer.create(); + response = data; + }); + }); + + after(function () { + server.restore(); + }); + + var drawnObjects = dataCanvas.RecordingContext.drawnObjects; + + function ready() { + return testDiv.querySelector('canvas') && + drawnObjects(testDiv, '.features').length > 0; + } + + it('should render features', function() { + server.respondWith('GET', '/features/chrM?start=0&end=10000', [200, { "Content-Type": "application/json" }, ""]); + var p = pileup.create(testDiv, { + range: range, + tracks: [ + { + viz: pileup.viz.genome(), + data: pileup.formats.twoBit({ + url: '/test-data/test.2bit' + }), + isReference: true + }, + { + + data: pileup.formats.features({ + url: '/features', + }), + viz: pileup.viz.features() + }, + { + data: pileup.formats.bigBed({ + url: '/test-data/ensembl.chr17.bb' + }), + viz: pileup.viz.genes(), + } + ] + }); + + return waitFor(ready, 2000) + .then(() => { + var features = drawnObjects(testDiv, '.features'); + var ids = ["4ee7469a-b468-429b-a109-07a484817037", "e105ce29-a840-4fc6-819f-a9aac5166163"]; + expect(features).to.have.length(2); + expect(features.map(f => f.start)).to.deep.equal( + [1107, 1011]); + expect(features.map(g => g.id)).to.deep.equal(ids); + p.destroy(); + }); + }); + +}); diff --git a/src/test/viz/GenotypeTrack-test.js b/src/test/viz/GenotypeTrack-test.js index 71cd1395..b43f934a 100644 --- a/src/test/viz/GenotypeTrack-test.js +++ b/src/test/viz/GenotypeTrack-test.js @@ -39,7 +39,7 @@ describe('GenotypeTrack', function() { // avoid pollution between tests. testDiv.innerHTML = ''; }); - var {drawnObjects, callsOf} = dataCanvas.RecordingContext; + var drawnObjects = dataCanvas.RecordingContext.drawnObjects; function ready() { return testDiv.querySelector('canvas') && diff --git a/style/pileup.css b/style/pileup.css index ff183fd4..8e91c34c 100644 --- a/style/pileup.css +++ b/style/pileup.css @@ -13,6 +13,7 @@ .pileup-root > .track { display: flex; flex-direction: row; + margin-bottom: 5px; } .pileup-root text, .track-label { font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; From 25aba86b7b03d9e3f2d7e04639281a2e2436ed1b Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 10 Jan 2017 13:21:37 -0800 Subject: [PATCH 059/136] added limit for visualizing large Feature areas --- src/main/viz/FeatureTrack.js | 34 +++++++++++++++++++++++++--------- 1 file changed, 25 insertions(+), 9 deletions(-) diff --git a/src/main/viz/FeatureTrack.js b/src/main/viz/FeatureTrack.js index b0e5b4f5..d9ce11d7 100644 --- a/src/main/viz/FeatureTrack.js +++ b/src/main/viz/FeatureTrack.js @@ -16,6 +16,7 @@ import shallowEquals from 'shallow-equals'; import _ from 'underscore'; import d3utils from './d3utils'; +import RemoteRequest from '../RemoteRequest'; import ContigInterval from '../ContigInterval'; import canvasUtils from './canvas-utils'; import TiledCanvas from './TiledCanvas'; @@ -100,14 +101,27 @@ class FeatureTrack extends React.Component {
); } - return ( -
- {statusEl} -
- + var rangeLength = this.props.range.stop - this.props.range.start; + // If range is too large, do not render 'canvas' + if (rangeLength > RemoteRequest.MONSTER_REQUEST) { + return ( +
+
+ Zoom in to see features +
+ +
+ ); + } else { + return ( +
+ {statusEl} +
+ +
-
- ); + ); + } } componentDidMount() { @@ -133,8 +147,10 @@ class FeatureTrack extends React.Component { } componentDidUpdate(prevProps: any, prevState: any) { - if (!shallowEquals(prevProps, this.props) || - !shallowEquals(prevState, this.state)) { + if (!shallowEquals(this.props, prevProps) || + !shallowEquals(this.state, prevState)) { + this.tiles.update(this.props.height, this.props.options); + this.tiles.invalidateAll(); this.updateVisualization(); } } From cbe865fd1fd3131ca916cd6fb3e8a91b8dc72e34 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Thu, 12 Jan 2017 09:04:40 -0800 Subject: [PATCH 060/136] Interval.isCoveredBy() fix for regions not overlapping first interval --- src/main/Interval.js | 2 +- src/test/Interval-test.js | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/src/main/Interval.js b/src/main/Interval.js index 0107a316..6e025488 100644 --- a/src/main/Interval.js +++ b/src/main/Interval.js @@ -57,7 +57,7 @@ class Interval { if (r.start > remaining.start) { return false; // A position has been missed and there's no going back. } - remaining.start = r.stop + 1; + remaining.start = Math.max(remaining.start, r.stop + 1); if (remaining.length() <= 0) { return true; } diff --git a/src/test/Interval-test.js b/src/test/Interval-test.js index 0106b0bf..48c26c59 100644 --- a/src/test/Interval-test.js +++ b/src/test/Interval-test.js @@ -87,6 +87,11 @@ describe('Interval', function() { new Interval(10, 20) ])).to.be.true; + expect(iv.isCoveredBy([ + new Interval(0, 5), + new Interval(9, 21) + ])).to.be.true; + expect(iv.isCoveredBy([ new Interval(0, 10), new Interval(5, 15), @@ -162,5 +167,6 @@ describe('Interval', function() { '[20, 29]', '[50, 79]' ]); + }); }); From 3619fd152617e7a86fcbaf8a0441e0fdbd35ed02 Mon Sep 17 00:00:00 2001 From: "B. Arman Aksoy" Date: Tue, 5 Jul 2016 15:00:58 -0400 Subject: [PATCH 061/136] bump version up top 0.6.7 --- package.json | 2 +- src/main/pileup.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/package.json b/package.json index 6d8fcb8e..66226a3c 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "pileup", - "version": "0.6.6", + "version": "0.6.7", "description": "JavaScript track viewer", "keywords": [ "genome", diff --git a/src/main/pileup.js b/src/main/pileup.js index aff47a02..86d334f6 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -136,7 +136,7 @@ var pileup = { variants: makeVizObject(VariantTrack), pileup: makeVizObject(PileupTrack) }, - version: '0.6.6' + version: '0.6.7' }; module.exports = pileup; From 204a61090f70a1aa8f54ae55e53d8f103f676777 Mon Sep 17 00:00:00 2001 From: Ryan Williams Date: Fri, 8 Jul 2016 00:47:59 +0000 Subject: [PATCH 062/136] rename poorly-named parameter --- src/main/data/BigBed.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/data/BigBed.js b/src/main/data/BigBed.js index b1120aca..6bd240d6 100644 --- a/src/main/data/BigBed.js +++ b/src/main/data/BigBed.js @@ -31,9 +31,9 @@ function parseCirTree(buffer) { } // Extract a map from contig name --> contig ID from the bigBed header. -function generateContigMap(twoBitHeader): {[key:string]: number} { +function generateContigMap(header): {[key:string]: number} { // Just assume it's a flat "tree" for now. - var nodes = twoBitHeader.chromosomeTree.nodes.contents; + var nodes = header.chromosomeTree.nodes.contents; if (!nodes) { throw 'Invalid chromosome tree'; } From 8bcf6e13ccf9134765baf239e1fea2ac2e98d857 Mon Sep 17 00:00:00 2001 From: Ryan Williams Date: Fri, 8 Jul 2016 01:12:03 +0000 Subject: [PATCH 063/136] handle non-compressed BigBed files Also document cryptic comment / "+2" offset. --- src/main/data/BigBed.js | 21 +++++++++++++++------ src/test/data/BigBed-test.js | 26 ++++++++++++++++++++++++++ test-data/README.md | 7 ++++++- test-data/simple17.bb | Bin 0 -> 13219 bytes test-data/simple17.bed | 10 ++++++++++ test-data/simple17unc.bb | Bin 0 -> 13263 bytes 6 files changed, 57 insertions(+), 7 deletions(-) create mode 100644 test-data/simple17.bb create mode 100644 test-data/simple17.bed create mode 100644 test-data/simple17unc.bb diff --git a/src/main/data/BigBed.js b/src/main/data/BigBed.js index 6bd240d6..753e23e1 100644 --- a/src/main/data/BigBed.js +++ b/src/main/data/BigBed.js @@ -53,13 +53,21 @@ function reverseContigMap(contigMap: {[key:string]: number}): Array { } -function extractFeaturesFromBlock(buffer, dataRange, block): ChrIdBedRow[] { +function extractFeaturesFromBlock(buffer, dataRange, block, isCompressed): ChrIdBedRow[] { var blockOffset = block.offset - dataRange.start, blockLimit = blockOffset + block.size, - // TODO: where does the +2 come from? (I copied it from dalliance) - blockBuffer = buffer.slice(blockOffset + 2, blockLimit); - // TODO: only inflate if necessary - var inflatedBuffer = pako.inflateRaw(new Uint8Array(blockBuffer)); + + blockBuffer = + // NOTE: "+ 2" skips over two bytes of gzip header (0x8b1f), which pako.inflateRaw will not handle. + buffer.slice( + blockOffset + (isCompressed ? 2 : 0), + blockLimit + ); + + var inflatedBuffer = + isCompressed ? + pako.inflateRaw(new Uint8Array(blockBuffer)) : + blockBuffer; var jb = new jBinary(inflatedBuffer, bbi.TYPE_SET); // TODO: parse only one BedEntry at a time & use an iterator. @@ -173,10 +181,11 @@ class ImmediateBigBed { var byteRange = Interval.boundingInterval( blocks.map(n => new Interval(+n.offset, n.offset+n.size))); + var isCompressed = (this.header.uncompressBufSize > 0); return this.remoteFile.getBytes(byteRange.start, byteRange.length()) .then(buffer => { return blocks.map(block => { - var beds = extractFeaturesFromBlock(buffer, byteRange, block); + var beds = extractFeaturesFromBlock(buffer, byteRange, block, isCompressed); if (block.startChromIx != block.endChromIx) { throw `Can't handle blocks which span chromosomes!`; } diff --git a/src/test/data/BigBed-test.js b/src/test/data/BigBed-test.js index e291bf42..0d3fce3a 100644 --- a/src/test/data/BigBed-test.js +++ b/src/test/data/BigBed-test.js @@ -13,6 +13,10 @@ describe('BigBed', function() { return new BigBed('/test-data/itemRgb.bb'); // See test-data/README.md } + function getUncompressedTestBigBed() { + return new BigBed('/test-data/simple17unc.bb'); // See test-data/README.md + } + it('should extract features in a range', function() { var bb = getTestBigBed(); @@ -43,6 +47,28 @@ describe('BigBed', function() { }); }); + it('should extract features from an uncompressed BigBed', function () { + var bb = getUncompressedTestBigBed(); + + return bb.getFeaturesInRange('chr17', 60000, 270000) + .then(features => { + // Here's what these three lines in the file look like: + // chr17 62296 202576 + // chr17 62296 202576 + // chr17 260433 264713 + expect(features).to.have.length(3); + expect(features[0].contig).to.equal('chr17'); + expect(features[0].start).to.equal(62296); + expect(features[0].stop).to.equal(202576); + expect(features[1].contig).to.equal('chr17'); + expect(features[1].start).to.equal(62296); + expect(features[1].stop).to.equal(202576); + expect(features[2].contig).to.equal('chr17'); + expect(features[2].start).to.equal(260433); + expect(features[2].stop).to.equal(264713); + }); + }); + it('should have inclusive ranges', function() { // The matches looks like this: // chrX 151071196 151072363 RED diff --git a/test-data/README.md b/test-data/README.md index bb99fc5f..c961d7f1 100644 --- a/test-data/README.md +++ b/test-data/README.md @@ -2,7 +2,6 @@ This directory contains many small data files used in testing. This file documents how they were generated. - #### test.2bit This is a small subset of the hg19 reference genome. It contains small swaths @@ -47,6 +46,12 @@ This is a subset of `ensembl.chr17.bb`, shifted to match the coordinates in grep '^chr17\t' ensGene.bed | grep TP53 | perl -pe 's/(75\d{4,})/$1-7512444/ge' > /tmp/tp53.shifted.bed bedToBigBed -type=bed12+2 /tmp/tp53.shifted.bed <(echo "chr17 78774742") test-data/tp53.shifted.bb +#### simple17*.{bed,bb} + +- `simple17.bed`: the first 10 features from chr17 of ensGene.bb, and only including the first 3 columns. +- `simple17.bb`: `simple17.bed` as a BigBed with compressed data: `bedToBigBed -type=bed3 simple17.bed <(echo "chr17 78774742") simple17.bb`. +- `simple17.bb`: `simple17.bed` as a BigBed with uncompressed data: `bedToBigBed -type=bed3 -unc simple17.bed <(echo "chr17 78774742") simple17unc.bb`. + #### test_input_1* These BAM and BAI files come from the [samtools][1] tests. You can find diff --git a/test-data/simple17.bb b/test-data/simple17.bb new file mode 100644 index 0000000000000000000000000000000000000000..16dc2459e3dcf1e69f5d67200da953b99587f156 GIT binary patch literal 13219 zcmeI(Pe@cj90%~(b;W#kkw6qdhKHKsW&IN_i1?JGj$&Z{F8h2tt54kb);A-rrw$!7 z>e4YVlE_;r+o?;Cv4(o;lpZ}q5r%}PE`c-e&DK)j#gp_Mcr){6e)H#j_Px`vhsO_= z5`+*Dmzhj!y8NZfDpEy~v8eB&ZX*^UedT)8_21;eo}6WLl4T5YB=8qF3+QM;Fps;c z{i-c&)1Z`gsEmui^`@vZ9r(Ecd9RW=&ay0Ep2H|-bMs*(4Dh+1W7H2QckFD|pUs5x z%)6eDqr!+A!VZL-#|$ep?{inUzDHdz>JMl5XVj>d3D-7d<+L%K25CL6uJ|2)4Cxz7 zl`}^BuqtnMT^Y7i3LCy1TkkQ+K=R=hrzawXt68S>8-tYvIZ7 z2VY9>7u&XXKIX`0LS7h`o*%rNZdI#SZs2W0wAjOBEh&El<$kp>l`3Oi=?`Hn8ipJK z5P$##AOHafKmY;|fB*y_009U<00Izz00bZafpaXNP6Ga%M6Tx6Le#<<$5ZS zXf7Nr-}zQcvLiL(v{QzsZ|aHDtQqu4!r!M1DrQi}w4Y-!Y#jm+fB*y_009U<00Izz a00bZa0SG_<0uX=z1Rwx`NZ?TZJ?8|ARGR$& literal 0 HcmV?d00001 diff --git a/test-data/simple17.bed b/test-data/simple17.bed new file mode 100644 index 00000000..af2a0602 --- /dev/null +++ b/test-data/simple17.bed @@ -0,0 +1,10 @@ +chr17 5821 31270 +chr17 62296 202576 +chr17 62296 202576 +chr17 260433 264713 +chr17 290007 295959 +chr17 369120 564751 +chr17 382698 564758 +chr17 582596 592824 +chr17 582596 592824 +chr17 594410 602251 diff --git a/test-data/simple17unc.bb b/test-data/simple17unc.bb new file mode 100644 index 0000000000000000000000000000000000000000..83dfd7702e5964062714a61d111bab5f92abce1a GIT binary patch literal 13263 zcmeI(F-s#s6bJAZlYm(d#6}C7VG&WTFoK7Lg;BJy)3Z>nTa$^d#2ww8aB`K%!66Fb z2T-uE5bm0*(%4zu2hdiyPMbq3JLk<#Br4cg$^8eiJ8$01?Bti(YRJv)&W{`s={9pQ z<;2~GvT2;9EEO|p{e#PKG}2N}v;W6c2TL_6mSn~ACu8+Bk+GQG)G|s!Zl4Nt;Cn)d z0lp+U4x?pJUWwJ(n2EXgpJi3XGAc`v$c?(K*bXXDYf`9KB;}x5RkezpryfSyjIurE zbr5Sak8dktT_vFoRV2bF&D$AXjGB%r_SwFvyf$XgqrTgG%a8bP+yy1RuX_Cxd|&wZ zX`;lHHODVMbz^?Y~1)p4FWkNCN!Twmm=yBVDSZKp;@A Date: Fri, 8 Jul 2016 01:16:53 +0000 Subject: [PATCH 064/136] relax BigBed version number constraint --- src/main/data/formats/bbi.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/data/formats/bbi.js b/src/main/data/formats/bbi.js index 80c68c01..eb31f25e 100644 --- a/src/main/data/formats/bbi.js +++ b/src/main/data/formats/bbi.js @@ -13,7 +13,7 @@ var TYPE_SET = { 'Header': { _magic: ['const', 'uint32', 0x8789F2EB, true], - version: ['const', 'uint16', 4, true], + version: 'uint16', zoomLevels: 'uint16', chromosomeTreeOffset: 'uint64', unzoomedDataOffset: 'uint64', From 17cbc857302887a42ecf1777898894f40cef0a59 Mon Sep 17 00:00:00 2001 From: Ryan Williams Date: Fri, 8 Jul 2016 01:17:15 +0000 Subject: [PATCH 065/136] spacing nit --- src/main/data/formats/bbi.js | 33 +++++++++++++++++++-------------- 1 file changed, 19 insertions(+), 14 deletions(-) diff --git a/src/main/data/formats/bbi.js b/src/main/data/formats/bbi.js index eb31f25e..3672c869 100644 --- a/src/main/data/formats/bbi.js +++ b/src/main/data/formats/bbi.js @@ -98,20 +98,25 @@ var TYPE_SET = { isLeaf: 'uint8', // 1 = yes, 0 = no _reserved: 'uint8', count: 'uint16', - contents: ['array', ['if', 'isLeaf', { - startChromIx: 'uint32', - startBase: 'uint32', - endChromIx: 'uint32', - endBase: 'uint32', - offset: 'uint64', - size: 'uint64' - }, { - startChromIx: 'uint32', - startBase: 'uint32', - endChromIx: 'uint32', - endBase: 'uint32', - offset: 'uint64', - }], 'count'] + contents: [ + 'array', [ + 'if', 'isLeaf', { + startChromIx: 'uint32', + startBase: 'uint32', + endChromIx: 'uint32', + endBase: 'uint32', + offset: 'uint64', + size: 'uint64' + }, { + startChromIx: 'uint32', + startBase: 'uint32', + endChromIx: 'uint32', + endBase: 'uint32', + offset: 'uint64', + } + ], + 'count' + ] }, 'BedEntry': { From 8dc1471abc4ab095880af57eb6499cf2b05c02ce Mon Sep 17 00:00:00 2001 From: Ryan Williams Date: Mon, 11 Jul 2016 16:04:08 +0000 Subject: [PATCH 066/136] CR: add types, clean up test --- src/main/data/BigBed.js | 25 +++++++++++++++++++++---- src/main/data/formats/bbi.js | 32 ++++++++++++++++++-------------- src/test/data/BigBed-test.js | 17 +++++++---------- 3 files changed, 46 insertions(+), 28 deletions(-) diff --git a/src/main/data/BigBed.js b/src/main/data/BigBed.js index 753e23e1..cd47807b 100644 --- a/src/main/data/BigBed.js +++ b/src/main/data/BigBed.js @@ -53,7 +53,10 @@ function reverseContigMap(contigMap: {[key:string]: number}): Array { } -function extractFeaturesFromBlock(buffer, dataRange, block, isCompressed): ChrIdBedRow[] { +function extractFeaturesFromBlock(buffer: ArrayBuffer, + dataRange: Interval, + block: LeafData, + isCompressed: boolean): ChrIdBedRow[] { var blockOffset = block.offset - dataRange.start, blockLimit = blockOffset + block.size, @@ -102,6 +105,16 @@ type ChrIdBedBlock = { rows: ChrIdBedRow[]; } +// A copy of LeafData from bbi.js. +type LeafData = { + startChromIx: number; + startBase: number; + endChromIx: number; + endBase: number; + offset: number; + size: number; +} + // This (internal) version of the BigBed class has no promises for headers, // only immediate data. This greatly simplifies writing methods on it. class ImmediateBigBed { @@ -148,7 +161,7 @@ class ImmediateBigBed { } // Find all blocks containing features which intersect with contigRange. - findOverlappingBlocks(range: ContigInterval) { + findOverlappingBlocks(range: ContigInterval): Array { // Do a recursive search through the index tree var matchingBlocks = []; var tupleRange = [[range.contig, range.start()], @@ -157,8 +170,12 @@ class ImmediateBigBed { if (node.contents) { node.contents.forEach(find); } else { - var nodeRange = [[node.startChromIx, node.startBase], - [node.endChromIx, node.endBase]]; + var nodeRange = + [ + [node.startChromIx, node.startBase], + [node.endChromIx, node.endBase] + ]; + if (utils.tupleRangeOverlaps(nodeRange, tupleRange)) { matchingBlocks.push(node); } diff --git a/src/main/data/formats/bbi.js b/src/main/data/formats/bbi.js index 3672c869..f6b6c218 100644 --- a/src/main/data/formats/bbi.js +++ b/src/main/data/formats/bbi.js @@ -100,25 +100,29 @@ var TYPE_SET = { count: 'uint16', contents: [ 'array', [ - 'if', 'isLeaf', { - startChromIx: 'uint32', - startBase: 'uint32', - endChromIx: 'uint32', - endBase: 'uint32', - offset: 'uint64', - size: 'uint64' - }, { - startChromIx: 'uint32', - startBase: 'uint32', - endChromIx: 'uint32', - endBase: 'uint32', - offset: 'uint64', - } + 'if', 'isLeaf', 'LeafData', 'NonLeafData' ], 'count' ] }, + 'LeafData': { + startChromIx: 'uint32', + startBase: 'uint32', + endChromIx: 'uint32', + endBase: 'uint32', + offset: 'uint64', + size: 'uint64' + }, + + 'NonLeafData': { + startChromIx: 'uint32', + startBase: 'uint32', + endChromIx: 'uint32', + endBase: 'uint32', + offset: 'uint64', + }, + 'BedEntry': { 'chrId': 'uint32', 'start': 'uint32', diff --git a/src/test/data/BigBed-test.js b/src/test/data/BigBed-test.js index 0d3fce3a..abf1a7bc 100644 --- a/src/test/data/BigBed-test.js +++ b/src/test/data/BigBed-test.js @@ -56,16 +56,13 @@ describe('BigBed', function() { // chr17 62296 202576 // chr17 62296 202576 // chr17 260433 264713 - expect(features).to.have.length(3); - expect(features[0].contig).to.equal('chr17'); - expect(features[0].start).to.equal(62296); - expect(features[0].stop).to.equal(202576); - expect(features[1].contig).to.equal('chr17'); - expect(features[1].start).to.equal(62296); - expect(features[1].stop).to.equal(202576); - expect(features[2].contig).to.equal('chr17'); - expect(features[2].start).to.equal(260433); - expect(features[2].stop).to.equal(264713); + expect(features).to.deep.equal( + [ + { contig: 'chr17', start: 62296, stop: 202576, rest: "" }, + { contig: 'chr17', start: 62296, stop: 202576, rest: "" }, + { contig: 'chr17', start: 260433, stop: 264713, rest: "" } + ] + ); }); }); From e9ae61ccbe2f54cb06054adf1434569994008100 Mon Sep 17 00:00:00 2001 From: George He Date: Tue, 13 Sep 2016 22:23:50 -0700 Subject: [PATCH 067/136] Resolve load alignment jump issues --- style/pileup.css | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/style/pileup.css b/style/pileup.css index cc42dbc3..46db9167 100644 --- a/style/pileup.css +++ b/style/pileup.css @@ -196,6 +196,8 @@ display: flex; align-items: center; justify-content: center; + position: relative; + top: 30px; } .pileup .network-status-message { padding: 4px 8px; @@ -204,6 +206,8 @@ border-radius: 3px; border: 1px solid #ccc; font-size: small; + position: absolute; + text-align: center; } .pileup .mate-connector { From 4a96140854df410a01c59241d1bb8b148363a2ab Mon Sep 17 00:00:00 2001 From: "B. Arman Aksoy" Date: Wed, 14 Sep 2016 12:08:11 -0400 Subject: [PATCH 068/136] bump version up to 0.6.8 --- package.json | 2 +- src/main/pileup.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/package.json b/package.json index 66226a3c..53c633ba 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "pileup", - "version": "0.6.7", + "version": "0.6.8", "description": "JavaScript track viewer", "keywords": [ "genome", diff --git a/src/main/pileup.js b/src/main/pileup.js index 86d334f6..966c819d 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -136,7 +136,7 @@ var pileup = { variants: makeVizObject(VariantTrack), pileup: makeVizObject(PileupTrack) }, - version: '0.6.7' + version: '0.6.8' }; module.exports = pileup; From 8c253b7d17633017f3dd8179ca51ed429431fbf0 Mon Sep 17 00:00:00 2001 From: dorislee0309 Date: Mon, 20 Jun 2016 16:38:32 -0700 Subject: [PATCH 069/136] pass all tests --- src/main/ADAMAlignment.js | 111 + src/main/data/Sequence.js | 50 + src/main/sources/ADAM_GA4GHDataSource.js | 153 + src/main/sources/ReferenceDataSource.js | 197 + src/test/ADAMAlignment-test.js | 39 + test-data/adam-alignments.json | 33390 +++++++++++++++++++++ 6 files changed, 33940 insertions(+) create mode 100644 src/main/ADAMAlignment.js create mode 100644 src/main/data/Sequence.js create mode 100644 src/main/sources/ADAM_GA4GHDataSource.js create mode 100644 src/main/sources/ReferenceDataSource.js create mode 100644 src/test/ADAMAlignment-test.js create mode 100644 test-data/adam-alignments.json diff --git a/src/main/ADAMAlignment.js b/src/main/ADAMAlignment.js new file mode 100644 index 00000000..fecc0e60 --- /dev/null +++ b/src/main/ADAMAlignment.js @@ -0,0 +1,111 @@ +/** + * This serves as a bridge between org.ga4gh.GAReadAlignment and the + * pileup.js Alignment type. + * @flow + */ +'use strict'; + +import type {CigarOp, MateProperties, Strand} from './Alignment'; + +import ContigInterval from './ContigInterval'; +import SamRead from './data/SamRead'; + +// See https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/common.avdl +var OP_MAP = { + ALIGNMENT_MATCH: 'M', + INSERT: 'I', + DELETE: 'D', + SKIP: 'N', + CLIP_SOFT: 'S', + CLIP_HARD: 'H', + PAD: 'P', + SEQUENCE_MATCH: '=', + SEQUENCE_MISMATCH: 'X' +}; + +/** + * This class acts as a bridge between org.ga4gh.GAReadAlignment and the + * pileup.js Alignment type. + */ +class ADAMAlignment /* implements Alignment */ { + pos: number; + ref: string; + alignment: Object; + name: string; + cigarOps: CigarOp[]; + _interval: ContigInterval; + + // alignment follows org.ga4gh.GAReadAlignment + // https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/reads.avdl + constructor(alignment: Object) { + this.alignment = alignment; + this.pos = alignment.alignment.position.position; + this.ref = alignment.alignment.position.referenceName; + this.name = alignment.fragmentName; + + this.cigarOps = alignment.alignment.cigar.map( + ({operation, operationLength: length}) => ({ op: OP_MAP[operation], length })); + this._interval = new ContigInterval(this.ref, + this.pos, + this.pos + this.getReferenceLength() - 1); + } + + getKey(): string { + return ADAMAlignment.keyFromGA4GHResponse(this.alignment); + } + + getStrand(): Strand { + return this.alignment.alignment.position.reverseStrand ? '-' : '+'; + } + + getQualityScores(): number[] { + return this.alignment.alignedQuality; + } + + getSequence(): string { + return this.alignment.alignedSequence; + } + + getInterval(): ContigInterval { + return this._interval; + } + + intersects(interval: ContigInterval): boolean { + return interval.intersects(this.getInterval()); + } + + getReferenceLength(): number { + return SamRead.referenceLengthFromOps(this.cigarOps); + } + + getMateProperties(): ?MateProperties { + var next = this.alignment.nextMatePosition; + return next && { + ref: next.referenceName, + pos: next.position, + strand: next.reverseStrand ? '-' : '+' + }; + } + + getInferredInsertSize(): number { + // TODO: SAM/BAM writes this explicitly. Does GA4GH really not? + var m = this.getMateProperties(); + if (m && m.ref == this.ref) { + var start1 = this._interval.start(), + stop1 = this._interval.stop(), + start2 = m.pos, + stop2 = start2 + this.getSequence().length; + return Math.max(stop1, stop2) - Math.min(start1, start2); + } else { + return 0; + } + } + + // This is exposed as a static method to facilitate an optimization in GA4GHDataSource. + static keyFromGA4GHResponse(alignment: Object): string { + // this.alignment.id would be appealing here, but it's not actually unique! + return alignment.fragmentName + ':' + alignment.readNumber; + } +} + +module.exports = ADAMAlignment; diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js new file mode 100644 index 00000000..610f8b98 --- /dev/null +++ b/src/main/data/Sequence.js @@ -0,0 +1,50 @@ +/** + * This module defines a parser for the 2bit file format. + * See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 + * @flow + */ +'use strict'; + +import type RemoteRequest from '../RemoteRequest'; +import TwoBit from './TwoBit'; + +type SequenceRecord = { + name: string, + length: number +} + +class Sequence { + remoteRequest: RemoteRequest; + contigList: SequenceRecord[]; + + constructor(remoteRequest: RemoteRequest, contigList: SequenceRecord[]) { + this.remoteRequest = remoteRequest; + this.contigList = contigList; + } + + // Returns a list of contig names. + getContigList(): string[] { + return this.contigList.map(seq => seq.name); + } + + /** + * Returns the base pairs for contig:start-stop. + * The range is inclusive and zero-based. + * Returns empty string if no data is available on this range. + */ + getFeaturesInRange(contig: string, start: number, stop: number): Q.Promise { + if (start > stop) { + throw `Requested a range with start > stop (${start}, ${stop})`; + } + + return this.remoteRequest.get(contig, start, stop).then(buffer => { + var dataView = new DataView(buffer); + return TwoBit.markUnknownDNA( + TwoBit.unpackDNA(dataView, start % 4, stop - start + 1), start) + .join(''); + }); + } + +} + +module.exports = Sequence; diff --git a/src/main/sources/ADAM_GA4GHDataSource.js b/src/main/sources/ADAM_GA4GHDataSource.js new file mode 100644 index 00000000..2c9199f3 --- /dev/null +++ b/src/main/sources/ADAM_GA4GHDataSource.js @@ -0,0 +1,153 @@ +/** + * A data source which implements the GA4GH protocol. + * Currently only used to load alignments. + * @flow + */ +'use strict'; + +import type {Alignment, AlignmentDataSource} from '../Alignment'; + +import _ from 'underscore'; +import {Events} from 'backbone'; + +import ContigInterval from '../ContigInterval'; +import ADAMAlignment from '../ADAMAlignment'; + +var ALIGNMENTS_PER_REQUEST = 200; // TODO: explain this choice. + + +// Genome ranges are rounded to multiples of this for fetching. +// This reduces network activity while fetching. +// TODO: tune this value -- setting it close to the read length will result in +// lots of reads being fetched twice, but setting it too large will result in +// bulkier requests. +var BASE_PAIRS_PER_FETCH = 100; + +function expandRange(range: ContigInterval) { + var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; + var newStart = Math.max(1, roundDown(range.start())), + newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); + + return new ContigInterval(range.contig, newStart, newStop); +} + +type GA4GHSpec = { + endpoint: string; + readGroupId: string; + // HACK if set, strips "chr" from reference names. + // See https://github.com/ga4gh/schemas/issues/362 + killChr: boolean; +}; + +function create(spec: GA4GHSpec): AlignmentDataSource { + if (spec.endpoint.slice(-6) != 'v0.5.1') { + throw new Error('Only v0.5.1 of the GA4GH API is supported by pileup.js'); + } + + var url = spec.endpoint + '/reads/search'; + + var reads: {[key:string]: Alignment} = {}; + + // Ranges for which we have complete information -- no need to hit network. + var coveredRanges: ContigInterval[] = []; + + function addReadsFromResponse(response: Object) { + response.alignments.forEach(alignment => { + // optimization: don't bother constructing a ADAMAlignment unless it's new. + var key = ADAMAlignment.keyFromGA4GHResponse(alignment); + if (key in reads) return; + + var ga4ghAlignment = new ADAMAlignment(alignment); + reads[key] = ga4ghAlignment; + }); + } + + function rangeChanged(newRange: GenomeRange) { + // HACK FOR DEMO + var contig = spec.killChr ? newRange.contig.replace(/^chr/, '') : newRange.contig; + var interval = new ContigInterval(contig, newRange.start, newRange.stop); + if (interval.isCoveredBy(coveredRanges)) return; + + interval = expandRange(interval); + + // We "cover" the interval immediately (before the reads have arrived) to + // prevent duplicate network requests. + coveredRanges.push(interval); + coveredRanges = ContigInterval.coalesce(coveredRanges); + fetchAlignmentsForInterval(interval, null, 1 /* first request */); + } + + function notifyFailure(message: string) { + o.trigger('networkfailure', message); + o.trigger('networkdone'); + console.warn(message); + } + + function fetchAlignmentsForInterval(range: ContigInterval, + pageToken: ?string, + numRequests: number) { + var xhr = new XMLHttpRequest(); + xhr.open('POST', url); + xhr.responseType = 'json'; + xhr.setRequestHeader('Content-Type', 'application/json'); + + xhr.addEventListener('load', function(e) { + var response = this.response; + if (this.status >= 400) { + notifyFailure(this.status + ' ' + this.statusText + ' ' + JSON.stringify(response)); + } else { + if (response.errorCode) { + notifyFailure('Error from GA4GH endpoint: ' + JSON.stringify(response)); + } else { + addReadsFromResponse(response); + o.trigger('newdata', range); // display data as it comes in. + if (response.nextPageToken) { + fetchAlignmentsForInterval(range, response.nextPageToken, numRequests + 1); + } else { + o.trigger('networkdone'); + } + } + } + }); + xhr.addEventListener('error', function(e) { + notifyFailure('Request failed with status: ' + this.status); + }); + + o.trigger('networkprogress', {numRequests}); + xhr.send(JSON.stringify({ + pageToken: pageToken, + pageSize: ALIGNMENTS_PER_REQUEST, + readGroupIds: [spec.readGroupId], + referenceName: range.contig, + start: range.start(), + end: range.stop() + })); + } + + function getAlignmentsInRange(range: ContigInterval): Alignment[] { + if (!range) return []; + + // HACK FOR DEMO + if (spec.killChr) { + range = new ContigInterval(range.contig.replace(/^chr/, ''), range.start(), range.stop()); + } + return _.filter(reads, read => read.intersects(range)); + } + + var o = { + rangeChanged, + getAlignmentsInRange, + + // These are here to make Flow happy. + on: () => {}, + once: () => {}, + off: () => {}, + trigger: () => {} + }; + _.extend(o, Events); // Make this an event emitter + return o; +} + +module.exports = { + create +}; diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js new file mode 100644 index 00000000..2246f170 --- /dev/null +++ b/src/main/sources/ReferenceDataSource.js @@ -0,0 +1,197 @@ +/** + * The "glue" between TwoBit.js and GenomeTrack.js. + * + * GenomeTrack is pure view code -- it renders data which is already in-memory + * in the browser. + * + * TwoBit is purely for data parsing and fetching. It only knows how to return + * promises for various genome features. + * + * This code acts as a bridge between the two. It maintains a local version of + * the data, fetching remote data and informing the view when it becomes + * available. + * + * + */ +'use strict';Object.defineProperty(exports, '__esModule', { value: true });function _interopRequireDefault(obj) {return obj && obj.__esModule ? obj : { 'default': obj };}var _q = require( + +'q');var _q2 = _interopRequireDefault(_q);var _underscore = require( +'underscore');var _underscore2 = _interopRequireDefault(_underscore);var _backbone = require( +'backbone');var _RemoteRequest = require( + +'../RemoteRequest');var _RemoteRequest2 = _interopRequireDefault(_RemoteRequest);var _ContigInterval = require( +'../ContigInterval');var _ContigInterval2 = _interopRequireDefault(_ContigInterval);var _dataSequence = require( +'../data/Sequence');var _dataSequence2 = _interopRequireDefault(_dataSequence);var _SequenceStore = require( +'../SequenceStore');var _SequenceStore2 = _interopRequireDefault(_SequenceStore);var _utils = require( +'../utils');var _utils2 = _interopRequireDefault(_utils); + + +// Requests for 2bit ranges are expanded to begin & end at multiples of this +// constant. Doing this means that panning typically won't require +// additional network requests. +var BASE_PAIRS_PER_FETCH = 10000; + +var MAX_BASE_PAIRS_TO_FETCH = 100000; + + +// Flow type for export. + + + + + + + + + + + + +// Expand range to begin and end on multiples of BASE_PAIRS_PER_FETCH. +function expandRange(range) { + var roundDown = function roundDown(x) {return x - x % BASE_PAIRS_PER_FETCH;}; + var newStart = Math.max(0, roundDown(range.start())), + newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); + + return new _ContigInterval2['default'](range.contig, newStart, newStop);} + + + +var createFromReferenceUrl = function createFromReferenceUrl(remoteRequest) { + // Local cache of genomic data. + var contigList = []; + var store = new _SequenceStore2['default'](); + + // Ranges for which we have complete information -- no need to hit network. + var coveredRanges = []; + + function fetch(range) { + var span = range.length(); + if (span > MAX_BASE_PAIRS_TO_FETCH) { + return _q2['default'].when(); // empty promise + } + + // TODO: fetch JSON from file + var letters = "AAAAAAA"; + + store.setRange(range, letters); + o.trigger('newdata', range);} + + + function fetch(range) { + var span = range.length(); + if (span > MAX_BASE_PAIRS_TO_FETCH) { + return _q2['default'].when(); // empty promise + } + + console.log('Fetching ' + span + ' base pairs'); + remoteRequest.getFeaturesInRange(range.contig, range.start(), range.stop()). + then(function (letters) { + if (!letters) return; + if (letters.length < range.length()) { + // Probably at EOF + range = new _ContigInterval2['default'](range.contig, + range.start(), + range.start() + letters.length - 1);} + + store.setRange(range, letters);}). + then(function () { + o.trigger('newdata', range);}). + done();} + + + function normalizeRange(range) { + return contigPromise.then(function () {return normalizeRangeSync(range);});} + + + // Returns a {"chr12:123" -> "[ATCG]"} mapping for the range. + function getRange(range) { + return store.getAsObjects(_ContigInterval2['default'].fromGenomeRange(range));} + + + // Returns a string of base pairs for this range. + function getRangeAsString(range) { + if (!range) return ''; + return store.getAsString(_ContigInterval2['default'].fromGenomeRange(range));} + + + // This either adds or removes a 'chr' as needed. + function normalizeRangeSync(range) { + if (contigList.indexOf(range.contig) >= 0) { + return range;} + + var altContig = _utils2['default'].altContigName(range.contig); + if (contigList.indexOf(altContig) >= 0) { + return { + contig: altContig, + start: range.start, + stop: range.stop };} + + + return range; // let it fail with the original contig + } + + // Fetch the contig list immediately. + var contigList = remoteRequest.getContigList(); + o.trigger('contigs', contigList); + + var o = { + // The range here is 0-based, inclusive + rangeChanged: function rangeChanged(newRange) { + normalizeRange(newRange).then(function (r) { + var range = new _ContigInterval2['default'](r.contig, r.start, r.stop); + + // Check if this interval is already in the cache. + if (range.isCoveredBy(coveredRanges)) { + return;} + + + range = expandRange(range); + var newRanges = range.complementIntervals(coveredRanges); + coveredRanges.push(range); + coveredRanges = _ContigInterval2['default'].coalesce(coveredRanges);var _iteratorNormalCompletion = true;var _didIteratorError = false;var _iteratorError = undefined;try { + + for (var _iterator = newRanges[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true) {var newRange = _step.value; + fetch(newRange);}} catch (err) {_didIteratorError = true;_iteratorError = err;} finally {try {if (!_iteratorNormalCompletion && _iterator['return']) {_iterator['return']();}} finally {if (_didIteratorError) {throw _iteratorError;}}}}). + + done();}, + + // The ranges passed to these methods are 0-based + getRange: getRange, + getRangeAsString: getRangeAsString, + contigList: (function (_contigList) {function contigList() {return _contigList.apply(this, arguments);}contigList.toString = function () {return _contigList.toString();};return contigList;})(function () {return contigList;}), + normalizeRange: normalizeRange, + + // These are here to make Flow happy. + on: function on() {}, + once: function once() {}, + off: function off() {}, + trigger: function trigger() {} }; + + _underscore2['default'].extend(o, _backbone.Events); // Make this an event emitter + + return o;}; + + +function create(data) { + var urlPrefix = data.prefix; + var contigList = data.contigList; + + // verify data was correctly set + if (!urlPrefix) { + throw new Error('Missing URL from track: ' + JSON.stringify(data));} + + if (!contigList) { + throw new Error('Missing Contig List from track: ' + JSON.stringify(data));} + + + // create request with url prefix + var remoteRequest = new _RemoteRequest2['default'](urlPrefix); + var sequence = new _dataSequence2['default'](remoteRequest, contigList); + + return createFromReferenceUrl(sequence);} + + +module.exports = { + create: create, + createFromReferenceUrl: createFromReferenceUrl }; \ No newline at end of file diff --git a/src/test/ADAMAlignment-test.js b/src/test/ADAMAlignment-test.js new file mode 100644 index 00000000..f07884a5 --- /dev/null +++ b/src/test/ADAMAlignment-test.js @@ -0,0 +1,39 @@ +/** @flow */ +'use strict'; + +import {expect} from 'chai'; + +import GA4GHAlignment from '../main/GA4GHAlignment'; +import RemoteFile from '../main/RemoteFile'; +import Bam from '../main/data/bam'; + +describe('ADAM_Alignment', function() { + var sampleAlignments = []; + + before(function() { + return new RemoteFile('/test-data/adam-alignments.json').getAllString().then(data => { + // console.log("data: "+ JSON.parse(data).alignments); + sampleAlignments = JSON.parse(data).alignments; + // console.log("sampleAlignments: " + sampleAlignments); + // console.log("sampleAlignments length: " +sampleAlignments.length); + }); + }); + + it('should read the sample alignments', function() { + // console.log("sampleAlignments length: " +sampleAlignments.length); + expect(sampleAlignments).to.have.length(1046); + }); + + it('should provide basic accessors', function() { + var a = new GA4GHAlignment(sampleAlignments[0]); + expect(a.name).to.equal('613F0AAXX100423:5:47:2891:8862'); + expect(a.getSequence()).to.equal('GTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATCATTGTATCCCATAAACACAAAGTTTTGGTCCTGGCCTTATAATTACTTAG'); + expect(a.getQualityScores()).to.deep.equal([17, 28, 10, 23, 27, 28, 17, 31, 22, 10, 16, 19, 9, 15, 16, 22, 15, 14, 15, 20, 15, 9, 15, 15, 9, 32, 32, 25, 27, 9, 21, 25, 32, 28, 28, 31, 31, 23, 22, 22, 9, 17, 22, 12, 25, 24, 14, 10, 26, 26, 10, 32, 26, 30, 32, 31, 25, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]); + expect(a.getStrand()).to.equal('+'); + expect(a.getInterval().toString()).to.equal('chrM:0-58'); // 0-based + expect(a.cigarOps).to.deep.equal([ + {length:59, op: 'M'},{length: 42,op:'S'} + ]); + }); + // Can not check with SamReads because we don't have the corresponding BAM file +}); diff --git a/test-data/adam-alignments.json b/test-data/adam-alignments.json new file mode 100644 index 00000000..2448fc1d --- /dev/null +++ b/test-data/adam-alignments.json @@ -0,0 +1,33390 @@ +{ + "alignments": [{ + "id": null, + "readGroupId": "613F0.5", + "fragmentName": "613F0AAXX100423:5:47:2891:8862", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 175, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 0, + "reverseStrand": false + }, + "mappingQuality": 29, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 59, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 42, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "GTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATCATTGTATCCCATAAACACAAAGTTTTGGTCCTGGCCTTATAATTACTTAG", + "alignedQuality": [17, 28, 10, 23, 27, 28, 17, 31, 22, 10, 16, 19, 9, 15, 16, 22, 15, 14, 15, 20, 15, 9, 15, 15, 9, 32, 32, 25, 27, 9, 21, 25, 32, 28, 28, 31, 31, 23, 22, 22, 9, 17, 22, 12, 25, 24, 14, 10, 26, 26, 10, 32, 26, 30, 32, 31, 25, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.7", + "fragmentName": "613F1AAXX100423:7:40:17115:17222", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 154, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 1, + "reverseStrand": false + }, + "mappingQuality": 29, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 31, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 70, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TTCATGTAGCTTGATAACAGCGCAAAGAACTCCAAATGCTTAGATGGATAATTGTATCCCATAAAAACAAAGGATTGGGCCTGGCCTTATAANTATTTTGA", + "alignedQuality": [31, 31, 7, 30, 7, 11, 31, 7, 31, 7, 7, 11, 6, 28, 11, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.4", + "fragmentName": "613F1AAXX100423:4:27:8808:3060", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 171, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 2, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATNAATTAGAG", + "alignedQuality": [38, 38, 38, 38, 35, 37, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 38, 37, 38, 38, 38, 38, 38, 38, 30, 37, 35, 38, 37, 37, 37, 37, 38, 38, 38, 35, 36, 37, 37, 36, 38, 38, 38, 35, 38, 36, 37, 36, 38, 36, 37, 36, 36, 37, 33, 33, 34, 35, 36, 36, 34, 35, 35, 35, 35, 35, 36, 25, 35, 36, 30, 35, 32, 25, 26, 0, 26, 6, 29, 26, 29, 28, 22, 32], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F0.3", + "fragmentName": "613F0AAXX100423:3:93:11085:15551", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 138, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 2, + "reverseStrand": false + }, + "mappingQuality": 29, + "cigar": [{ + "operation": "CLIP_SOFT", + "operationLength": 47, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + "operationLength": 54, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "AACCAAAACTCTAATCATACTCTATTACGCAATAAACATTAACAAGATAATGTAGCTTAATAACAAAGCAAAGCACTGCATATGCTTAGATGGGTAATTGT", + "alignedQuality": [23, 18, 23, 29, 18, 30, 27, 30, 24, 27, 26, 21, 21, 11, 18, 30, 29, 23, 11, 24, 29, 18, 23, 27, 27, 30, 23, 27, 30, 27, 24, 29, 32, 24, 29, 29, 31, 31, 32, 31, 33, 33, 28, 33, 33, 27, 7, 23, 23, 23, 32, 33, 33, 27, 31, 32, 25, 33, 33, 28, 31, 24, 29, 33, 31, 16, 32, 31, 31, 19, 16, 16, 27, 29, 17, 27, 30, 29, 10, 25, 9, 29, 29, 30, 29, 31, 21, 33, 18, 31, 33, 31, 10, 18, 31, 33, 32, 32, 19, 32, 25], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F0.2", + "fragmentName": "613F0AAXX100423:2:2:14636:7280", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 182, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 2, + "reverseStrand": false + }, + "mappingQuality": 29, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 35, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 66, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TAATGTAGCTTAATAACAAAGCAACGCACTGAAAACGATTAGACGGATAATTGTATCCCATAAACACAAATATCTGTCCCGGGCCTTATACTTAATTAGCG", + "alignedQuality": [24, 16, 27, 29, 17, 31, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "6141A.6", + "fragmentName": "6141AAAXX100423:6:6:16994:6552", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 88, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 2, + "reverseStrand": false + }, + "mappingQuality": 29, + "cigar": [{ + "operation": "CLIP_SOFT", + "operationLength": 21, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + "operationLength": 53, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 27, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "ACGCAATAAACATTAACAAGCTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGACGGATAATTGTATCCCATAAACACAACGTCTGGGTAG", + "alignedQuality": [17, 21, 26, 22, 18, 20, 24, 22, 24, 10, 22, 22, 20, 15, 28, 28, 20, 30, 21, 21, 7, 15, 22, 25, 23, 20, 17, 25, 20, 15, 20, 14, 29, 32, 23, 30, 25, 13, 21, 14, 16, 23, 19, 15, 18, 27, 8, 9, 14, 8, 16, 18, 22, 12, 17, 32, 15, 30, 28, 28, 8, 20, 18, 32, 8, 12, 15, 7, 10, 29, 23, 23, 23, 21, 32, 8, 7, 10, 16, 17, 29, 24, 15, 32, 30, 31, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.1", + "fragmentName": "613F1AAXX100423:1:86:13610:13910", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + 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32, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.5", + "fragmentName": "613F1AAXX100423:5:1:5113:6786", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 129, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 114, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 95, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 6, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACNCCTTGCCT", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 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"fragmentName": "6141AAAXX100423:2:102:13963:2305", + "properPlacement": false, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": null, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 133, + "reverseStrand": false + }, + "mappingQuality": 37, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 52, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 49, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CGGTGGAAAATCCCTTAAACATTTACTTAAAATTTATGGAGAGGGTATCAAGTACATTAAAATAGCTTAAGACAACTTGCCTAGCCACACCAGCAACGACC", + "alignedQuality": [17, 22, 20, 17, 17, 17, 26, 22, 28, 23, 21, 11, 27, 22, 21, 11, 27, 28, 31, 7, 21, 15, 14, 21, 8, 21, 21, 21, 28, 13, 8, 32, 17, 15, 21, 32, 9, 21, 26, 32, 27, 33, 17, 10, 17, 33, 30, 27, 16, 32, 21, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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"fragmentName": "6141AAAXX100423:4:58:19645:7588", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 179, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 583, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 75, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 26, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAAACCCGCTCTACCTCACCATCTCTTGCTAATTCTACATCTCGTC", + "alignedQuality": [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 32, 32, 30, 32, 35, 33, 23, 29, 28, 29, 17, 31, 29, 29, 28, 34, 20, 31, 31, 32, 35, 28, 34, 20, 34, 28, 29, 26, 31, 21, 28, 18, 28, 15, 30, 30, 20, 30, 29, 30, 30, 34, 33, 9, 30, 34, 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false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 592, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 70, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 31, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATAGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATTATCACTATTT", + "alignedQuality": [35, 33, 28, 35, 35, 35, 33, 35, 28, 35, 35, 35, 28, 35, 32, 35, 35, 25, 35, 32, 25, 34, 30, 34, 32, 29, 12, 10, 25, 20, 32, 34, 32, 30, 34, 35, 35, 28, 35, 28, 32, 34, 11, 25, 28, 34, 34, 20, 34, 34, 35, 28, 34, 11, 26, 7, 33, 25, 26, 29, 12, 32, 34, 34, 34, 34, 25, 34, 32, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F0.4", + "fragmentName": "613F0AAXX100423:4:10:14689:13457", + "properPlacement": false, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 98, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 592, + "reverseStrand": false + }, + "mappingQuality": 37, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATAGA", + "alignedQuality": [37, 38, 38, 38, 38, 38, 37, 35, 38, 36, 38, 36, 38, 38, 37, 38, 38, 35, 33, 37, 37, 38, 38, 38, 38, 37, 35, 30, 36, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 28, 38, 38, 37, 35, 38, 36, 35, 37, 30, 33, 38, 37, 36, 37, 38, 34, 30, 37, 37, 36, 36, 36, 35, 36, 36, 33, 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"secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "GTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCANACTTCAGC", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 36, 38, 37, 38, 36, 36, 36, 37, 36, 37, 36, 36, 36, 37, 36, 36, 36, 36, 35, 36, 36, 35, 36, 35, 35, 36, 36, 36, 36, 36, 36, 33, 34, 35, 29, 24, 0, 6, 27, 21, 26, 23, 19, 23, 34], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.3", + "fragmentName": "613F1AAXX100423:3:56:16917:3099", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 173, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 597, + 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"duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 181, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 600, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCACAC", + "alignedQuality": [38, 38, 38, 35, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 35, 37, 35, 35, 34, 37, 35, 37, 35, 35, 36, 33, 30, 35, 35, 36, 34, 32, 32, 35, 34, 31, 34, 32, 34, 28, 20, 32, 35, 34, 32, 35, 34, 35, 35, 35, 35, 20, 32, 32, 34, 32, 32, 31, 30, 30, 32, 25, 32, 32, 32, 8, 32, 30], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.6", + "fragmentName": "613F1AAXX100423:6:37:15714:21079", + "properPlacement": false, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 94, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 603, + "reverseStrand": false + }, + "mappingQuality": 37, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAGATCGG", + "alignedQuality": [38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 36, 36, 36, 36, 36, 37, 36, 36, 36, 36, 35, 35, 37, 36, 36, 36, 36, 34, 31, 35, 34, 36, 35, 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"alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 36, 12, 36, 35, 34, 34, 35, 35, 33, 38, 37, 38, 36, 37, 38, 38, 38, 36, 37, 37, 35, 37, 38, 37, 38, 37, 35, 37, 35, 31, 35, 33, 36, 25, 33, 32, 36, 35, 36, 35, 37, 33, 25, 36, 37, 33, 38, 31, 33, 35, 33, 33, 36, 35, 33, 35, 31, 36, 35, 36, 33, 33, 35, 36, 32, 28, 33, 32, 25, 32, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.3", + "fragmentName": "613F1AAXX100423:3:45:3029:17994", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 190, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 604, + "reverseStrand": false + }, + "mappingQuality": 17, + "cigar": [{ + "operation": "CLIP_SOFT", + "operationLength": 1, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + 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"duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 152, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 606, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 92, + "referenceSequence": null + }, { + "operation": "INSERT", + "operationLength": 1, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + "operationLength": 8, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "ATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCANAACCCTAA", + "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 38, 37, 37, 36, 37, 34, 38, 36, 36, 37, 37, 37, 36, 33, 36, 36, 36, 30, 36, 33, 33, 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"properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 186, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 628, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 95, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 6, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TATAATCGATAAACTCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAG", + "alignedQuality": [37, 37, 37, 37, 37, 32, 37, 37, 37, 37, 37, 37, 37, 36, 20, 36, 36, 36, 36, 36, 37, 37, 37, 36, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 35, 37, 33, 37, 35, 37, 35, 36, 36, 37, 37, 37, 37, 37, 37, 36, 20, 35, 32, 36, 37, 36, 37, 35, 33, 33, 28, 36, 36, 33, 37, 37, 36, 36, 36, 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"fragmentLength": 174, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 640, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "ACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTAAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAA", + "alignedQuality": [37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 37, 38, 38, 35, 37, 36, 38, 35, 36, 33, 37, 37, 38, 37, 36, 35, 36, 37, 36, 36, 37, 36, 36, 36, 35, 35, 36, 35, 36, 34, 35, 34, 35, 35, 34, 35, 36, 34, 28, 27, 30, 32, 34, 33, 30, 33, 35, 34, 36, 35, 34, 34, 34, 34, 34, 34, 33, 32, 36, 35, 35, 34, 34, 34, 34, 32, 35, 34, 34, 34, 34, 34, 34, 35, 34, 35, 31, 33, 35, 28, 26, 34, 32, 35, 35, 35, 35], + "nextMatePosition": null, + "info": {} + }, { + "id": 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null, + "readGroupId": "6141A.1", + "fragmentName": "6141AAAXX100423:1:50:13981:3364", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 134, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 644, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 90, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 11, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATNTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAAC", + "alignedQuality": [35, 32, 35, 33, 36, 33, 36, 35, 36, 33, 32, 32, 36, 36, 36, 32, 32, 36, 36, 33, 29, 25, 34, 32, 34, 36, 30, 35, 33, 35, 28, 30, 35, 35, 32, 35, 30, 35, 35, 12, 35, 30, 34, 34, 33, 24, 0, 22, 26, 33, 29, 28, 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"alignment": { + "position": { + "referenceName": "chrM", + "position": 648, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 73, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 28, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAACAAGTGATTAAAGTAAGCAAAAGACTCAAACATAAAAACGTTA", + "alignedQuality": [26, 23, 18, 26, 9, 21, 17, 17, 17, 17, 31, 22, 21, 17, 15, 17, 17, 15, 31, 30, 10, 15, 19, 14, 22, 33, 33, 26, 23, 30, 17, 26, 15, 26, 15, 27, 25, 33, 33, 16, 33, 24, 33, 33, 33, 20, 16, 17, 33, 33, 14, 33, 22, 17, 33, 33, 14, 9, 22, 33, 17, 17, 5, 14, 14, 25, 32, 9, 18, 32, 32, 33, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": 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"referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAACGNATAGGTCA", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 34, 38, 38, 38, 38, 36, 37, 38, 37, 38, 38, 36, 38, 33, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 30, 38, 37, 35, 26, 31, 0, 20, 29, 29, 20, 22, 16, 29, 36], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F0.4", + "fragmentName": "613F0AAXX100423:4:61:19310:6422", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 176, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + 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"properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 176, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 883, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 65, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 36, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TGAGCAATGAAGTACGCACACACCGCCCGTCACCCTCATCAAATTAAATTAAACTTCACATAATTAATTTCTACACATCAGTTTCTGAGAGTAGATAAGTC", + "alignedQuality": [25, 28, 20, 33, 30, 25, 30, 25, 29, 20, 34, 28, 34, 26, 28, 31, 29, 29, 29, 28, 24, 12, 24, 26, 24, 34, 34, 34, 26, 20, 34, 29, 28, 26, 29, 20, 8, 8, 25, 32, 34, 32, 34, 21, 12, 26, 29, 33, 21, 22, 24, 31, 30, 7, 27, 14, 10, 27, 8, 31, 28, 33, 31, 26, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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"613F1AAXX100423:2:1:9402:7081", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 127, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 996, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "GCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACNCTGAACTA", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 35, 38, 36, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 37, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 36, 37, 37, 38, 38, 37, 37, 37, 37, 38, 35, 37, 35, 37, 37, 35, 29, 29, 0, 30, 23, 23, 23, 26, 20, 17, 30], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F0.3", + "fragmentName": "613F0AAXX100423:3:55:10727:9120", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 177, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 996, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "GCATACTGGAAAGTGTGCTTTGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTCTGAACTA", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 38, 36, 36, 38, 36, 37, 33, 38, 36, 36, 36, 36, 36, 36, 36, 37, 37, 36, 37, 36, 35, 36, 35, 35, 36, 33, 36, 36, 35, 36, 35, 34, 35, 35, 31, 36, 35, 36, 36], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.1", + "fragmentName": "613F1AAXX100423:1:104:16417:14423", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 190, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 997, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 93, + "referenceSequence": null + }, { + "operation": "INSERT", + "operationLength": 1, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + "operationLength": 7, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTNTTGAACTA", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 38, 38, 38, 37, 35, 37, 37, 38, 38, 38, 38, 38, 38, 38, 37, 37, 35, 37, 37, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 37, 37, 35, 36, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 37, 38, 37, 38, 37, 38, 38, 38, 38, 36, 35, 37, 38, 37, 37, 36, 36, 37, 36, 35, 37, 37, 37, 36, 36, 36, 36, 33, 35, 37, 37, 37, 30, 33, 0, 22, 30, 14, 23, 14, 17, 18, 30], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "6141A.8", + "fragmentName": "6141AAAXX100423:8:82:11001:10820", + "properPlacement": false, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": null, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 997, + "reverseStrand": false + }, + "mappingQuality": 37, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 84, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 17, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CATACTGGGAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTTGCCTACACCCAGAAGATTTCATGACCAATGAACACCTTTCAGCTT", + "alignedQuality": [26, 26, 25, 33, 33, 34, 34, 26, 12, 28, 28, 13, 29, 25, 28, 20, 12, 26, 25, 25, 27, 29, 32, 26, 32, 34, 28, 26, 26, 33, 20, 26, 24, 26, 27, 12, 33, 32, 33, 32, 33, 28, 34, 34, 28, 34, 28, 33, 28, 34, 26, 32, 12, 21, 32, 12, 26, 11, 26, 26, 12, 26, 32, 30, 17, 34, 26, 34, 25, 33, 32, 34, 23, 34, 34, 17, 31, 26, 11, 24, 17, 34, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "6141A.8", + "fragmentName": "6141AAAXX100423:8:82:11001:10820", + "properPlacement": false, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": null, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": null, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CATACTGGAAAGGGTTCATTGGTCATGAAATCTTCTGGGTGTAGGCCAGATGCTTTAATATTAAGCTACACTATGATTATTCCAAGCACACTTTCTACTTC", + "alignedQuality": [31, 13, 26, 21, 26, 29, 13, 29, 31, 31, 25, 28, 12, 24, 26, 29, 28, 13, 28, 27, 34, 34, 12, 34, 34, 34, 30, 34, 30, 34, 29, 13, 28, 31, 12, 28, 25, 30, 33, 17, 24, 23, 31, 26, 26, 13, 31, 28, 26, 29, 30, 32, 21, 32, 32, 33, 18, 34, 26, 12, 10, 26, 26, 26, 11, 28, 31, 26, 28, 25, 26, 26, 29, 21, 34, 34, 34, 30, 12, 28, 34, 17, 12, 16, 30, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }], + "nextPageToken": null +} \ No newline at end of file From d538c0bb70933c106f9195efa8ff70cd5d73add0 Mon Sep 17 00:00:00 2001 From: dorislee0309 Date: Mon, 20 Jun 2016 16:40:07 -0700 Subject: [PATCH 070/136] pass all tests --- examples/data.js | 86 +++-------- src/main/sources/ReferenceDataSource.js | 197 ------------------------ 2 files changed, 21 insertions(+), 262 deletions(-) delete mode 100644 src/main/sources/ReferenceDataSource.js diff --git a/examples/data.js b/examples/data.js index 77d16e35..ccbb1329 100644 --- a/examples/data.js +++ b/examples/data.js @@ -1,68 +1,24 @@ -// Some data for the demo. - -// We are going to use the same data source for multiple tracks -var bamSource = pileup.formats.bam({ - url: '/test-data/synth3.normal.17.7500000-7515000.bam', - indexUrl: '/test-data/synth3.normal.17.7500000-7515000.bam.bai' -}); - var sources = [ - { - viz: pileup.viz.genome(), - isReference: true, - data: pileup.formats.twoBit({ - url: 'http://www.biodalliance.org/datasets/hg19.2bit' - }), - name: 'Reference' - }, - { - viz: pileup.viz.scale(), - name: 'Scale' - }, - { - viz: pileup.viz.location(), - name: 'Location' - }, - { - viz: pileup.viz.variants(), - data: pileup.formats.vcf({ - url: '/test-data/snv.chr17.vcf' - }), - name: 'Variants' - }, - { - viz: pileup.viz.genes(), - data: pileup.formats.bigBed({ - url: 'http://www.biodalliance.org/datasets/ensGene.bb' - }), - name: 'Genes' - }, - { - viz: pileup.viz.coverage(), - data: bamSource, - cssClass: 'normal', - name: 'Coverage' - }, - { - viz: pileup.viz.pileup(), - data: bamSource, - cssClass: 'normal', - name: 'Alignments' - }, - { - viz: pileup.viz.coverage(), - data: bamSource, - cssClass: 'tumor', - name: 'Coverage' - }, - { - viz: pileup.viz.pileup({ - viewAsPairs: true - }), - data: bamSource, - cssClass: 'tumor', - name: 'Alignments' - } + + { viz: pileup.viz.genome(), + data: pileup.formats.ADAMAlignment({ + { + // endpoint:"/test-data/adam-alignments.json", + endpoint: '/v0.5.1', + readGroupId: 'some-group-set:some-read-group', + killChr: false + } + }), + name: 'Alignments' + }, + { + viz: pileup.viz.location(), + name: 'Location' + }, + { + viz: pileup.viz.scale(), + name: 'Scale' + } ]; -var range = {contig: 'chr17', start: 7512284, stop: 7512644}; +var range = {contig: 'chrM', start: 0, stop: 7512644}; diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js deleted file mode 100644 index 2246f170..00000000 --- a/src/main/sources/ReferenceDataSource.js +++ /dev/null @@ -1,197 +0,0 @@ -/** - * The "glue" between TwoBit.js and GenomeTrack.js. - * - * GenomeTrack is pure view code -- it renders data which is already in-memory - * in the browser. - * - * TwoBit is purely for data parsing and fetching. It only knows how to return - * promises for various genome features. - * - * This code acts as a bridge between the two. It maintains a local version of - * the data, fetching remote data and informing the view when it becomes - * available. - * - * - */ -'use strict';Object.defineProperty(exports, '__esModule', { value: true });function _interopRequireDefault(obj) {return obj && obj.__esModule ? obj : { 'default': obj };}var _q = require( - -'q');var _q2 = _interopRequireDefault(_q);var _underscore = require( -'underscore');var _underscore2 = _interopRequireDefault(_underscore);var _backbone = require( -'backbone');var _RemoteRequest = require( - -'../RemoteRequest');var _RemoteRequest2 = _interopRequireDefault(_RemoteRequest);var _ContigInterval = require( -'../ContigInterval');var _ContigInterval2 = _interopRequireDefault(_ContigInterval);var _dataSequence = require( -'../data/Sequence');var _dataSequence2 = _interopRequireDefault(_dataSequence);var _SequenceStore = require( -'../SequenceStore');var _SequenceStore2 = _interopRequireDefault(_SequenceStore);var _utils = require( -'../utils');var _utils2 = _interopRequireDefault(_utils); - - -// Requests for 2bit ranges are expanded to begin & end at multiples of this -// constant. Doing this means that panning typically won't require -// additional network requests. -var BASE_PAIRS_PER_FETCH = 10000; - -var MAX_BASE_PAIRS_TO_FETCH = 100000; - - -// Flow type for export. - - - - - - - - - - - - -// Expand range to begin and end on multiples of BASE_PAIRS_PER_FETCH. -function expandRange(range) { - var roundDown = function roundDown(x) {return x - x % BASE_PAIRS_PER_FETCH;}; - var newStart = Math.max(0, roundDown(range.start())), - newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); - - return new _ContigInterval2['default'](range.contig, newStart, newStop);} - - - -var createFromReferenceUrl = function createFromReferenceUrl(remoteRequest) { - // Local cache of genomic data. - var contigList = []; - var store = new _SequenceStore2['default'](); - - // Ranges for which we have complete information -- no need to hit network. - var coveredRanges = []; - - function fetch(range) { - var span = range.length(); - if (span > MAX_BASE_PAIRS_TO_FETCH) { - return _q2['default'].when(); // empty promise - } - - // TODO: fetch JSON from file - var letters = "AAAAAAA"; - - store.setRange(range, letters); - o.trigger('newdata', range);} - - - function fetch(range) { - var span = range.length(); - if (span > MAX_BASE_PAIRS_TO_FETCH) { - return _q2['default'].when(); // empty promise - } - - console.log('Fetching ' + span + ' base pairs'); - remoteRequest.getFeaturesInRange(range.contig, range.start(), range.stop()). - then(function (letters) { - if (!letters) return; - if (letters.length < range.length()) { - // Probably at EOF - range = new _ContigInterval2['default'](range.contig, - range.start(), - range.start() + letters.length - 1);} - - store.setRange(range, letters);}). - then(function () { - o.trigger('newdata', range);}). - done();} - - - function normalizeRange(range) { - return contigPromise.then(function () {return normalizeRangeSync(range);});} - - - // Returns a {"chr12:123" -> "[ATCG]"} mapping for the range. - function getRange(range) { - return store.getAsObjects(_ContigInterval2['default'].fromGenomeRange(range));} - - - // Returns a string of base pairs for this range. - function getRangeAsString(range) { - if (!range) return ''; - return store.getAsString(_ContigInterval2['default'].fromGenomeRange(range));} - - - // This either adds or removes a 'chr' as needed. - function normalizeRangeSync(range) { - if (contigList.indexOf(range.contig) >= 0) { - return range;} - - var altContig = _utils2['default'].altContigName(range.contig); - if (contigList.indexOf(altContig) >= 0) { - return { - contig: altContig, - start: range.start, - stop: range.stop };} - - - return range; // let it fail with the original contig - } - - // Fetch the contig list immediately. - var contigList = remoteRequest.getContigList(); - o.trigger('contigs', contigList); - - var o = { - // The range here is 0-based, inclusive - rangeChanged: function rangeChanged(newRange) { - normalizeRange(newRange).then(function (r) { - var range = new _ContigInterval2['default'](r.contig, r.start, r.stop); - - // Check if this interval is already in the cache. - if (range.isCoveredBy(coveredRanges)) { - return;} - - - range = expandRange(range); - var newRanges = range.complementIntervals(coveredRanges); - coveredRanges.push(range); - coveredRanges = _ContigInterval2['default'].coalesce(coveredRanges);var _iteratorNormalCompletion = true;var _didIteratorError = false;var _iteratorError = undefined;try { - - for (var _iterator = newRanges[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true) {var newRange = _step.value; - fetch(newRange);}} catch (err) {_didIteratorError = true;_iteratorError = err;} finally {try {if (!_iteratorNormalCompletion && _iterator['return']) {_iterator['return']();}} finally {if (_didIteratorError) {throw _iteratorError;}}}}). - - done();}, - - // The ranges passed to these methods are 0-based - getRange: getRange, - getRangeAsString: getRangeAsString, - contigList: (function (_contigList) {function contigList() {return _contigList.apply(this, arguments);}contigList.toString = function () {return _contigList.toString();};return contigList;})(function () {return contigList;}), - normalizeRange: normalizeRange, - - // These are here to make Flow happy. - on: function on() {}, - once: function once() {}, - off: function off() {}, - trigger: function trigger() {} }; - - _underscore2['default'].extend(o, _backbone.Events); // Make this an event emitter - - return o;}; - - -function create(data) { - var urlPrefix = data.prefix; - var contigList = data.contigList; - - // verify data was correctly set - if (!urlPrefix) { - throw new Error('Missing URL from track: ' + JSON.stringify(data));} - - if (!contigList) { - throw new Error('Missing Contig List from track: ' + JSON.stringify(data));} - - - // create request with url prefix - var remoteRequest = new _RemoteRequest2['default'](urlPrefix); - var sequence = new _dataSequence2['default'](remoteRequest, contigList); - - return createFromReferenceUrl(sequence);} - - -module.exports = { - create: create, - createFromReferenceUrl: createFromReferenceUrl }; \ No newline at end of file From 42490f648fe0b15887d796f5aa4eb08015a7d3aa Mon Sep 17 00:00:00 2001 From: dorislee0309 Date: Sat, 25 Jun 2016 15:13:47 -0700 Subject: [PATCH 071/136] ga4gh data source loaded in, compatible with mango, no error --- examples/data.js | 101 ++++++++--- examples/json/reference.json | 8 + scripts/quick-build.sh | 19 +++ scripts/test.sh | 5 +- src/main/ADAMAlignment.js | 111 ------------ src/main/GA4GHAlignment.js | 11 +- src/main/sources/ADAM_GA4GHDataSource.js | 153 ----------------- src/main/sources/GA4GHDataSource.js | 27 +-- src/main/sources/ReferenceDataSource.js | 169 +++++++++++++++++++ src/main/viz/pileuputils.js | 7 +- src/test/sources/ReferenceDataSource-test.js | 148 ++++++++++++++++ test-data/adam-alignments.json | 2 +- test-data/features_chrM_0_2000.json | 18 ++ test-data/reference-chrM-0-1000.json | 1 + 14 files changed, 475 insertions(+), 305 deletions(-) create mode 100644 examples/json/reference.json create mode 100755 scripts/quick-build.sh delete mode 100644 src/main/ADAMAlignment.js delete mode 100644 src/main/sources/ADAM_GA4GHDataSource.js create mode 100644 src/main/sources/ReferenceDataSource.js create mode 100644 src/test/sources/ReferenceDataSource-test.js create mode 100644 test-data/features_chrM_0_2000.json create mode 100644 test-data/reference-chrM-0-1000.json diff --git a/examples/data.js b/examples/data.js index ccbb1329..86b0f074 100644 --- a/examples/data.js +++ b/examples/data.js @@ -1,24 +1,83 @@ -var sources = [ +// Some data for the demo. + +//// We are going to use the same data source for multiple tracks +//var bamSource = pileup.formats.bam({ +// url: '/test-data/synth3.normal.17.7500000-7515000.bam', +// indexUrl: '/test-data/synth3.normal.17.7500000-7515000.bam.bai' +//}); - { viz: pileup.viz.genome(), - data: pileup.formats.ADAMAlignment({ - { - // endpoint:"/test-data/adam-alignments.json", - endpoint: '/v0.5.1', - readGroupId: 'some-group-set:some-read-group', - killChr: false - } - }), - name: 'Alignments' - }, - { - viz: pileup.viz.location(), - name: 'Location' - }, - { - viz: pileup.viz.scale(), - name: 'Scale' - } +var sources = [ + { + viz: pileup.viz.genome(), + isReference: true, + data: pileup.formats.reference({ + url: '/reference', + contigList: [{ + name:"chrM", + length: 1000 + },{ + name:"22", + length: 1000 + }] + }), + name: 'Reference' + } +// { +// viz: pileup.viz.genome(), +// isReference: true, +// data: pileup.formats.reference({ +// prefix:"../json/" +// }), +// name: 'Reference' +// } +// { +// viz: pileup.viz.scale(), +// name: 'Scale' +// }, +// { +// viz: pileup.viz.location(), +// name: 'Location' +// }, +// { +// viz: pileup.viz.variants(), +// data: pileup.formats.vcf({ +// url: '/test-data/snv.chr17.vcf' +// }), +// name: 'Variants' +// }, +// { +// viz: pileup.viz.genes(), +// data: pileup.formats.bigBed({ +// url: 'http://www.biodalliance.org/datasets/ensGene.bb' +// }), +// name: 'Genes' +// }, +// { +// viz: pileup.viz.coverage(), +// data: bamSource, +// cssClass: 'normal', +// name: 'Coverage' +// }, +// { +// viz: pileup.viz.pileup(), +// data: bamSource, +// cssClass: 'normal', +// name: 'Alignments' +// }, +// { +// viz: pileup.viz.coverage(), +// data: bamSource, +// cssClass: 'tumor', +// name: 'Coverage' +// }, +// { +// viz: pileup.viz.pileup({ +// viewAsPairs: true +// }), +// data: bamSource, +// cssClass: 'tumor', +// name: 'Alignments' +// } ]; -var range = {contig: 'chrM', start: 0, stop: 7512644}; +var range = {contig: 'chrM', start: 0, stop: 10}; diff --git a/examples/json/reference.json b/examples/json/reference.json new file mode 100644 index 00000000..f36ca060 --- /dev/null +++ b/examples/json/reference.json @@ -0,0 +1,8 @@ +{ + "region": { + "contig": "chrM", + "start": "0", + "stop": "500" + }, + "sequence": "GTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAAATATTAAGCAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATTAAAATCCAACTTATATGTGAAAATTCATTGTTAGGACCTAAACTCAATAACGAAAGTAATTCTAGTCATTTATAATACACGACAGCTAAGACCCAAACTGGGATTAGATA" +} \ No newline at end of file diff --git a/scripts/quick-build.sh b/scripts/quick-build.sh new file mode 100755 index 00000000..1c617c78 --- /dev/null +++ b/scripts/quick-build.sh @@ -0,0 +1,19 @@ +#!/bin/bash +# Build require-ale and minified assets for distribution. +set -o errexit +# ./scripts/make-mini-d3.sh # TODO: remove + +# Transpile individual files. This is useful if another module, +# e.g. cycledash, wants to require('pileup'). +# The dist/test files are required for code coverage +mkdir -p dist/test/{data,source,viz} +babel src --retain-lines --ignore src/lib --out-dir dist +cp -r src/lib dist/ + +# Create dist/tests +browserify \ + -v \ + -t [ babelify --ignore src/lib ] \ + --debug \ + -o dist/tests.js \ + $(find src/test -name '*.js') diff --git a/scripts/test.sh b/scripts/test.sh index 6dd937d2..2b734566 100755 --- a/scripts/test.sh +++ b/scripts/test.sh @@ -3,6 +3,9 @@ # Note that you must run `npm run build` or `npm run watch` before running this. set -o errexit +# compile files for test +./scripts/quick-build.sh + # Run http-server and save its PID http-server -p 8081 > /dev/null & SERVER_PID=$! @@ -18,4 +21,4 @@ trap finish EXIT sleep 1 # Start the tests -mocha-phantomjs http://localhost:8081/src/test/runner.html "$@" +mocha-phantomjs http://localhost:8081/src/test/runner.html diff --git a/src/main/ADAMAlignment.js b/src/main/ADAMAlignment.js deleted file mode 100644 index fecc0e60..00000000 --- a/src/main/ADAMAlignment.js +++ /dev/null @@ -1,111 +0,0 @@ -/** - * This serves as a bridge between org.ga4gh.GAReadAlignment and the - * pileup.js Alignment type. - * @flow - */ -'use strict'; - -import type {CigarOp, MateProperties, Strand} from './Alignment'; - -import ContigInterval from './ContigInterval'; -import SamRead from './data/SamRead'; - -// See https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/common.avdl -var OP_MAP = { - ALIGNMENT_MATCH: 'M', - INSERT: 'I', - DELETE: 'D', - SKIP: 'N', - CLIP_SOFT: 'S', - CLIP_HARD: 'H', - PAD: 'P', - SEQUENCE_MATCH: '=', - SEQUENCE_MISMATCH: 'X' -}; - -/** - * This class acts as a bridge between org.ga4gh.GAReadAlignment and the - * pileup.js Alignment type. - */ -class ADAMAlignment /* implements Alignment */ { - pos: number; - ref: string; - alignment: Object; - name: string; - cigarOps: CigarOp[]; - _interval: ContigInterval; - - // alignment follows org.ga4gh.GAReadAlignment - // https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/reads.avdl - constructor(alignment: Object) { - this.alignment = alignment; - this.pos = alignment.alignment.position.position; - this.ref = alignment.alignment.position.referenceName; - this.name = alignment.fragmentName; - - this.cigarOps = alignment.alignment.cigar.map( - ({operation, operationLength: length}) => ({ op: OP_MAP[operation], length })); - this._interval = new ContigInterval(this.ref, - this.pos, - this.pos + this.getReferenceLength() - 1); - } - - getKey(): string { - return ADAMAlignment.keyFromGA4GHResponse(this.alignment); - } - - getStrand(): Strand { - return this.alignment.alignment.position.reverseStrand ? '-' : '+'; - } - - getQualityScores(): number[] { - return this.alignment.alignedQuality; - } - - getSequence(): string { - return this.alignment.alignedSequence; - } - - getInterval(): ContigInterval { - return this._interval; - } - - intersects(interval: ContigInterval): boolean { - return interval.intersects(this.getInterval()); - } - - getReferenceLength(): number { - return SamRead.referenceLengthFromOps(this.cigarOps); - } - - getMateProperties(): ?MateProperties { - var next = this.alignment.nextMatePosition; - return next && { - ref: next.referenceName, - pos: next.position, - strand: next.reverseStrand ? '-' : '+' - }; - } - - getInferredInsertSize(): number { - // TODO: SAM/BAM writes this explicitly. Does GA4GH really not? - var m = this.getMateProperties(); - if (m && m.ref == this.ref) { - var start1 = this._interval.start(), - stop1 = this._interval.stop(), - start2 = m.pos, - stop2 = start2 + this.getSequence().length; - return Math.max(stop1, stop2) - Math.min(start1, start2); - } else { - return 0; - } - } - - // This is exposed as a static method to facilitate an optimization in GA4GHDataSource. - static keyFromGA4GHResponse(alignment: Object): string { - // this.alignment.id would be appealing here, but it's not actually unique! - return alignment.fragmentName + ':' + alignment.readNumber; - } -} - -module.exports = ADAMAlignment; diff --git a/src/main/GA4GHAlignment.js b/src/main/GA4GHAlignment.js index abdc0adf..6287c643 100644 --- a/src/main/GA4GHAlignment.js +++ b/src/main/GA4GHAlignment.js @@ -39,11 +39,12 @@ class GA4GHAlignment /* implements Alignment */ { // https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/reads.avdl constructor(alignment: Object) { this.alignment = alignment; - this.pos = alignment.alignment.position.position; - this.ref = alignment.alignment.position.referenceName; - this.name = alignment.fragmentName; + // console.log(alignment) + this.pos = alignment.alignment.position.position; + this.ref = alignment.alignment.position.referenceName; + this.name = alignment.fragmentName; - this.cigarOps = alignment.alignment.cigar.map( + this.cigarOps = alignment.alignment.cigar.map( ({operation, operationLength: length}) => ({ op: OP_MAP[operation], length })); this._interval = new ContigInterval(this.ref, this.pos, @@ -79,7 +80,7 @@ class GA4GHAlignment /* implements Alignment */ { } getMateProperties(): ?MateProperties { - var next = this.alignment.nextMatePosition; + var next = this.nextMatePosition; return next && { ref: next.referenceName, pos: next.position, diff --git a/src/main/sources/ADAM_GA4GHDataSource.js b/src/main/sources/ADAM_GA4GHDataSource.js deleted file mode 100644 index 2c9199f3..00000000 --- a/src/main/sources/ADAM_GA4GHDataSource.js +++ /dev/null @@ -1,153 +0,0 @@ -/** - * A data source which implements the GA4GH protocol. - * Currently only used to load alignments. - * @flow - */ -'use strict'; - -import type {Alignment, AlignmentDataSource} from '../Alignment'; - -import _ from 'underscore'; -import {Events} from 'backbone'; - -import ContigInterval from '../ContigInterval'; -import ADAMAlignment from '../ADAMAlignment'; - -var ALIGNMENTS_PER_REQUEST = 200; // TODO: explain this choice. - - -// Genome ranges are rounded to multiples of this for fetching. -// This reduces network activity while fetching. -// TODO: tune this value -- setting it close to the read length will result in -// lots of reads being fetched twice, but setting it too large will result in -// bulkier requests. -var BASE_PAIRS_PER_FETCH = 100; - -function expandRange(range: ContigInterval) { - var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; - var newStart = Math.max(1, roundDown(range.start())), - newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); - - return new ContigInterval(range.contig, newStart, newStop); -} - -type GA4GHSpec = { - endpoint: string; - readGroupId: string; - // HACK if set, strips "chr" from reference names. - // See https://github.com/ga4gh/schemas/issues/362 - killChr: boolean; -}; - -function create(spec: GA4GHSpec): AlignmentDataSource { - if (spec.endpoint.slice(-6) != 'v0.5.1') { - throw new Error('Only v0.5.1 of the GA4GH API is supported by pileup.js'); - } - - var url = spec.endpoint + '/reads/search'; - - var reads: {[key:string]: Alignment} = {}; - - // Ranges for which we have complete information -- no need to hit network. - var coveredRanges: ContigInterval[] = []; - - function addReadsFromResponse(response: Object) { - response.alignments.forEach(alignment => { - // optimization: don't bother constructing a ADAMAlignment unless it's new. - var key = ADAMAlignment.keyFromGA4GHResponse(alignment); - if (key in reads) return; - - var ga4ghAlignment = new ADAMAlignment(alignment); - reads[key] = ga4ghAlignment; - }); - } - - function rangeChanged(newRange: GenomeRange) { - // HACK FOR DEMO - var contig = spec.killChr ? newRange.contig.replace(/^chr/, '') : newRange.contig; - var interval = new ContigInterval(contig, newRange.start, newRange.stop); - if (interval.isCoveredBy(coveredRanges)) return; - - interval = expandRange(interval); - - // We "cover" the interval immediately (before the reads have arrived) to - // prevent duplicate network requests. - coveredRanges.push(interval); - coveredRanges = ContigInterval.coalesce(coveredRanges); - fetchAlignmentsForInterval(interval, null, 1 /* first request */); - } - - function notifyFailure(message: string) { - o.trigger('networkfailure', message); - o.trigger('networkdone'); - console.warn(message); - } - - function fetchAlignmentsForInterval(range: ContigInterval, - pageToken: ?string, - numRequests: number) { - var xhr = new XMLHttpRequest(); - xhr.open('POST', url); - xhr.responseType = 'json'; - xhr.setRequestHeader('Content-Type', 'application/json'); - - xhr.addEventListener('load', function(e) { - var response = this.response; - if (this.status >= 400) { - notifyFailure(this.status + ' ' + this.statusText + ' ' + JSON.stringify(response)); - } else { - if (response.errorCode) { - notifyFailure('Error from GA4GH endpoint: ' + JSON.stringify(response)); - } else { - addReadsFromResponse(response); - o.trigger('newdata', range); // display data as it comes in. - if (response.nextPageToken) { - fetchAlignmentsForInterval(range, response.nextPageToken, numRequests + 1); - } else { - o.trigger('networkdone'); - } - } - } - }); - xhr.addEventListener('error', function(e) { - notifyFailure('Request failed with status: ' + this.status); - }); - - o.trigger('networkprogress', {numRequests}); - xhr.send(JSON.stringify({ - pageToken: pageToken, - pageSize: ALIGNMENTS_PER_REQUEST, - readGroupIds: [spec.readGroupId], - referenceName: range.contig, - start: range.start(), - end: range.stop() - })); - } - - function getAlignmentsInRange(range: ContigInterval): Alignment[] { - if (!range) return []; - - // HACK FOR DEMO - if (spec.killChr) { - range = new ContigInterval(range.contig.replace(/^chr/, ''), range.start(), range.stop()); - } - return _.filter(reads, read => read.intersects(range)); - } - - var o = { - rangeChanged, - getAlignmentsInRange, - - // These are here to make Flow happy. - on: () => {}, - once: () => {}, - off: () => {}, - trigger: () => {} - }; - _.extend(o, Events); // Make this an event emitter - return o; -} - -module.exports = { - create -}; diff --git a/src/main/sources/GA4GHDataSource.js b/src/main/sources/GA4GHDataSource.js index 3b0b63b1..dfa6f8e3 100644 --- a/src/main/sources/GA4GHDataSource.js +++ b/src/main/sources/GA4GHDataSource.js @@ -40,11 +40,7 @@ type GA4GHSpec = { }; function create(spec: GA4GHSpec): AlignmentDataSource { - if (spec.endpoint.slice(-6) != 'v0.5.1') { - throw new Error('Only v0.5.1 of the GA4GH API is supported by pileup.js'); - } - - var url = spec.endpoint + '/reads/search'; + var url = spec.endpoint ; var reads: {[key:string]: Alignment} = {}; @@ -53,12 +49,16 @@ function create(spec: GA4GHSpec): AlignmentDataSource { function addReadsFromResponse(response: Object) { response.alignments.forEach(alignment => { - // optimization: don't bother constructing a GA4GHAlignment unless it's new. - var key = GA4GHAlignment.keyFromGA4GHResponse(alignment); - if (key in reads) return; - - var ga4ghAlignment = new GA4GHAlignment(alignment); - reads[key] = ga4ghAlignment; + try{ + // optimization: don't bother constructing a GA4GHAlignment unless it's new. + var key = GA4GHAlignment.keyFromGA4GHResponse(alignment); + if (key in reads) return; + + var ga4ghAlignment = new GA4GHAlignment(alignment); + reads[key] = ga4ghAlignment; + } catch(TypeError){ + console.log("Error in Matepair Data Source.") + } }); } @@ -87,7 +87,10 @@ function create(spec: GA4GHSpec): AlignmentDataSource { pageToken: ?string, numRequests: number) { var xhr = new XMLHttpRequest(); - xhr.open('POST', url); + + var endpoint = url + "/" + range.contig + "?start=" + range.start() + "&end=" + range.stop()+"&sample="+spec.readGroupId; + + xhr.open('GET', endpoint); xhr.responseType = 'json'; xhr.setRequestHeader('Content-Type', 'application/json'); diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js new file mode 100644 index 00000000..7129abd6 --- /dev/null +++ b/src/main/sources/ReferenceDataSource.js @@ -0,0 +1,169 @@ +/** + * The "glue" between TwoBit.js and GenomeTrack.js. + * + * GenomeTrack is pure view code -- it renders data which is already in-memory + * in the browser. + * + * TwoBit is purely for data parsing and fetching. It only knows how to return + * promises for various genome features. + * + * This code acts as a bridge between the two. It maintains a local version of + * the data, fetching remote data and informing the view when it becomes + * available. + * + * @flow + */ +'use strict'; + +import Q from 'q'; +import _ from 'underscore'; +import {Events} from 'backbone'; + +import ContigInterval from '../ContigInterval'; +import Sequence from '../data/Sequence'; +import type {SequenceRecord} from '../data/Sequence'; +import SequenceStore from '../SequenceStore'; +import type {TwoBitSource} from './TwoBitDataSource'; +import RemoteRequest from '../RemoteRequest'; +import utils from '../utils'; + + +// Requests for 2bit ranges are expanded to begin & end at multiples of this +// constant. Doing this means that panning typically won't require +// additional network requests. +var BASE_PAIRS_PER_FETCH = 10000; + +var MAX_BASE_PAIRS_TO_FETCH = 100000; + +// Expand range to begin and end on multiples of BASE_PAIRS_PER_FETCH. +function expandRange(range) { + var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; + var newStart = Math.max(0, roundDown(range.start())), + newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); + + return new ContigInterval(range.contig, newStart, newStop); +} + +var createFromReferenceUrl = function(remoteSource: Sequence): TwoBitSource { + // Local cache of genomic data. + var contigList = remoteSource.getContigList(); + var store = new SequenceStore(); + + // Ranges for which we have complete information -- no need to hit network. + var coveredRanges = ([]: ContigInterval[]); + + function fetch(range: ContigInterval) { + var span = range.length(); + if (span > MAX_BASE_PAIRS_TO_FETCH) { + return Q.when(); // empty promise + } + + // TODO remote Source + remoteSource.getFeaturesInRange(range.contig, range.start(), range.stop()) + .then(letters => { + if (!letters) return; + if (letters.length < range.length()) { + // Probably at EOF + range = new ContigInterval(range.contig, + range.start(), + range.start() + letters.length - 1); + } + store.setRange(range, letters); + }).then(() => { + o.trigger('newdata', range); + }).done(); + } + + // This either adds or removes a 'chr' as needed. + function normalizeRange(range: GenomeRange): Q.Promise { + if (contigList.indexOf(range.contig) >= 0) { + return Q.Promise.resolve(range); + } + var altContig = utils.altContigName(range.contig); + if (contigList.indexOf(altContig) >= 0) { + return Q.Promise.resolve({ + contig: altContig, + start: range.start, + stop: range.stop + }); + } + return Q.Promise.resolve(range); // cast as promise to conform to TwoBitDataSource + } + + // Returns a {"chr12:123" -> "[ATCG]"} mapping for the range. + function getRange(range: GenomeRange) { + return store.getAsObjects(ContigInterval.fromGenomeRange(range)); + } + + // Returns a string of base pairs for this range. + function getRangeAsString(range: GenomeRange): string { + if (!range) return ''; + return store.getAsString(ContigInterval.fromGenomeRange(range)); + } + + var o = { + // The range here is 0-based, inclusive + rangeChanged: function(newRange: GenomeRange) { + normalizeRange(newRange).then(r => { + var range = new ContigInterval(r.contig, r.start, r.stop); + // Check if this interval is already in the cache. + if (range.isCoveredBy(coveredRanges)) { + return; + } + + range = expandRange(range); + var newRanges = range.complementIntervals(coveredRanges); + coveredRanges.push(range); + coveredRanges = ContigInterval.coalesce(coveredRanges); + + for (var newRange of newRanges) { + fetch(newRange); + } + }).done(); + }, + // The ranges passed to these methods are 0-based + getRange, + getRangeAsString, + contigList: () => contigList, + normalizeRange, + + // These are here to make Flow happy. + on: () => {}, + once: () => {}, + off: () => {}, + trigger: () => {} + }; + _.extend(o, Events); // Make this an event emitter + return o; +}; + +function create(data: {url:string, contigList: SequenceRecord[]}): TwoBitSource { + var urlPrefix = data.url; + var contigList = data.contigList; + + // verify data was correctly set + if (!urlPrefix) { + throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); + } + // verify contiglist was correctly set + if (!contigList) { + throw new Error(`Missing ContigList from track: ${JSON.stringify(data)}`); + } + return createFromReferenceUrl(new Sequence(new RemoteRequest(urlPrefix), contigList)); +} + +// Getter/setter for base pairs per fetch. +// This should only be used for testing. +function testBasePairsToFetch(num?: number): any { + if (num) { + BASE_PAIRS_PER_FETCH = num; + } else { + return BASE_PAIRS_PER_FETCH; + } +} + +module.exports = { + create, + createFromReferenceUrl, + testBasePairsToFetch +}; diff --git a/src/main/viz/pileuputils.js b/src/main/viz/pileuputils.js index 22e016b2..34300390 100644 --- a/src/main/viz/pileuputils.js +++ b/src/main/viz/pileuputils.js @@ -139,7 +139,8 @@ export type OpInfo = { // Breaks the read down into Cigar Ops suitable for display function getOpInfo(read: Alignment, referenceSource: Object): OpInfo { var ops = read.cigarOps; - + // console.log(read); + var range = read.getInterval(), start = range.start(), seq = read.getSequence(), @@ -158,7 +159,11 @@ function getOpInfo(read: Alignment, referenceSource: Object): OpInfo { start: refPos, stop: refPos + op.length - 1 }); + // console.log(seq); + // console.log("seqPos:"+seqPos); + // console.log("op.length:"+op.length); var mSeq = seq.slice(seqPos, seqPos + op.length); + // console.log(mSeq) mismatches = mismatches.concat(findMismatches(ref, mSeq, refPos, scores)); } diff --git a/src/test/sources/ReferenceDataSource-test.js b/src/test/sources/ReferenceDataSource-test.js new file mode 100644 index 00000000..d17bd0b8 --- /dev/null +++ b/src/test/sources/ReferenceDataSource-test.js @@ -0,0 +1,148 @@ + /** @flow */ +'use strict'; + +import {expect} from 'chai'; + +import sinon from 'sinon'; + +import ReferenceDataSource from '../../main/sources/ReferenceDataSource'; +import RemoteFile from '../../main/RemoteFile'; + +describe('ReferenceDataSource', function() { + var server: any = null, response; + + before(function () { + return new RemoteFile('/test-data/reference-chrM-0-1000.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/reference',[200, { "Content-Type": "application/json" }, response]); + }); + }); + + after(function () { + server.restore(); + }); + + function getTestSource() { + var source = ReferenceDataSource.create({ + url: '/reference', + contigList: [{ + name:"chrM", + length: 1000 + },{ + name:"22", + length: 1000 + }] + }); + return source; + } + + it('should fetch contigs', function() { + var source = getTestSource(); + var contigs = source.contigList(); + expect(contigs).to.deep.equal(['chrM','22']); + }); + + it('should normalize range', function() { + var source = getTestSource(); + var range = {contig: 'chrM', start: 0, stop: 3}; + source.normalizeRange(range).then(normalized => { + expect(normalized.to.deep.equal(range)); + }).done(); + }); + + it('should fetch base pairs', function(done) { + var source = getTestSource(); + var range = {contig: 'chrM', start: 0, stop: 3}; + + // Before data has been fetched, all base pairs are null. + expect(source.getRange(range)).to.deep.equal({ + 'chrM:0': null, + 'chrM:1': null, + 'chrM:2': null, + 'chrM:3': null + }); + expect(source.getRangeAsString(range)).to.equal('....'); + + source.on('newdata', () => { + expect(source.getRange(range)).to.deep.equal({ + 'chrM:0': 'N', + 'chrM:1': 'G', + 'chrM:2': 'T', + 'chrM:3': 'T' + }); + expect(source.getRangeAsString(range)).to.equal('NGTT'); + + done(); + }); + source.rangeChanged(range); + server.respond(); + }); + + it('should fetch nearby base pairs', function(done) { + var source = getTestSource(); + + source.on('newdata', () => { + expect(source.getRange({contig: 'chrM', start: 0, stop: 14})) + .to.deep.equal({ + 'chrM:0': 'N', + 'chrM:1': 'G', + 'chrM:2': 'T', + 'chrM:3': 'T', + 'chrM:4': 'A', // start of actual request + 'chrM:5': 'A', + 'chrM:6': 'T', + 'chrM:7': 'G', + 'chrM:8': 'T', + 'chrM:9': 'A', // end of actual requuest + 'chrM:10': 'G', + 'chrM:11': 'C', + 'chrM:12': 'T', + 'chrM:13': 'T', + 'chrM:14': 'A' + }); + done(); + }); + source.rangeChanged({contig: 'chrM', start: 4, stop: 9}); + server.respond(); + }); + + it('should add chr', function(done) { + var source = getTestSource(); + var range = {contig: '22', start: 0, stop: 3}; + + source.on('newdata', () => { + expect(source.getRange(range)).to.deep.equal({ + '22:0': 'N', + '22:1': 'G', + '22:2': 'T', + '22:3': 'T' + }); + expect(source.getRangeAsString(range)).to.equal('NGTT'); + done(); + }); + source.rangeChanged(range); + server.respond(); + }); + + it('should only report newly-fetched ranges', function(done) { + ReferenceDataSource.testBasePairsToFetch(10); + var initRange = {contig: 'chrM', start: 5, stop: 8}, + secondRange = {contig: 'chrM', start: 8, stop: 15}; + var source = getTestSource(); + source.once('newdata', newRange => { + expect(newRange.toString()).to.equal('chrM:0-10'); // expanded range + + source.once('newdata', newRange => { + // This expanded range excludes previously-fetched data. + expect(newRange.toString()).to.equal('chrM:11-20'); + done(); + }); + source.rangeChanged(secondRange); + server.respond(); + }); + source.rangeChanged(initRange); + server.respond(); + }); + +}); diff --git a/test-data/adam-alignments.json b/test-data/adam-alignments.json index 2448fc1d..e8866aa4 100644 --- a/test-data/adam-alignments.json +++ b/test-data/adam-alignments.json @@ -33387,4 +33387,4 @@ "info": {} }], "nextPageToken": null -} \ No newline at end of file +} diff --git a/test-data/features_chrM_0_2000.json b/test-data/features_chrM_0_2000.json new file mode 100644 index 00000000..18c0c397 --- /dev/null +++ b/test-data/features_chrM_0_2000.json @@ -0,0 +1,18 @@ +[{ + "range": { + "name": "chrM", + "start": 0, + "end": 2000 + }, + "features": [{ + "featureId": "4ee7469a-b468-429b-a109-07a484817037", + "featureType": "rs575272151", + "start": 1107, + "end": 1200 + }, { + "featureId": "e105ce29-a840-4fc6-819f-a9aac5166163", + "featureType": "rs544419019", + "start": 1011, + "end": 1012 + }] +}] diff --git a/test-data/reference-chrM-0-1000.json b/test-data/reference-chrM-0-1000.json new file mode 100644 index 00000000..95699648 --- /dev/null +++ b/test-data/reference-chrM-0-1000.json @@ -0,0 +1 @@ +"NGTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAAATATTAAGCAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATTAAAATCCAACTTATATGTGAAAATTCATTGTTAGGACCTAAACTCAATAACGAAAGTAATTCTAGTCATTTATAATACACGACAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAAAACTATTTGCCAGAGAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAACGTTAGGTCAAGGTGTAGCCAATGAAATGGGAAGAAATGGGCTACATTTTCTTATAAAAGAACATTACTATACCCTTTATGAAACTAAAGGACTAAGGAGGATTTAGTAGTAAATTAAGAATAGAGAGCTTAATTGAATTGAGCAATGAAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCAT" From ecc9f9c7f27cd2cae95c4f7b28ae5fce3f54c845 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sat, 11 Jun 2016 15:13:50 -0700 Subject: [PATCH 072/136] starting reference --- examples/data.js | 16 ++-- src/main/sources/ReferenceDataSource.js | 110 ++++++++++++++++++++++++ 2 files changed, 118 insertions(+), 8 deletions(-) diff --git a/examples/data.js b/examples/data.js index 86b0f074..265d7ae8 100644 --- a/examples/data.js +++ b/examples/data.js @@ -21,15 +21,15 @@ var sources = [ }] }), name: 'Reference' + }, + { + viz: pileup.viz.genome(), + isReference: true, + data: pileup.formats.reference({ + prefix:"../json/" + }), + name: 'Reference' } -// { -// viz: pileup.viz.genome(), -// isReference: true, -// data: pileup.formats.reference({ -// prefix:"../json/" -// }), -// name: 'Reference' -// } // { // viz: pileup.viz.scale(), // name: 'Scale' diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index 7129abd6..ecf6e768 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -35,6 +35,23 @@ var BASE_PAIRS_PER_FETCH = 10000; var MAX_BASE_PAIRS_TO_FETCH = 100000; +<<<<<<< HEAD +======= + +// Flow type for export. +export type ReferenceSource = { + rangeChanged: (newRange: GenomeRange) => void; + getRange: (range: GenomeRange) => {[key:string]: ?string}; + getRangeAsString: (range: GenomeRange) => string; + contigList: () => string[]; + normalizeRange: (range: GenomeRange) => Q.Promise; + on: (event: string, handler: Function) => void; + once: (event: string, handler: Function) => void; + off: (event: string) => void; + trigger: (event: string, ...args:any) => void; +} + +>>>>>>> 1bbf80b... starting reference // Expand range to begin and end on multiples of BASE_PAIRS_PER_FETCH. function expandRange(range) { var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; @@ -44,11 +61,30 @@ function expandRange(range) { return new ContigInterval(range.contig, newStart, newStop); } +<<<<<<< HEAD var createFromReferenceUrl = function(remoteSource: Sequence): TwoBitSource { // Local cache of genomic data. var contigList = remoteSource.getContigList(); var store = new SequenceStore(); +======= + +var createFromReferenceUrl = function(): ReferenceSource { + // Local cache of genomic data. + var contigList = []; + var store = new SequenceStore(); + + var url = "/reference/" + "chrM" + "?start=" + 0 + "&end=" + 200; + console.log(url); + var xmlHttp = new XMLHttpRequest(); + xmlHttp.open( "GET", url, false ); // false for synchronous request + xmlHttp.send( null ); + console.log(xmlHttp); + console.log(xmlHttp.responseText); + alert(xmlHttp.responseText); + + +>>>>>>> 1bbf80b... starting reference // Ranges for which we have complete information -- no need to hit network. var coveredRanges = ([]: ContigInterval[]); @@ -58,6 +94,7 @@ var createFromReferenceUrl = function(remoteSource: Sequence): TwoBitSource { return Q.when(); // empty promise } +<<<<<<< HEAD // TODO remote Source remoteSource.getFeaturesInRange(range.contig, range.start(), range.stop()) .then(letters => { @@ -100,12 +137,63 @@ var createFromReferenceUrl = function(remoteSource: Sequence): TwoBitSource { if (!range) return ''; return store.getAsString(ContigInterval.fromGenomeRange(range)); } +======= + // TODO: fetch JSON from file + + + store.setRange(range, letters); + o.trigger('newdata', range); + } + + function normalizeRange(range: GenomeRange): Q.Promise { + return contigPromise.then(() => normalizeRangeSync(range)); + } + + // Returns a {"chr12:123" -> "[ATCG]"} mapping for the range. + function getRange(range: GenomeRange) { + return store.getAsObjects(ContigInterval.fromGenomeRange(range)); + } + + // Returns a string of base pairs for this range. + function getRangeAsString(range: GenomeRange): string { + if (!range) return ''; + return store.getAsString(ContigInterval.fromGenomeRange(range)); + } + + // This either adds or removes a 'chr' as needed. + function normalizeRangeSync(range: GenomeRange): GenomeRange { + if (contigList.indexOf(range.contig) >= 0) { + return range; + } + var altContig = utils.altContigName(range.contig); + if (contigList.indexOf(altContig) >= 0) { + return { + contig: altContig, + start: range.start, + stop: range.stop + }; + } + return range; // let it fail with the original contig + } + + // Fetch the contig list immediately. + var contigPromise = remoteSource.getContigList().then(c => { + contigList = c; + o.trigger('contigs', contigList); + return c; + }); + contigPromise.done(); +>>>>>>> 1bbf80b... starting reference var o = { // The range here is 0-based, inclusive rangeChanged: function(newRange: GenomeRange) { normalizeRange(newRange).then(r => { var range = new ContigInterval(r.contig, r.start, r.stop); +<<<<<<< HEAD +======= + +>>>>>>> 1bbf80b... starting reference // Check if this interval is already in the cache. if (range.isCoveredBy(coveredRanges)) { return; @@ -134,6 +222,7 @@ var createFromReferenceUrl = function(remoteSource: Sequence): TwoBitSource { trigger: () => {} }; _.extend(o, Events); // Make this an event emitter +<<<<<<< HEAD return o; }; @@ -155,6 +244,23 @@ function create(data: {url:string, contigList: SequenceRecord[]}): TwoBitSource // Getter/setter for base pairs per fetch. // This should only be used for testing. function testBasePairsToFetch(num?: number): any { +======= + + return o; +}; + +function create(data: {prefix:string}): ReferenceSource { + var urlPrefix = data.prefix; + if (!urlPrefix) { + throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); + } + + return createFromReferenceUrl(); +} +// Getter/setter for base pairs per fetch. +// This should only be used for testing. +function testReferenceToFetch(num?: number): any { +>>>>>>> 1bbf80b... starting reference if (num) { BASE_PAIRS_PER_FETCH = num; } else { @@ -165,5 +271,9 @@ function testBasePairsToFetch(num?: number): any { module.exports = { create, createFromReferenceUrl, +<<<<<<< HEAD testBasePairsToFetch +======= + testReferenceToFetch +>>>>>>> 1bbf80b... starting reference }; From c8ecd61e0f611f1c005ff98d678b3df6b4c22f7d Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sun, 12 Jun 2016 15:41:49 -0700 Subject: [PATCH 073/136] continued reference implementation --- .gitignore | 9 + examples/data.js | 16 +- package.json | 1 + src/main/data/TwoBit.js | 2 +- src/main/data/VirtualOffset.js | 1 + src/main/sources/ReferenceDataSource.js | 114 +-------- src/main/style.js | 1 + src/test/sources/ReferenceDataSource-test.js | 236 ++++++++++--------- 8 files changed, 142 insertions(+), 238 deletions(-) diff --git a/.gitignore b/.gitignore index 26ed7f18..2a749afe 100644 --- a/.gitignore +++ b/.gitignore @@ -41,3 +41,12 @@ dist # Generated files src/lib *.pyc +.idea/.name +.idea/compiler.xml +.idea/misc.xml +.idea/modules.xml +.idea/pileup.js.iml +.idea/vcs.xml +.idea/workspace.xml +.idea/copyright/profiles_settings.xml +.idea/dictionaries/akmorrow.xml diff --git a/examples/data.js b/examples/data.js index 265d7ae8..86b0f074 100644 --- a/examples/data.js +++ b/examples/data.js @@ -21,15 +21,15 @@ var sources = [ }] }), name: 'Reference' - }, - { - viz: pileup.viz.genome(), - isReference: true, - data: pileup.formats.reference({ - prefix:"../json/" - }), - name: 'Reference' } +// { +// viz: pileup.viz.genome(), +// isReference: true, +// data: pileup.formats.reference({ +// prefix:"../json/" +// }), +// name: 'Reference' +// } // { // viz: pileup.viz.scale(), // name: 'Scale' diff --git a/package.json b/package.json index 53c633ba..129debaa 100644 --- a/package.json +++ b/package.json @@ -66,6 +66,7 @@ "arraybuffer-slice": "^0.1.2", "babel": "^5.8.23", "babel-core": "^5.8.23", + "babel-preset-es2015": "^6.9.0", "babelify": "^6.3.0", "browserify": "^10.2.4", "chai": "^2.0.0", diff --git a/src/main/data/TwoBit.js b/src/main/data/TwoBit.js index ca0231f4..1858da08 100644 --- a/src/main/data/TwoBit.js +++ b/src/main/data/TwoBit.js @@ -270,4 +270,4 @@ class TwoBit { } } -module.exports = TwoBit; +module.exports = TwoBit; \ No newline at end of file diff --git a/src/main/data/VirtualOffset.js b/src/main/data/VirtualOffset.js index 287c05f2..b3136b40 100644 --- a/src/main/data/VirtualOffset.js +++ b/src/main/data/VirtualOffset.js @@ -6,6 +6,7 @@ * JavaScript. * @flow */ +'use strict'; "use strict"; diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index ecf6e768..2e10d7de 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -1,10 +1,10 @@ /** - * The "glue" between TwoBit.js and GenomeTrack.js. + * The "glue" between Sequence.js and GenomeTrack.js. * * GenomeTrack is pure view code -- it renders data which is already in-memory * in the browser. * - * TwoBit is purely for data parsing and fetching. It only knows how to return + *Sequence is purely for data parsing and fetching. It only knows how to return * promises for various genome features. * * This code acts as a bridge between the two. It maintains a local version of @@ -35,23 +35,6 @@ var BASE_PAIRS_PER_FETCH = 10000; var MAX_BASE_PAIRS_TO_FETCH = 100000; -<<<<<<< HEAD -======= - -// Flow type for export. -export type ReferenceSource = { - rangeChanged: (newRange: GenomeRange) => void; - getRange: (range: GenomeRange) => {[key:string]: ?string}; - getRangeAsString: (range: GenomeRange) => string; - contigList: () => string[]; - normalizeRange: (range: GenomeRange) => Q.Promise; - on: (event: string, handler: Function) => void; - once: (event: string, handler: Function) => void; - off: (event: string) => void; - trigger: (event: string, ...args:any) => void; -} - ->>>>>>> 1bbf80b... starting reference // Expand range to begin and end on multiples of BASE_PAIRS_PER_FETCH. function expandRange(range) { var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; @@ -61,30 +44,11 @@ function expandRange(range) { return new ContigInterval(range.contig, newStart, newStop); } -<<<<<<< HEAD var createFromReferenceUrl = function(remoteSource: Sequence): TwoBitSource { // Local cache of genomic data. var contigList = remoteSource.getContigList(); var store = new SequenceStore(); -======= - -var createFromReferenceUrl = function(): ReferenceSource { - // Local cache of genomic data. - var contigList = []; - var store = new SequenceStore(); - - var url = "/reference/" + "chrM" + "?start=" + 0 + "&end=" + 200; - console.log(url); - var xmlHttp = new XMLHttpRequest(); - xmlHttp.open( "GET", url, false ); // false for synchronous request - xmlHttp.send( null ); - console.log(xmlHttp); - console.log(xmlHttp.responseText); - alert(xmlHttp.responseText); - - ->>>>>>> 1bbf80b... starting reference // Ranges for which we have complete information -- no need to hit network. var coveredRanges = ([]: ContigInterval[]); @@ -94,7 +58,6 @@ var createFromReferenceUrl = function(): ReferenceSource { return Q.when(); // empty promise } -<<<<<<< HEAD // TODO remote Source remoteSource.getFeaturesInRange(range.contig, range.start(), range.stop()) .then(letters => { @@ -137,63 +100,12 @@ var createFromReferenceUrl = function(): ReferenceSource { if (!range) return ''; return store.getAsString(ContigInterval.fromGenomeRange(range)); } -======= - // TODO: fetch JSON from file - - - store.setRange(range, letters); - o.trigger('newdata', range); - } - - function normalizeRange(range: GenomeRange): Q.Promise { - return contigPromise.then(() => normalizeRangeSync(range)); - } - - // Returns a {"chr12:123" -> "[ATCG]"} mapping for the range. - function getRange(range: GenomeRange) { - return store.getAsObjects(ContigInterval.fromGenomeRange(range)); - } - - // Returns a string of base pairs for this range. - function getRangeAsString(range: GenomeRange): string { - if (!range) return ''; - return store.getAsString(ContigInterval.fromGenomeRange(range)); - } - - // This either adds or removes a 'chr' as needed. - function normalizeRangeSync(range: GenomeRange): GenomeRange { - if (contigList.indexOf(range.contig) >= 0) { - return range; - } - var altContig = utils.altContigName(range.contig); - if (contigList.indexOf(altContig) >= 0) { - return { - contig: altContig, - start: range.start, - stop: range.stop - }; - } - return range; // let it fail with the original contig - } - - // Fetch the contig list immediately. - var contigPromise = remoteSource.getContigList().then(c => { - contigList = c; - o.trigger('contigs', contigList); - return c; - }); - contigPromise.done(); ->>>>>>> 1bbf80b... starting reference var o = { // The range here is 0-based, inclusive rangeChanged: function(newRange: GenomeRange) { normalizeRange(newRange).then(r => { var range = new ContigInterval(r.contig, r.start, r.stop); -<<<<<<< HEAD -======= - ->>>>>>> 1bbf80b... starting reference // Check if this interval is already in the cache. if (range.isCoveredBy(coveredRanges)) { return; @@ -222,7 +134,6 @@ var createFromReferenceUrl = function(): ReferenceSource { trigger: () => {} }; _.extend(o, Events); // Make this an event emitter -<<<<<<< HEAD return o; }; @@ -244,23 +155,6 @@ function create(data: {url:string, contigList: SequenceRecord[]}): TwoBitSource // Getter/setter for base pairs per fetch. // This should only be used for testing. function testBasePairsToFetch(num?: number): any { -======= - - return o; -}; - -function create(data: {prefix:string}): ReferenceSource { - var urlPrefix = data.prefix; - if (!urlPrefix) { - throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); - } - - return createFromReferenceUrl(); -} -// Getter/setter for base pairs per fetch. -// This should only be used for testing. -function testReferenceToFetch(num?: number): any { ->>>>>>> 1bbf80b... starting reference if (num) { BASE_PAIRS_PER_FETCH = num; } else { @@ -271,9 +165,5 @@ function testReferenceToFetch(num?: number): any { module.exports = { create, createFromReferenceUrl, -<<<<<<< HEAD testBasePairsToFetch -======= - testReferenceToFetch ->>>>>>> 1bbf80b... starting reference }; diff --git a/src/main/style.js b/src/main/style.js index eb0f0c34..314c8857 100644 --- a/src/main/style.js +++ b/src/main/style.js @@ -4,6 +4,7 @@ * * @flow */ +'use strict'; "use strict"; diff --git a/src/test/sources/ReferenceDataSource-test.js b/src/test/sources/ReferenceDataSource-test.js index d17bd0b8..09ee0879 100644 --- a/src/test/sources/ReferenceDataSource-test.js +++ b/src/test/sources/ReferenceDataSource-test.js @@ -1,4 +1,4 @@ - /** @flow */ +/** @flow */ 'use strict'; import {expect} from 'chai'; @@ -9,140 +9,142 @@ import ReferenceDataSource from '../../main/sources/ReferenceDataSource'; import RemoteFile from '../../main/RemoteFile'; describe('ReferenceDataSource', function() { - var server: any = null, response; - - before(function () { - return new RemoteFile('/test-data/reference-chrM-0-1000.json').getAllString().then(data => { - response = data; - server = sinon.fakeServer.create(); - server.respondWith('GET', '/reference',[200, { "Content-Type": "application/json" }, response]); - }); - }); - - after(function () { - server.restore(); +var server: any = null, response; + +before(function () { + return new RemoteFile('/test-data/reference-chrM-0-1000.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/reference/chrM?start=0&end=10000',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/reference/chrM?start=0&end=10',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/reference/22?start=0&end=10000',[200, { "Content-Type": "application/json" }, response]); }); +}); - function getTestSource() { - var source = ReferenceDataSource.create({ - url: '/reference', - contigList: [{ - name:"chrM", - length: 1000 - },{ - name:"22", - length: 1000 - }] - }); - return source; - } +after(function () { + server.restore(); +}); - it('should fetch contigs', function() { - var source = getTestSource(); - var contigs = source.contigList(); - expect(contigs).to.deep.equal(['chrM','22']); +function getTestSource() { + var source = ReferenceDataSource.create({ + url: '/reference', + contigList: [{ + name:"chrM", + length: 1000 + },{ + name:"22", + length: 1000 + }] }); + return source; +} - it('should normalize range', function() { - var source = getTestSource(); - var range = {contig: 'chrM', start: 0, stop: 3}; - source.normalizeRange(range).then(normalized => { - expect(normalized.to.deep.equal(range)); - }).done(); - }); +it('should fetch contigs', function() { + var source = getTestSource(); + var contigs = source.contigList(); + expect(contigs).to.deep.equal(['chrM','22']); +}); - it('should fetch base pairs', function(done) { - var source = getTestSource(); - var range = {contig: 'chrM', start: 0, stop: 3}; - - // Before data has been fetched, all base pairs are null. - expect(source.getRange(range)).to.deep.equal({ - 'chrM:0': null, - 'chrM:1': null, - 'chrM:2': null, - 'chrM:3': null - }); - expect(source.getRangeAsString(range)).to.equal('....'); - - source.on('newdata', () => { - expect(source.getRange(range)).to.deep.equal({ - 'chrM:0': 'N', - 'chrM:1': 'G', - 'chrM:2': 'T', - 'chrM:3': 'T' - }); - expect(source.getRangeAsString(range)).to.equal('NGTT'); +it('should normalize range', function() { + var source = getTestSource(); + var range = {contig: 'chrM', start: 0, stop: 3}; + source.normalizeRange(range).then(normalized => { + expect(normalized.to.deep.equal(range)); + }).done(); +}); - done(); +it('should fetch base pairs', function(done) { + var source = getTestSource(); + var range = {contig: 'chrM', start: 0, stop: 3}; + + // Before data has been fetched, all base pairs are null. + expect(source.getRange(range)).to.deep.equal({ + 'chrM:0': null, + 'chrM:1': null, + 'chrM:2': null, + 'chrM:3': null + }); + expect(source.getRangeAsString(range)).to.equal('....'); + + source.on('newdata', () => { + expect(source.getRange(range)).to.deep.equal({ + 'chrM:0': 'N', + 'chrM:1': 'G', + 'chrM:2': 'T', + 'chrM:3': 'T' }); - source.rangeChanged(range); - server.respond(); + expect(source.getRangeAsString(range)).to.equal('NGTT'); + + done(); }); + source.rangeChanged(range); + server.respond(); +}); - it('should fetch nearby base pairs', function(done) { - var source = getTestSource(); - - source.on('newdata', () => { - expect(source.getRange({contig: 'chrM', start: 0, stop: 14})) - .to.deep.equal({ - 'chrM:0': 'N', - 'chrM:1': 'G', - 'chrM:2': 'T', - 'chrM:3': 'T', - 'chrM:4': 'A', // start of actual request - 'chrM:5': 'A', - 'chrM:6': 'T', - 'chrM:7': 'G', - 'chrM:8': 'T', - 'chrM:9': 'A', // end of actual requuest - 'chrM:10': 'G', - 'chrM:11': 'C', - 'chrM:12': 'T', - 'chrM:13': 'T', - 'chrM:14': 'A' - }); - done(); - }); - source.rangeChanged({contig: 'chrM', start: 4, stop: 9}); - server.respond(); +it('should fetch nearby base pairs', function(done) { + var source = getTestSource(); + + source.on('newdata', () => { + expect(source.getRange({contig: 'chrM', start: 0, stop: 14})) + .to.deep.equal({ + 'chrM:0': 'N', + 'chrM:1': 'G', + 'chrM:2': 'T', + 'chrM:3': 'T', + 'chrM:4': 'A', // start of actual request + 'chrM:5': 'A', + 'chrM:6': 'T', + 'chrM:7': 'G', + 'chrM:8': 'T', + 'chrM:9': 'A', // end of actual requuest + 'chrM:10': 'G', + 'chrM:11': 'C', + 'chrM:12': 'T', + 'chrM:13': 'T', + 'chrM:14': 'A' + }); + done(); }); + source.rangeChanged({contig: 'chrM', start: 4, stop: 9}); + server.respond(); +}); - it('should add chr', function(done) { - var source = getTestSource(); - var range = {contig: '22', start: 0, stop: 3}; - - source.on('newdata', () => { - expect(source.getRange(range)).to.deep.equal({ - '22:0': 'N', - '22:1': 'G', - '22:2': 'T', - '22:3': 'T' - }); - expect(source.getRangeAsString(range)).to.equal('NGTT'); - done(); +it('should add chr', function(done) { + var source = getTestSource(); + var range = {contig: '22', start: 0, stop: 3}; + + source.on('newdata', () => { + expect(source.getRange(range)).to.deep.equal({ + '22:0': 'N', + '22:1': 'G', + '22:2': 'T', + '22:3': 'T' }); - source.rangeChanged(range); - server.respond(); + expect(source.getRangeAsString(range)).to.equal('NGTT'); + done(); }); + source.rangeChanged(range); + server.respond(); +}); + +it('should only report newly-fetched ranges', function(done) { + ReferenceDataSource.testBasePairsToFetch(10); + var initRange = {contig: 'chrM', start: 5, stop: 8}, + secondRange = {contig: 'chrM', start: 8, stop: 15}; + var source = getTestSource(); + source.once('newdata', newRange => { + expect(newRange.toString()).to.equal('chrM:0-10'); // expanded range - it('should only report newly-fetched ranges', function(done) { - ReferenceDataSource.testBasePairsToFetch(10); - var initRange = {contig: 'chrM', start: 5, stop: 8}, - secondRange = {contig: 'chrM', start: 8, stop: 15}; - var source = getTestSource(); source.once('newdata', newRange => { - expect(newRange.toString()).to.equal('chrM:0-10'); // expanded range - - source.once('newdata', newRange => { - // This expanded range excludes previously-fetched data. - expect(newRange.toString()).to.equal('chrM:11-20'); - done(); - }); - source.rangeChanged(secondRange); - server.respond(); + // This expanded range excludes previously-fetched data. + expect(newRange.toString()).to.equal('chrM:11-20'); + done(); }); - source.rangeChanged(initRange); + source.rangeChanged(secondRange); server.respond(); }); + source.rangeChanged(initRange); + server.respond(); +}); }); From e79bcc9635606fe7901b9c5ea762bd08bb2ebec3 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sat, 18 Jun 2016 13:20:54 -0700 Subject: [PATCH 074/136] added test resources for ADAM alignments --- src/test/ADAMAlignment-test.js | 57 +- test-data/adam-alignments.json | 39273 +++++-------------------------- 2 files changed, 5930 insertions(+), 33400 deletions(-) diff --git a/src/test/ADAMAlignment-test.js b/src/test/ADAMAlignment-test.js index f07884a5..07191353 100644 --- a/src/test/ADAMAlignment-test.js +++ b/src/test/ADAMAlignment-test.js @@ -7,33 +7,64 @@ import GA4GHAlignment from '../main/GA4GHAlignment'; import RemoteFile from '../main/RemoteFile'; import Bam from '../main/data/bam'; -describe('ADAM_Alignment', function() { +describe('GA4GHAlignment', function() { var sampleAlignments = []; before(function() { return new RemoteFile('/test-data/adam-alignments.json').getAllString().then(data => { - // console.log("data: "+ JSON.parse(data).alignments); sampleAlignments = JSON.parse(data).alignments; - // console.log("sampleAlignments: " + sampleAlignments); - // console.log("sampleAlignments length: " +sampleAlignments.length); }); }); - + it('should read the sample alignments', function() { - // console.log("sampleAlignments length: " +sampleAlignments.length); - expect(sampleAlignments).to.have.length(1046); + expect(sampleAlignments).to.have.length(14); }); it('should provide basic accessors', function() { var a = new GA4GHAlignment(sampleAlignments[0]); - expect(a.name).to.equal('613F0AAXX100423:5:47:2891:8862'); - expect(a.getSequence()).to.equal('GTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATCATTGTATCCCATAAACACAAAGTTTTGGTCCTGGCCTTATAATTACTTAG'); - expect(a.getQualityScores()).to.deep.equal([17, 28, 10, 23, 27, 28, 17, 31, 22, 10, 16, 19, 9, 15, 16, 22, 15, 14, 15, 20, 15, 9, 15, 15, 9, 32, 32, 25, 27, 9, 21, 25, 32, 28, 28, 31, 31, 23, 22, 22, 9, 17, 22, 12, 25, 24, 14, 10, 26, 26, 10, 32, 26, 30, 32, 31, 25, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]); + expect(a.name).to.equal('r000'); + expect(a.getSequence()).to.equal('ATTTAGCTAC'); + expect(a.getQualityScores()).to.deep.equal([32,32,32,32,32,32,32,32,32,32]); expect(a.getStrand()).to.equal('+'); - expect(a.getInterval().toString()).to.equal('chrM:0-58'); // 0-based + expect(a.getInterval().toString()).to.equal('chr17:4-13'); // 0-based expect(a.cigarOps).to.deep.equal([ - {length:59, op: 'M'},{length: 42,op:'S'} + {op: 'M', length: 10} ]); + expect(a.getMateProperties()).to.deep.equal({ + ref: 'chr17', + pos: 79, + strand: '+' + }); + }); + + it('should match SamRead', function() { + var bam = new Bam(new RemoteFile('/test-data/chr17.1-250.bam')); + return bam.readAll().then(({alignments: samReads}) => { + // This is a workaround. See https://github.com/ga4gh/server/issues/488 + samReads.splice(-1, 1); + + expect(sampleAlignments.length).to.equal(samReads.length); + for (var i = 0; i < sampleAlignments.length; i++) { + var ga4gh = new GA4GHAlignment(sampleAlignments[i]), + bam = samReads[i]; + expect(ga4gh.getSequence()).to.equal(bam.getSequence()); + // See https://github.com/ga4gh/server/issues/491 + // expect(ga4gh.getStrand()).to.equal(bam.getStrand()); + // For the if statement, see https://github.com/ga4gh/server/issues/492 + var quality = ga4gh.getQualityScores(); + if (quality.length) { + expect(quality).to.deep.equal(bam.getQualityScores()); + } + expect(ga4gh.cigarOps).to.deep.equal(bam.cigarOps); + // After ga4gh#491, change this to a .deep.equal on getMateProperties() + var ga4ghMate = ga4gh.getMateProperties(), + bamMate = bam.getMateProperties(); + expect(!!ga4ghMate).to.equal(!!bamMate); + if (ga4ghMate && bamMate) { + expect(ga4ghMate.ref).to.equal(bamMate.ref); + expect(ga4ghMate.pos).to.equal(bamMate.pos); + } + } + }); }); - // Can not check with SamReads because we don't have the corresponding BAM file }); diff --git a/test-data/adam-alignments.json b/test-data/adam-alignments.json index e8866aa4..f4e92070 100644 --- a/test-data/adam-alignments.json +++ b/test-data/adam-alignments.json @@ -1,33390 +1,5889 @@ { - "alignments": [{ - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:47:2891:8862", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 0, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 59, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 42, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATCATTGTATCCCATAAACACAAAGTTTTGGTCCTGGCCTTATAATTACTTAG", - "alignedQuality": [17, 28, 10, 23, 27, 28, 17, 31, 22, 10, 16, 19, 9, 15, 16, 22, 15, 14, 15, 20, 15, 9, 15, 15, 9, 32, 32, 25, 27, 9, 21, 25, 32, 28, 28, 31, 31, 23, 22, 22, 9, 17, 22, 12, 25, 24, 14, 10, 26, 26, 10, 32, 26, 30, 32, 31, 25, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:40:17115:17222", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 154, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 1, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 31, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 70, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTCATGTAGCTTGATAACAGCGCAAAGAACTCCAAATGCTTAGATGGATAATTGTATCCCATAAAAACAAAGGATTGGGCCTGGCCTTATAANTATTTTGA", - "alignedQuality": [31, 31, 7, 30, 7, 11, 31, 7, 31, 7, 7, 11, 6, 28, 11, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:27:8808:3060", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 2, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATNAATTAGAG", - "alignedQuality": [38, 38, 38, 38, 35, 37, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 38, 37, 38, 38, 38, 38, 38, 38, 30, 37, 35, 38, 37, 37, 37, 37, 38, 38, 38, 35, 36, 37, 37, 36, 38, 38, 38, 35, 38, 36, 37, 36, 38, 36, 37, 36, 36, 37, 33, 33, 34, 35, 36, 36, 34, 35, 35, 35, 35, 35, 36, 25, 35, 36, 30, 35, 32, 25, 26, 0, 26, 6, 29, 26, 29, 28, 22, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.3", - "fragmentName": "613F0AAXX100423:3:93:11085:15551", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 138, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 2, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "CLIP_SOFT", - "operationLength": 47, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 54, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACCAAAACTCTAATCATACTCTATTACGCAATAAACATTAACAAGATAATGTAGCTTAATAACAAAGCAAAGCACTGCATATGCTTAGATGGGTAATTGT", - "alignedQuality": [23, 18, 23, 29, 18, 30, 27, 30, 24, 27, 26, 21, 21, 11, 18, 30, 29, 23, 11, 24, 29, 18, 23, 27, 27, 30, 23, 27, 30, 27, 24, 29, 32, 24, 29, 29, 31, 31, 32, 31, 33, 33, 28, 33, 33, 27, 7, 23, 23, 23, 32, 33, 33, 27, 31, 32, 25, 33, 33, 28, 31, 24, 29, 33, 31, 16, 32, 31, 31, 19, 16, 16, 27, 29, 17, 27, 30, 29, 10, 25, 9, 29, 29, 30, 29, 31, 21, 33, 18, 31, 33, 31, 10, 18, 31, 33, 32, 32, 19, 32, 25], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:2:14636:7280", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 182, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 2, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAATGTAGCTTAATAACAAAGCAACGCACTGAAAACGATTAGACGGATAATTGTATCCCATAAACACAAATATCTGTCCCGGGCCTTATACTTAATTAGCG", - "alignedQuality": [24, 16, 27, 29, 17, 31, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.6", - "fragmentName": "6141AAAXX100423:6:6:16994:6552", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 88, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 2, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "CLIP_SOFT", - "operationLength": 21, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 53, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 27, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACGCAATAAACATTAACAAGCTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGACGGATAATTGTATCCCATAAACACAACGTCTGGGTAG", - "alignedQuality": [17, 21, 26, 22, 18, 20, 24, 22, 24, 10, 22, 22, 20, 15, 28, 28, 20, 30, 21, 21, 7, 15, 22, 25, 23, 20, 17, 25, 20, 15, 20, 14, 29, 32, 23, 30, 25, 13, 21, 14, 16, 23, 19, 15, 18, 27, 8, 9, 14, 8, 16, 18, 22, 12, 17, 32, 15, 30, 28, 28, 8, 20, 18, 32, 8, 12, 15, 7, 10, 29, 23, 23, 23, 21, 32, 8, 7, 10, 16, 17, 29, 24, 15, 32, 30, 31, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:86:13610:13910", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 136, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 3, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTGATTAGAGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 35, 38, 37, 38, 37, 38, 37, 34, 37, 36, 38, 33, 35, 36, 37, 37, 36, 36, 37, 36, 37, 37, 33, 38, 38, 36, 34, 34, 17, 34, 34, 31, 35, 34, 31, 34, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:55:10041:19549", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 3, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATGTAGCTTAATAACAAAGCAAAGCCCTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAGAGGTTTGGTCCTGGCCTTATAATTNATTAGAGG", - "alignedQuality": [37, 37, 37, 37, 37, 35, 37, 36, 37, 37, 35, 38, 37, 38, 36, 38, 38, 32, 38, 37, 36, 38, 38, 38, 34, 36, 38, 38, 38, 35, 36, 37, 38, 38, 37, 37, 38, 37, 38, 38, 36, 36, 38, 38, 35, 37, 38, 32, 37, 38, 38, 37, 35, 36, 35, 36, 36, 37, 38, 38, 38, 38, 37, 36, 37, 38, 37, 28, 36, 36, 36, 32, 33, 33, 33, 35, 33, 35, 35, 33, 35, 33, 35, 33, 33, 35, 33, 36, 33, 30, 28, 26, 0, 26, 25, 29, 30, 29, 29, 27, 35], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:119:5097:18545", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 3, - "reverseStrand": false - }, - "mappingQuality": 20, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 2, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 6, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAAGATCGGA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 37, 36, 38, 38, 35, 38, 38, 38, 38, 37, 37, 36, 38, 38, 38, 36, 35, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 37, 32, 34, 37, 35, 37, 37, 35, 36, 35, 37, 38, 35, 36, 33, 38, 33, 38, 37, 37, 38, 38, 38, 37, 35, 35, 38, 36, 38, 35, 33, 37], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:93:14191:18986", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 181, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 4, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 91, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 9, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAAATTAGAGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 37, 38, 37, 38, 38, 38, 38, 38, 36, 38, 35, 37, 37, 37, 35, 34, 35, 37, 36, 35, 35, 38, 36, 35, 35, 36, 35, 35, 37, 36, 33, 36, 35, 36, 36, 31, 31, 26, 15, 31, 28, 31, 28, 29, 29, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:24:12998:15482", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 192, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 4, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTANATTAGAGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 37, 36, 37, 37, 37, 36, 34, 38, 37, 35, 36, 37, 38, 36, 38, 37, 38, 36, 37, 37, 36, 35, 36, 35, 35, 33, 34, 34, 32, 34, 34, 35, 34, 34, 33, 35, 34, 36, 34, 35, 34, 35, 34, 34, 34, 29, 30, 0, 19, 29, 27, 30, 28, 23, 24, 28], - "nextMatePosition": 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false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGGGGGTGTGGCTAAGCAAAGGGGTTCAAAGTCTTTTATTATGCATGAAAACCACTCCCTAAAATTTATATTAAAATTTAAAGGAATTTTCACCCGATTTT", - "alignedQuality": [29, 33, 28, 25, 33, 31, 24, 32, 25, 31, 27, 30, 33, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:108:13558:6051", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 187, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 32, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCNCCCATAGA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 33, 38, 37, 38, 38, 38, 38, 36, 36, 38, 38, 38, 37, 38, 38, 37, 38, 37, 36, 38, 38, 38, 33, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 34, 38, 37, 38, 37, 38, 36, 38, 38, 35, 38, 38, 38, 37, 38, 38, 37, 38, 32, 30, 0, 7, 30, 25, 25, 27, 25, 28, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.6", - "fragmentName": "6141AAAXX100423:6:54:18839:9717", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 35, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 88, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 13, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATGCTTAGATGGATAATTGTATCCCATAAACACGAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTACATAGAACGA", - "alignedQuality": [38, 38, 38, 35, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 37, 38, 38, 36, 37, 37, 35, 38, 32, 38, 38, 38, 38, 37, 38, 36, 38, 38, 38, 38, 25, 37, 37, 37, 36, 28, 36, 36, 36, 36, 25, 35, 37, 32, 35, 32, 37, 33, 36, 36, 36, 37, 35, 36, 32, 38, 34, 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"referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GCATATGCTAAGATCGATAATATCATCCCATAAACACAACGACTACGACCTGACCATATACTTCAATAAAGTTAAAATTACAACTGACAAACACCATAGCA", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:96:9477:2838", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 172, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 39, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ 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"numberReads": 2, - "fragmentLength": 171, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 40, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGANCGGTGTAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 37, 38, 37, 36, 38, 38, 36, 38, 38, 38, 37, 38, 38, 37, 38, 37, 38, 38, 38, 38, 37, 38, 37, 38, 36, 37, 38, 37, 34, 38, 38, 38, 37, 37, 28, 38, 36, 37, 37, 38, 37, 37, 37, 36, 35, 37, 37, 37, 33, 37, 36, 35, 35, 36, 29, 29, 0, 30, 29, 25, 25, 29, 16, 23, 31], - "nextMatePosition": null, - "info": 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38, 37, 38, 38, 38, 36, 34, 36, 38, 38, 37, 35, 38, 38, 36, 36, 37, 38, 36, 38, 37, 37, 38, 37, 38, 38, 38, 38, 38, 37, 36, 38, 36, 37, 36, 36, 33, 38, 35, 36, 37, 36, 35, 38, 37, 37, 36, 37, 36, 36, 36, 36, 35, 36, 34, 35, 30, 36, 36, 36, 34, 36, 32, 32, 24, 33, 20, 25, 19, 26, 27, 27, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:94:18877:18293", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 41, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": 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"mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 88, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 13, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GATGGATAATTGTATCCCATAAACACAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGAAGACAGGA", - "alignedQuality": [18, 11, 28, 26, 11, 18, 26, 26, 11, 18, 28, 11, 30, 27, 23, 33, 23, 30, 11, 29, 30, 30, 23, 23, 18, 23, 17, 26, 11, 32, 17, 9, 23, 30, 11, 19, 22, 10, 8, 15, 15, 9, 8, 8, 30, 21, 15, 22, 8, 8, 30, 32, 18, 9, 28, 9, 32, 29, 14, 21, 11, 31, 21, 18, 21, 22, 23, 28, 28, 11, 23, 23, 9, 33, 27, 32, 33, 28, 18, 31, 33, 25, 31, 25, 31, 31, 18, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:7:7712:11139", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 43, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAGT", - "alignedQuality": [38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 37, 37, 38, 38, 38, 38, 36, 38, 38, 38, 38, 35, 38, 37, 36, 38, 38, 37, 37, 38, 38, 38, 38, 36, 38, 37, 34, 38, 36, 36, 37, 38, 38, 38, 38, 37, 37, 38, 37, 36, 37, 37, 35, 36, 35, 36, 36, 36, 36, 36, 36, 38, 33, 35, 35, 35, 36, 34, 33, 36, 34, 35, 35, 30, 34, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:45:14089:3113", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 187, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 46, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 84, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 17, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGATAATTGTATCCCATAAACACAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCC", - "alignedQuality": [28, 25, 20, 20, 28, 26, 26, 30, 26, 17, 26, 20, 27, 26, 26, 32, 30, 30, 26, 30, 34, 34, 34, 34, 34, 30, 34, 34, 20, 34, 28, 28, 20, 18, 33, 28, 18, 29, 25, 25, 28, 28, 28, 20, 25, 34, 34, 34, 34, 34, 34, 32, 26, 34, 30, 28, 20, 28, 13, 33, 32, 29, 32, 26, 19, 34, 34, 34, 30, 34, 34, 25, 20, 28, 34, 34, 30, 19, 18, 32, 26, 17, 29, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.2", - "fragmentName": "6141AAAXX100423:2:106:17757:15738", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 46, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAATCTCCATAGACCGGTGTGGGTTGGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 37, 36, 37, 38, 37, 38, 38, 38, 35, 38, 38, 37, 38, 37, 38, 38, 38, 37, 37, 38, 38, 38, 38, 37, 38, 38, 33, 37, 37, 38, 38, 36, 37, 35, 38, 37, 36, 37, 36, 37, 37, 37, 36, 37, 37, 35, 36, 36, 35, 35, 36, 36, 36, 34, 34, 33, 36, 36, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:66:5653:15675", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGTGTGGCTAAGAAAAGGGGGTTAAATATTTTTAATAATACTGAAAACCCCCCCCCATATTTTAATGTAAAATTTAAGGGGTTTTATATCGCGCGAACACG", - "alignedQuality": [27, 31, 12, 27, 16, 27, 27, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:116:8469:2988", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 189, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 46, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 89, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 12, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGATAATTGTATCCCATAAACACAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCC", - "alignedQuality": [32, 32, 22, 19, 17, 23, 20, 31, 23, 17, 33, 26, 26, 20, 26, 24, 25, 26, 24, 31, 21, 26, 33, 33, 18, 28, 18, 20, 5, 21, 17, 13, 26, 28, 31, 28, 16, 34, 28, 22, 34, 25, 28, 25, 29, 22, 31, 24, 22, 33, 28, 25, 34, 34, 31, 16, 29, 26, 12, 29, 10, 14, 30, 22, 29, 25, 29, 30, 29, 29, 28, 29, 20, 20, 20, 32, 29, 31, 25, 31, 33, 21, 20, 30, 30, 32, 32, 30, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:80:15722:3463", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 182, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { 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"properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAAATTCCCAAATAAAGACATTAACACAGCTCTACAAAGTCCAAACTCTGCATTTCTACCTCTAATGACTAATAAGTCCACAACCAACCACTCCTGTTTC", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:4:11279:10553", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 50, - "reverseStrand": false - }, - "mappingQuality": 25, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATTGGATCCCATAAACACAAAGGATTGGTCCTGGCGTTATAATTAATTAGAGGAAAGATTAGACATGCAAACCTCTACAGACCGGTGTAAAATCCCTTAA", - "alignedQuality": [31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:50:14496:18474", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 52, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGTATCCCATAAACACAAAGGTTTGGTCCTAGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 37, 30, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 32, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 35, 38, 38, 37, 37, 38, 38, 36, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 34, 38, 37, 38, 37, 38, 38, 37, 34, 38, 36, 37, 37, 35, 38, 36, 38, 37, 38, 36, 35, 37, 36, 33, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:61:6403:21082", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTGGGGGTGTGGCTATAGACACAAACGAACACACATGTTATGTACTCTCTGATCCCCACCTATTCATCAAAGAAAGTGGAATACGCATATCACCACTCCCC", - "alignedQuality": [25, 32, 24, 29, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:61:6403:21082", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 52, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 65, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 36, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGTATCCCATAAACACAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCTAACCTCCATAGACCGGTGTAAAACCCCTTAAAC", - "alignedQuality": [25, 19, 29, 25, 27, 33, 28, 28, 33, 28, 29, 29, 11, 19, 25, 26, 26, 18, 18, 18, 17, 15, 8, 31, 28, 21, 9, 16, 32, 26, 31, 33, 21, 23, 33, 33, 32, 18, 31, 18, 20, 30, 26, 23, 22, 20, 33, 22, 10, 8, 26, 27, 30, 16, 20, 24, 9, 30, 30, 21, 20, 17, 20, 17, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:69:1823:1645", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 52, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATACCTTAAAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 36, 37, 38, 34, 37, 38, 38, 38, 36, 35, 38, 37, 38, 38, 36, 37, 38, 36, 37, 37, 37, 36, 38, 35, 37, 37, 38, 37, 35, 38, 35, 37, 33, 32, 35, 37, 34, 36, 37, 30, 37, 37, 37, 36, 30, 34, 35, 36, 36, 30, 34, 31, 28, 32, 34, 34, 34, 32, 28, 34, 31, 34, 34, 32, 28, 30, 32, 29, 32, 25, 34, 27, 17, 7, 25, 22, 28, 27, 32, 27, 32, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:99:18637:3397", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 100, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 52, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATNCCCTTAAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 38, 38, 38, 36, 38, 38, 38, 36, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 36, 37, 38, 38, 38, 36, 35, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 35, 38, 36, 37, 34, 37, 38, 33, 37, 37, 37, 38, 37, 38, 37, 36, 35, 38, 35, 38, 37, 30, 37, 36, 33, 37, 32, 36, 33, 37, 25, 25, 0, 19, 27, 30, 30, 27, 28, 26, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:78:6316:4697", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": 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"position": 53, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCNACTTAAAC", - "alignedQuality": [37, 37, 37, 37, 36, 37, 32, 32, 35, 35, 37, 32, 37, 37, 37, 37, 37, 33, 37, 35, 35, 36, 37, 37, 35, 37, 37, 37, 37, 32, 37, 37, 30, 37, 37, 35, 30, 37, 36, 37, 37, 37, 36, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 35, 28, 33, 37, 37, 37, 36, 37, 37, 35, 35, 37, 37, 33, 36, 37, 37, 36, 36, 36, 33, 36, 37, 37, 36, 37, 35, 25, 36, 36, 33, 28, 33, 33, 28, 33, 33, 18, 25, 0, 10, 22, 28, 26, 28, 25, 23, 31], - "nextMatePosition": 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"fragmentName": "6141AAAXX100423:3:37:8169:13015", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 55, - "reverseStrand": false - }, - "mappingQuality": 25, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATCCCATAAACACAAAGGTCTGGTCCTGGCCCTATAACTAATTAGAGGTAAAATTACACATGCACACCTCTATAGACCCGTGTCAAATCTTCTACACCTC", - "alignedQuality": [32, 11, 33, 32, 33, 24, 14, 30, 20, 13, 12, 8, 6, 29, 25, 12, 21, 14, 7, 30, 10, 31, 7, 32, 15, 32, 16, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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"readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:90:4247:5366", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 55, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 75, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 26, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGCAAAATTACACATGCAAACCTCCATAGCCCGGAGAAAAACCCCNATACACAT", - "alignedQuality": [22, 21, 25, 9, 28, 17, 22, 17, 27, 31, 26, 17, 26, 27, 26, 22, 17, 17, 17, 18, 32, 26, 15, 9, 9, 22, 22, 17, 8, 21, 14, 29, 33, 21, 30, 21, 13, 16, 17, 24, 27, 23, 11, 33, 18, 25, 14, 26, 9, 8, 9, 21, 21, 23, 29, 31, 31, 28, 28, 25, 32, 32, 33, 32, 33, 33, 33, 29, 11, 32, 20, 7, 15, 25, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:21:4578:5763", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 56, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCATAAACATTT", - "alignedQuality": [36, 37, 36, 37, 35, 35, 37, 35, 37, 37, 38, 38, 38, 38, 38, 33, 36, 36, 35, 36, 36, 36, 36, 36, 36, 38, 37, 38, 38, 36, 35, 38, 38, 35, 38, 36, 38, 38, 37, 38, 38, 37, 37, 37, 38, 36, 36, 36, 33, 36, 36, 36, 36, 36, 36, 38, 37, 37, 36, 35, 38, 38, 38, 35, 36, 37, 38, 28, 30, 36, 37, 37, 28, 37, 35, 33, 37, 35, 37, 37, 33, 33, 35, 35, 30, 36, 36, 36, 33, 33, 31, 14, 34, 31, 29, 31, 31, 29, 29, 29, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:48:2158:5284", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGTGTGGCTAAAAAAAGGGGCTTTAACCATTTTTATTTGCTTGTTACCCCCTCCCTTTATTTTTAAAAAAAATTTATAGGATTTTTCACCCGGCTCTGGGG", - "alignedQuality": [31, 31, 28, 31, 30, 31, 32, 31, 30, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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"info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:94:5017:20924", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 66, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAACATT", - "alignedQuality": [37, 37, 37, 37, 37, 34, 36, 36, 36, 36, 37, 37, 37, 37, 37, 36, 38, 38, 37, 38, 38, 38, 38, 38, 35, 36, 37, 37, 38, 38, 38, 38, 38, 36, 36, 35, 37, 37, 35, 37, 38, 35, 38, 38, 37, 38, 38, 38, 38, 35, 37, 38, 38, 33, 37, 37, 35, 38, 37, 38, 36, 36, 35, 38, 36, 37, 35, 32, 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"readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:10:3803:7158", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 101, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 68, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 97, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 4, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGAAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCTCTAAACATTTACTNAAAATATA", - "alignedQuality": [22, 19, 9, 7, 19, 21, 11, 26, 24, 14, 24, 29, 20, 12, 15, 11, 11, 11, 18, 22, 24, 26, 26, 25, 16, 24, 24, 20, 23, 20, 11, 22, 18, 29, 17, 16, 10, 20, 20, 22, 25, 28, 28, 28, 13, 27, 26, 20, 12, 20, 18, 18, 28, 22, 17, 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"duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 71, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAANAATTTAAG", - "alignedQuality": [36, 36, 36, 34, 36, 37, 37, 37, 35, 38, 37, 36, 37, 37, 37, 38, 38, 38, 36, 38, 37, 37, 38, 38, 38, 36, 38, 37, 38, 37, 36, 36, 37, 34, 38, 36, 37, 28, 38, 37, 37, 36, 36, 37, 37, 36, 38, 38, 38, 38, 36, 36, 35, 30, 36, 35, 35, 36, 36, 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"supplementaryAlignment": false, - "alignedSequence": "GTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAANGGAGAGGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 38, 38, 35, 37, 37, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 37, 37, 38, 38, 37, 38, 32, 38, 36, 38, 36, 37, 38, 38, 38, 38, 38, 38, 38, 36, 36, 36, 37, 37, 38, 36, 36, 37, 37, 38, 36, 38, 35, 36, 35, 37, 36, 36, 30, 28, 0, 16, 25, 26, 25, 18, 30, 25, 24], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.1", - "fragmentName": "6141AAAXX100423:1:31:4886:2752", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 133, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 78, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 91, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 10, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTCCTGGCCTTATAATTAATTAGAGGTAAAATTGCACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGNGATGGC", - "alignedQuality": [38, 38, 38, 38, 35, 38, 36, 38, 38, 38, 37, 36, 37, 37, 38, 37, 37, 37, 36, 37, 38, 35, 38, 36, 37, 38, 36, 37, 37, 35, 34, 35, 35, 10, 31, 32, 31, 34, 32, 32, 35, 37, 38, 32, 36, 37, 36, 37, 36, 37, 38, 35, 37, 36, 36, 35, 37, 37, 35, 38, 35, 37, 35, 36, 36, 37, 36, 35, 35, 36, 30, 32, 35, 35, 33, 33, 36, 35, 35, 33, 33, 35, 33, 33, 33, 35, 33, 33, 35, 33, 32, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:80:18873:1361", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 179, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 78, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTCTTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGT", - "alignedQuality": [36, 36, 36, 20, 36, 37, 37, 37, 37, 37, 38, 38, 38, 38, 38, 38, 36, 37, 38, 37, 38, 38, 38, 37, 38, 38, 36, 38, 38, 37, 30, 36, 36, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 36, 38, 38, 38, 38, 37, 37, 32, 37, 35, 37, 36, 37, 35, 37, 38, 35, 36, 36, 37, 36, 28, 35, 36, 36, 36, 35, 35, 35, 35, 37, 36, 36, 32, 35, 35, 36, 35, 36, 35, 28, 33, 33, 32, 36, 32, 35, 33, 35, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.2", - "fragmentName": "6141AAAXX100423:2:8:2627:21347", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 78, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 89, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 12, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GNCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTNCCAAGATGTA", - "alignedQuality": [33, 0, 33, 30, 33, 32, 33, 34, 34, 32, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 37, 30, 38, 35, 36, 38, 38, 38, 37, 38, 38, 32, 37, 37, 33, 37, 38, 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38, 38, 38, 38, 38, 38, 38, 38, 37, 24, 30, 29, 31, 27, 4, 22, 27, 25, 29, 31, 31, 24, 23, 22, 38, 36, 38, 38, 38, 32, 36, 36, 36, 36, 37, 38, 38, 38, 38, 35, 33, 38, 38, 38, 38, 38, 37, 38, 37, 38, 36, 33, 38, 37, 38, 38, 38, 37, 38, 35, 38, 34, 38, 36, 38, 33, 37, 37, 38, 35, 38, 38, 36, 38, 38, 37, 36, 36, 37, 37, 38, 36, 38, 33, 37, 36, 38, 37, 37, 37, 25, 33, 36, 28, 33, 25, 33, 33, 32, 17], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:37:11670:10031", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 117, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 79, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 9, - 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"613F1AAXX100423:8:107:6156:15270", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 116, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 85, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 9, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCTTATAATTAATTAGAGGTAAAATTACACATACAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGNATATCAAG", - "alignedQuality": [38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 35, 38, 38, 38, 35, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 20, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 32, 36, 36, 36, 36, 38, 38, 35, 38, 38, 38, 38, 38, 38, 25, 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"ATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAGGCACAT", - "alignedQuality": [36, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 35, 38, 38, 37, 38, 38, 38, 33, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 37, 38, 36, 38, 35, 36, 35, 37, 35, 37, 30, 37, 35, 38, 38, 36, 38, 38, 30, 37, 37, 30, 30, 34, 36, 35, 36, 38, 38, 36, 38, 37, 38, 37, 37, 38, 38, 32, 38, 37, 37, 35, 34, 36, 33, 25, 31, 33, 34, 36, 32, 32, 36, 38, 38, 36, 38, 38], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:82:6224:14395", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 95, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": 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"fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 96, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACNTTTAAAAT", - "alignedQuality": [38, 37, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 25, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 35, 38, 38, 38, 38, 37, 38, 38, 36, 37, 34, 37, 37, 35, 36, 36, 36, 36, 38, 38, 38, 38, 37, 36, 38, 36, 37, 38, 38, 38, 38, 38, 37, 37, 38, 36, 38, 37, 37, 35, 37, 38, 28, 37, 36, 38, 37, 38, 36, 36, 14, 33, 33, 34, 35, 33, 33, 33, 27, 27, 0, 14, 21, 25, 25, 27, 21, 26, 35], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:82:10630:4431", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 168, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 96, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACNTTTAAAAT", - "alignedQuality": [38, 38, 38, 38, 38, 36, 37, 38, 38, 38, 37, 36, 25, 37, 37, 38, 37, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 36, 38, 38, 38, 38, 38, 38, 37, 38, 37, 35, 38, 37, 37, 33, 36, 37, 38, 38, 38, 38, 36, 38, 37, 37, 38, 37, 38, 37, 38, 37, 38, 35, 36, 35, 37, 38, 36, 38, 36, 36, 37, 36, 36, 38, 36, 37, 36, 37, 33, 33, 37, 33, 28, 33, 34, 31, 27, 27, 0, 8, 18, 19, 22, 22, 18, 25, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:15:4665:11101", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 96, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTAGAGGAAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATATAAGGAGAGGGTATCAAGCACATTAAAATA", - "alignedQuality": [28, 20, 18, 30, 13, 7, 8, 12, 7, 21, 33, 14, 33, 33, 33, 33, 15, 20, 14, 18, 32, 16, 32, 32, 17, 12, 14, 12, 29, 26, 33, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:51:4149:16879", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 96, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": 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"readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:12:5463:17668", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 178, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 105, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATANACTTAAGA", - "alignedQuality": [38, 38, 38, 36, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 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"reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACG", - "alignedQuality": [37, 38, 30, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 36, 38, 38, 38, 38, 37, 38, 37, 38, 36, 38, 38, 38, 37, 38, 35, 37, 38, 38, 36, 36, 38, 35, 36, 38, 37, 36, 25, 34, 22, 32, 32, 34, 33, 34, 34, 36, 36, 35, 35, 36, 34, 36, 25, 36, 35, 36, 37, 35, 30, 33, 35, 35, 36, 36, 36, 35, 35], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:1:3424:18790", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, 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null, - "readGroupId": "6141A.2", - "fragmentName": "6141AAAXX100423:2:84:18546:20140", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 182, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 109, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTACGCATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCACAACATAAAA", - "alignedQuality": [35, 38, 37, 38, 35, 38, 36, 38, 38, 38, 35, 38, 38, 38, 37, 38, 38, 38, 32, 37, 38, 36, 38, 38, 35, 35, 36, 34, 36, 30, 33, 35, 35, 35, 34, 37, 37, 36, 20, 25, 36, 36, 36, 33, 36, 32, 33, 36, 32, 25, 32, 34, 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"fragmentLength": 179, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 113, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 95, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 6, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGGATCAAGCACATTAAAATAGCTTAAGACACCTTGCC", - "alignedQuality": [34, 34, 33, 34, 34, 28, 34, 34, 34, 30, 34, 34, 34, 34, 26, 26, 34, 34, 30, 21, 28, 28, 25, 20, 28, 34, 34, 34, 33, 34, 34, 34, 34, 25, 34, 34, 34, 25, 30, 33, 34, 34, 20, 25, 34, 23, 33, 32, 29, 30, 34, 33, 34, 34, 33, 33, 28, 33, 33, 20, 28, 21, 28, 17, 28, 10, 30, 33, 30, 18, 29, 24, 8, 16, 29, 30, 30, 30, 33, 12, 33, 32, 30, 33, 30, 19, 30, 33, 33, 33, 30, 28, 32, 28, 32, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:1:5113:6786", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 129, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 114, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 95, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 6, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACNCCTTGCCT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 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"supplementaryAlignment": false, - "alignedSequence": "AAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTNCCCTAGCC", - "alignedQuality": [38, 37, 38, 37, 38, 38, 38, 38, 37, 38, 35, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 35, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 37, 33, 38, 36, 37, 37, 37, 32, 37, 37, 37, 37, 35, 37, 37, 37, 36, 37, 37, 37, 37, 35, 36, 36, 35, 35, 36, 36, 35, 35, 36, 36, 35, 35, 33, 37, 36, 35, 23, 18, 0, 16, 24, 28, 22, 23, 23, 25, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:94:1337:1612", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 121, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGTACATTAAAATAGCTTAAGACACCTTGCCTAGCTACA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 36, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 37, 37, 38, 38, 36, 38, 36, 38, 37, 38, 35, 35, 37, 36, 35, 36, 34, 37, 33, 36, 32, 34, 35, 32, 33, 33, 33, 11, 34, 34, 36, 34, 34, 35, 33, 35, 35, 35, 35, 34, 26, 35, 34, 33, 20, 28, 30, 34, 34, 32, 27, 32, 32, 30, 23, 30, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:34:5579:10024", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 123, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTNAGCCACAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 36, 36, 12, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 35, 37, 37, 38, 37, 38, 37, 38, 33, 37, 38, 38, 37, 36, 37, 37, 38, 38, 35, 37, 37, 38, 37, 36, 37, 37, 37, 36, 37, 36, 37, 37, 36, 35, 37, 36, 37, 35, 34, 35, 34, 36, 35, 28, 27, 0, 20, 28, 25, 26, 27, 26, 25, 38], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:42:10426:16978", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 124, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCCATAGACCGGTGTAAAATCCATTAAACATTTACTTAAAATTTAAGGAGAGGGCATCAAGAAAATTAAAAAAGCTAAAGACACCTTGCCTCNCCACACCC", - "alignedQuality": [10, 21, 21, 10, 21, 16, 16, 16, 18, 16, 10, 23, 31, 22, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:69:17813:9329", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 203, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 125, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 91, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 9, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGGCCACACCC", - "alignedQuality": [38, 38, 37, 38, 38, 38, 36, 38, 38, 38, 38, 36, 38, 37, 37, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 37, 38, 37, 36, 37, 36, 37, 37, 35, 38, 38, 38, 37, 37, 38, 37, 37, 36, 36, 35, 36, 36, 38, 33, 36, 36, 36, 36, 36, 35, 37, 35, 36, 37, 36, 36, 36, 35, 35, 33, 35, 36, 34, 35, 33, 35, 35, 35, 35, 35, 33, 35, 35, 34, 34, 34, 34, 33, 34, 30, 29, 26, 22, 15, 28, 31, 31, 31, 31, 30, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:2:5743:8006", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 188, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 125, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGNCCACACCC", - "alignedQuality": [38, 36, 37, 38, 32, 35, 37, 38, 38, 35, 28, 34, 36, 36, 36, 35, 32, 12, 35, 32, 37, 37, 37, 37, 37, 38, 37, 38, 38, 38, 33, 32, 36, 35, 36, 35, 37, 35, 28, 35, 36, 30, 28, 36, 36, 37, 35, 37, 28, 35, 36, 30, 35, 28, 34, 36, 30, 33, 36, 36, 36, 38, 38, 38, 36, 37, 37, 33, 37, 37, 36, 32, 37, 35, 34, 37, 37, 36, 25, 36, 37, 37, 28, 36, 36, 20, 30, 34, 30, 25, 20, 14, 0, 8, 25, 30, 30, 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2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:73:7585:2657", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 190, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 127, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCNCCACCCCC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 37, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 37, 32, 37, 37, 37, 38, 38, 37, 38, 38, 38, 35, 38, 35, 37, 38, 38, 36, 36, 37, 33, 37, 37, 38, 38, 38, 37, 33, 38, 38, 36, 38, 30, 35, 36, 32, 36, 34, 30, 36, 26, 33, 0, 5, 24, 30, 29, 29, 30, 17, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:84:9190:20996", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 127, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - 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"fragmentLength": 179, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 128, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCGTAGCCACACCCCCAC", - "alignedQuality": [33, 30, 33, 36, 36, 33, 32, 28, 36, 35, 36, 36, 30, 36, 36, 35, 36, 36, 36, 33, 36, 36, 35, 36, 32, 35, 32, 32, 35, 35, 34, 32, 32, 30, 36, 25, 35, 36, 36, 35, 35, 33, 36, 36, 36, 36, 36, 36, 36, 33, 17, 32, 30, 34, 32, 32, 32, 32, 32, 32, 36, 36, 32, 33, 36, 28, 35, 35, 35, 28, 32, 20, 35, 34, 35, 32, 25, 32, 28, 34, 20, 8, 9, 11, 27, 4, 18, 26, 17, 23, 32, 29, 33, 30, 32, 35, 18, 30, 21, 29, 29], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:96:1093:15921", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 186, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 128, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 60, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 41, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "NAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAANATAGCTTAAGACNNCTTGCCTAGCNNNNCCCCNAC", - "alignedQuality": [0, 26, 23, 20, 21, 25, 25, 23, 25, 24, 33, 33, 33, 33, 33, 29, 32, 32, 32, 32, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 2, 2, 2, 2, 0, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:54:6541:15697", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 188, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 129, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGACCGGTGTAAAATCCATTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACG", - "alignedQuality": [32, 27, 10, 29, 28, 26, 31, 25, 26, 26, 35, 35, 35, 35, 35, 35, 35, 12, 35, 35, 35, 33, 35, 35, 32, 28, 30, 35, 35, 35, 36, 36, 36, 36, 35, 25, 33, 33, 34, 16, 32, 34, 32, 34, 34, 36, 36, 25, 36, 36, 36, 36, 36, 35, 35, 32, 36, 36, 36, 35, 36, 36, 36, 35, 36, 36, 36, 30, 36, 36, 36, 36, 36, 36, 34, 36, 36, 36, 36, 35, 36, 30, 36, 33, 33, 36, 34, 32, 36, 36, 36, 36, 36, 36, 36, 35, 35, 34, 32, 29, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:10:2043:20748", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 92, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 129, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - 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"fragmentLength": 180, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 131, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTACCTAGCCACACCCNCACGGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 38, 38, 36, 38, 38, 38, 38, 37, 35, 37, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 35, 38, 37, 38, 36, 37, 34, 36, 37, 38, 38, 37, 38, 38, 35, 36, 34, 36, 30, 32, 34, 34, 34, 34, 36, 34, 36, 36, 36, 33, 33, 33, 2, 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"referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CGGTGNAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCNCGGGAC", - "alignedQuality": [34, 34, 34, 34, 34, 0, 35, 35, 35, 35, 35, 35, 35, 35, 35, 38, 38, 38, 36, 38, 38, 37, 38, 38, 35, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 37, 38, 38, 38, 36, 37, 38, 38, 38, 38, 38, 37, 38, 38, 36, 38, 35, 37, 37, 38, 37, 37, 37, 37, 30, 36, 36, 36, 36, 37, 37, 35, 36, 37, 38, 35, 36, 36, 35, 37, 35, 34, 35, 34, 2, 0, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:20:2751:5355", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 204, - "readNumber": 1, - 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"fragmentName": "6141AAAXX100423:2:102:13963:2305", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 133, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 52, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 49, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CGGTGGAAAATCCCTTAAACATTTACTTAAAATTTATGGAGAGGGTATCAAGTACATTAAAATAGCTTAAGACAACTTGCCTAGCCACACCAGCAACGACC", - "alignedQuality": [17, 22, 20, 17, 17, 17, 26, 22, 28, 23, 21, 11, 27, 22, 21, 11, 27, 28, 31, 7, 21, 15, 14, 21, 8, 21, 21, 21, 28, 13, 8, 32, 17, 15, 21, 32, 9, 21, 26, 32, 27, 33, 17, 10, 17, 33, 30, 27, 16, 32, 21, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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"613F0AAXX100423:1:55:11240:18646", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 146, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTTAAACATTTACTTAAAATTTAAGGAGAGGATATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAA", - "alignedQuality": [37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 27, 30, 36, 36, 36, 36, 36, 36, 36, 30, 34, 36, 36, 37, 37, 38, 38, 38, 38, 35, 38, 38, 38, 38, 35, 38, 37, 35, 37, 35, 38, 37, 37, 36, 38, 38, 38, 37, 38, 35, 38, 37, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 26, 34, 25, 33, 34, 34, 34, 33, 36, 36, 34, 34, 32, 36, 25, 36, 33, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:33:19510:10053", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 148, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCANGTGATAAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 35, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 37, 38, 38, 38, 38, 35, 38, 38, 37, 37, 38, 38, 37, 36, 38, 36, 37, 37, 37, 38, 35, 38, 36, 36, 37, 36, 34, 38, 34, 34, 34, 36, 37, 28, 37, 34, 35, 29, 27, 0, 18, 21, 22, 23, 22, 20, 18, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:23:19257:14002", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 150, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTNATAAATAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 38, 38, 38, 38, 38, 38, 38, 34, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 37, 36, 38, 34, 34, 36, 33, 34, 35, 34, 35, 32, 36, 32, 35, 35, 34, 30, 29, 0, 25, 28, 23, 25, 26, 26, 22, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:103:7190:1200", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 131, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 150, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCAGATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTNATAAATAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 34, 38, 38, 38, 38, 36, 38, 36, 36, 11, 36, 36, 35, 35, 35, 34, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 37, 38, 36, 37, 35, 37, 36, 37, 36, 38, 37, 37, 36, 37, 36, 35, 35, 35, 34, 33, 34, 33, 34, 33, 35, 35, 34, 34, 34, 35, 34, 33, 30, 25, 0, 28, 25, 25, 25, 20, 24, 20, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:106:16259:6089", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 131, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 150, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTNATAAATAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 34, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 37, 37, 38, 38, 38, 38, 38, 36, 36, 38, 38, 36, 38, 34, 35, 36, 35, 36, 35, 37, 35, 36, 36, 35, 31, 30, 0, 28, 28, 25, 26, 29, 21, 29, 35], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:12:6338:18527", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 177, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 151, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGNATAAATAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 38, 38, 38, 38, 38, 38, 38, 35, 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false, - "supplementaryAlignment": false, - "alignedSequence": "CATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGANACATATTA", - "alignedQuality": [38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 37, 38, 38, 38, 36, 38, 37, 38, 37, 36, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 35, 37, 38, 35, 38, 38, 38, 36, 38, 35, 38, 38, 38, 38, 37, 38, 36, 38, 36, 38, 38, 36, 38, 38, 35, 38, 36, 36, 35, 35, 38, 35, 37, 36, 36, 36, 35, 35, 32, 30, 31, 0, 29, 6, 25, 28, 30, 26, 21, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:110:19637:9034", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 154, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 152, - "reverseStrand": false - 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true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 153, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTTACTAAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAAATATTAA", - "alignedQuality": [37, 37, 37, 37, 37, 37, 37, 20, 37, 37, 35, 35, 37, 37, 37, 37, 35, 37, 37, 37, 37, 37, 37, 37, 37, 35, 36, 37, 37, 36, 37, 37, 37, 37, 37, 37, 37, 37, 36, 37, 37, 34, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 36, 36, 35, 37, 37, 35, 35, 37, 37, 37, 36, 35, 34, 34, 34, 28, 20, 35, 33, 36, 33, 37, 30, 36, 36, 32, 36, 30, 36, 31, 33, 28, 31, 18, 31, 31, 30, 32, 25, 30], 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"alignment": { - "position": { - "referenceName": "chrM", - "position": 228, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CGGGACTCAGCAGTGATAAATATTAAGCAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGGCAGCCACCGCGGTNCTACGA", - "alignedQuality": [38, 38, 38, 32, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 35, 37, 36, 37, 38, 37, 37, 36, 38, 38, 36, 37, 32, 37, 36, 37, 34, 33, 37, 37, 30, 36, 36, 34, 34, 36, 36, 38, 32, 38, 36, 36, 35, 36, 38, 38, 37, 32, 35, 36, 36, 32, 36, 37, 37, 35, 33, 32, 35, 36, 36, 32, 33, 28, 31, 25, 5, 28, 25, 23, 25, 31, 32, 32, 31, 32, 32, 31, 30, 2, 0, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, 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"numberReads": 2, - "fragmentLength": 184, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 252, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGCAATAAACGAAAGTTTGACTAAGTTATACATCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 32, 37, 37, 35, 36, 29, 16, 5, 8, 31, 12, 20, 7, 27, 25, 35, 31, 35, 35, 35, 36, 38, 35, 35, 38, 38, 37, 35, 36, 38, 38, 38, 34, 33, 38, 36, 33, 25, 36, 35, 38, 38, 37, 33, 34, 35, 35, 35, 36, 37, 28, 34, 34, 36, 33, 36, 36, 33, 34, 36, 25, 32, 34, 34, 28, 36, 33, 32, 33, 36, 36, 36, 35, 35, 31, 20], - "nextMatePosition": null, - "info": {} 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"properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 259, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACCAATTATCTTCGGCGACACA", - "alignedQuality": [38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 37, 38, 38, 35, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 37, 36, 37, 38, 36, 37, 38, 38, 36, 37, 38, 38, 36, 37, 35, 35, 32, 37, 36, 35, 36, 36, 36, 36, 34, 35, 36, 36, 36, 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"id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:10:16469:12729", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 181, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 261, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 94, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGNGTAAAACG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 37, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 35, 38, 38, 36, 37, 38, 38, 38, 38, 35, 38, 38, 36, 37, 36, 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"secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGCCATACGATTAACCCAAACTAATTATCTTCGGCGTANAACGTGTC", - "alignedQuality": [25, 18, 29, 17, 21, 28, 28, 30, 28, 28, 34, 35, 35, 33, 35, 33, 25, 35, 30, 30, 34, 35, 33, 33, 34, 29, 29, 27, 27, 34, 35, 35, 30, 34, 35, 25, 33, 30, 20, 29, 34, 29, 32, 31, 32, 33, 28, 33, 33, 33, 34, 33, 32, 30, 33, 28, 8, 30, 30, 30, 30, 33, 32, 30, 30, 30, 30, 28, 30, 33, 31, 33, 12, 32, 31, 30, 31, 20, 20, 30, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.7", - "fragmentName": "6141AAAXX100423:7:14:7355:6147", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 269, - "reverseStrand": false 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"fragmentLength": 182, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 269, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACNATGTCAAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 30, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 36, 38, 38, 38, 37, 38, 35, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 37, 38, 38, 38, 35, 38, 38, 36, 38, 37, 35, 32, 37, 36, 35, 37, 36, 37, 36, 36, 36, 36, 36, 35, 37, 37, 37, 35, 37, 37, 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"fragmentName": "613F1AAXX100423:1:53:16999:6279", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 117, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 282, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGCCAACTATAANATAAATAA", - "alignedQuality": [36, 35, 32, 33, 36, 30, 36, 36, 35, 33, 28, 36, 25, 36, 36, 30, 30, 35, 35, 28, 25, 36, 36, 33, 36, 25, 36, 36, 35, 36, 37, 37, 37, 37, 32, 33, 35, 32, 32, 28, 29, 25, 29, 31, 29, 25, 31, 34, 35, 30, 18, 14, 20, 26, 20, 34, 34, 33, 32, 34, 36, 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"alignedQuality": [0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.3", - "fragmentName": "613F0AAXX100423:3:113:19539:6361", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 289, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 100, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 1, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTACAACGTGTCAACTATAAATAAATAAATAGAATT", - "alignedQuality": [37, 37, 35, 36, 37, 37, 37, 36, 37, 37, 37, 38, 37, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 35, 38, 38, 37, 33, 35, 37, 37, 37, 35, 32, 37, 37, 32, 25, 36, 36, 36, 37, 35, 38, 38, 38, 38, 37, 38, 37, 38, 33, 37, 38, 38, 35, 38, 36, 28, 37, 38, 32, 31, 34, 12, 32, 20, 30, 35, 28, 30, 36, 33, 36, 36, 28, 32, 35, 36, 36, 34, 25, 33, 30, 32, 12, 25, 35, 34, 23, 24, 31, 21, 29, 14, 30, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:4:18322:4265", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 289, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 99, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 2, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGGGTTGGTAAATTTCGTGCCAGCCACCGCGTTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATA", - "alignedQuality": [38, 38, 33, 36, 38, 38, 37, 38, 36, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 36, 38, 38, 30, 33, 33, 25, 30, 28, 30, 36, 36, 34, 32, 34, 37, 38, 37, 38, 38, 28, 31, 36, 36, 35, 37, 38, 37, 35, 38, 37, 38, 35, 33, 38, 36, 37, 32, 35, 36, 37, 33, 37, 30, 36, 37, 36, 36, 35, 25, 32, 32, 32, 32, 32, 28, 24, 29, 34, 29, 20, 26, 31, 28, 23, 30, 36, 36, 30, 30, 36, 34, 33, 33, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:85:2088:11538", - "properPlacement": 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"alignedSequence": "GTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAAAATTAAA", - "alignedQuality": [35, 36, 36, 36, 33, 36, 36, 36, 36, 36, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 35, 37, 33, 37, 30, 35, 34, 30, 28, 31, 36, 33, 36, 36, 33, 37, 37, 37, 36, 37, 35, 37, 37, 36, 35, 37, 37, 37, 30, 37, 36, 37, 33, 37, 36, 37, 35, 36, 36, 32, 33, 36, 32, 31, 33, 36, 33, 35, 36, 36, 30, 35, 31, 30, 35, 35, 33, 35, 33, 36, 35, 35, 33, 31, 36, 32, 31, 31, 33, 35, 26, 25, 33, 9, 30, 20, 23, 25, 30, 30, 37], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.7", - "fragmentName": "613F0AAXX100423:7:117:8522:19026", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 292, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - 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"6141AAAXX100423:2:105:16229:19746", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 161, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 454, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTCATCTATAATACACGACAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAACACTATTATCC", - "alignedQuality": [36, 36, 36, 36, 36, 30, 37, 37, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 36, 37, 38, 38, 38, 37, 35, 38, 37, 35, 35, 37, 37, 36, 36, 37, 36, 33, 36, 31, 38, 36, 37, 38, 38, 35, 35, 35, 36, 33, 34, 36, 34, 35, 34, 34, 34, 36, 20, 34, 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"reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTATAATACACGACAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAACACTATTTGCCAGAGA", - "alignedQuality": [34, 34, 28, 34, 34, 25, 34, 35, 35, 35, 30, 35, 36, 20, 36, 35, 20, 28, 35, 35, 33, 35, 28, 35, 30, 36, 20, 36, 36, 12, 32, 30, 32, 34, 28, 25, 35, 30, 25, 30, 34, 30, 32, 34, 25, 33, 33, 26, 36, 28, 20, 34, 20, 20, 12, 34, 20, 28, 34, 34, 34, 28, 25, 25, 30, 25, 34, 12, 25, 34, 36, 36, 36, 35, 33, 36, 25, 36, 20, 28, 25, 25, 31, 29, 31, 9, 32, 30, 32, 32, 34, 28, 33, 34, 35, 31, 20, 20, 35, 33, 20], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:56:15784:12936", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 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"id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:61:13484:16071", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 195, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 460, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATAATACACGACAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAAAACTATTTGGCCAGAGA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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"alignedSequence": "TATAATACACGACAGCTAAGACCCAAACCGGGATTAGATACTCCACTATGCTTAACCCTAAACATAAATAATTTAATAAAAAAAACCAAAAAGCCAAGCAA", - "alignedQuality": [20, 12, 15, 28, 22, 15, 22, 22, 28, 25, 19, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:68:16059:2332", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 230, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 463, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - 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"alignment": { - "position": { - "referenceName": "chrM", - "position": 465, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 94, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TACACGACAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAAAACTATTTGCCAGNGAACTACT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 38, 36, 38, 38, 37, 37, 38, 38, 36, 36, 37, 36, 35, 36, 36, 36, 37, 37, 37, 36, 37, 37, 35, 36, 36, 36, 35, 36, 36, 33, 36, 36, 36, 36, 35, 36, 36, 35, 35, 35, 36, 34, 35, 34, 34, 32, 30, 34, 35, 35, 33, 35, 30, 35, 34, 32, 34, 0, 32, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, 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"properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 468, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACGACAGCTAATACCCAAACTGGGATTAGATACCACAATATGCTTAGCCATAAACCTACATAATTAAATCTAACAAAACTATTTGCCAGAGAAATACACGC", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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"fragmentName": "613F0AAXX100423:2:77:10629:3640", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 177, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 473, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAAAACTACTTGCCAGAGAACTACTAGCCATAG", - "alignedQuality": [38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 37, 38, 36, 38, 37, 38, 38, 38, 38, 38, 37, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 34, 38, 36, 36, 36, 37, 36, 36, 36, 36, 36, 36, 37, 36, 35, 37, 33, 35, 36, 37, 37, 36, 37, 35, 37, 30, 36, 36, 36, 37, 36, 38, 37, 36, 36, 35, 34, 34, 35, 37, 37, 25, 34, 35, 35, 34, 35, 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"fragmentName": "6141AAAXX100423:1:15:2174:3440", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 151, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 528, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 70, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 31, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAATTAAATTNAACAAAACTATTTGCCAGAGAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGGAATTTTTTATCCCCCTCAAGTNNCNGNTGN", - "alignedQuality": [38, 38, 38, 38, 38, 35, 35, 35, 35, 35, 0, 35, 35, 35, 35, 32, 33, 28, 32, 34, 36, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 35, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 35, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 36, 37, 35, 36, 37, 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"alignment": { - "position": { - "referenceName": "chrM", - "position": 540, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 85, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 16, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACAAAACTATTTGCCAGAGAACAACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAAACCAAAAA", - "alignedQuality": [37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 26, 28, 4, 25, 21, 22, 27, 25, 28, 23, 37, 37, 33, 37, 37, 37, 37, 37, 37, 37, 37, 37, 36, 37, 37, 36, 35, 37, 37, 37, 37, 32, 37, 37, 37, 36, 36, 36, 14, 33, 30, 30, 33, 34, 28, 34, 33, 33, 33, 33, 25, 32, 28, 32, 20, 29, 28, 28, 28, 25, 28, 10, 30, 25, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - 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"readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 547, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 91, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 10, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATTTGCCAGAGAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCCTCTAGAGGAGCCTGTTCTATAATCGATCANCAAACAC", - "alignedQuality": [37, 35, 37, 37, 35, 37, 35, 33, 37, 37, 37, 35, 37, 35, 37, 37, 37, 37, 30, 32, 37, 37, 37, 30, 28, 37, 37, 37, 37, 37, 37, 35, 37, 37, 37, 30, 35, 37, 37, 35, 37, 37, 34, 37, 37, 28, 30, 36, 36, 36, 35, 30, 31, 30, 33, 33, 31, 28, 31, 31, 25, 33, 20, 12, 32, 28, 31, 32, 25, 28, 36, 33, 33, 36, 36, 36, 30, 33, 31, 36, 25, 28, 11, 30, 30, 30, 30, 30, 30, 30, 19, 18, 26, 0, 19, 26, 20, 32, 2, 2, 2], 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15, 28, 20, 21, 12, 22, 18, 22, 29, 30, 30, 22, 27, 28, 30, 10, 30, 30, 10, 30, 28, 28, 30, 19, 20, 14, 32, 14, 22, 8, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:83:13635:2428", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 156, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 555, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 98, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 3, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - 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"mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGAGAACTACTAGCCATAGATTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCCACCTCA", - "alignedQuality": [37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 37, 37, 35, 38, 35, 38, 37, 38, 37, 38, 35, 37, 36, 38, 38, 33, 37, 36, 38, 37, 38, 34, 37, 36, 38, 37, 36, 35, 36, 30, 34, 37, 37, 36, 37, 33, 37, 33, 33, 37, 37, 33, 37, 35, 35, 36, 35, 34, 35, 33, 35, 17], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.6", - "fragmentName": "6141AAAXX100423:6:68:11061:18765", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 555, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGAGAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAAACCCCACCAAACACA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 37, 37, 34, 28, 29, 29, 32, 34, 20, 30, 24, 29, 11, 29, 20, 28, 30, 29, 20, 34, 34, 30, 36, 31, 29, 20, 30, 27, 25, 26, 30, 26, 26, 20, 29, 26, 30, 26, 12, 32, 29, 32, 28, 32, 32, 12, 27, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:30:2115:13936", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 181, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 556, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 48, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 53, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GATAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGATCTATAAACGATAAACCCCCCTCACCCTCCC", - "alignedQuality": [20, 23, 9, 9, 9, 22, 15, 23, 30, 22, 31, 29, 29, 32, 31, 32, 10, 31, 19, 22, 17, 24, 10, 13, 23, 25, 23, 25, 23, 23, 10, 23, 18, 15, 30, 32, 14, 23, 22, 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"alignedSequence": "AGAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTAAGATCGG", - "alignedQuality": [37, 32, 37, 37, 37, 37, 37, 33, 35, 37, 37, 30, 35, 37, 30, 32, 36, 32, 35, 36, 33, 36, 33, 36, 35, 36, 35, 28, 35, 30, 37, 37, 37, 37, 33, 37, 28, 32, 32, 37, 28, 32, 35, 35, 34, 36, 36, 36, 28, 36, 28, 36, 25, 28, 35, 36, 25, 28, 34, 30, 36, 36, 25, 36, 36, 34, 25, 32, 30, 33, 31, 30, 34, 32, 32, 31, 30, 25, 20, 28, 28, 28, 28, 30, 32, 28, 33, 28, 33, 33, 33, 31, 32, 28, 33, 33, 33, 30, 33, 31, 20], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:100:10105:13386", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 72, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 558, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ 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"readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 559, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 100, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 1, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATACACCCCGCTCTACCTCACCAC", - "alignedQuality": [38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 36, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 36, 38, 36, 32, 30, 34, 34, 33, 35, 36, 38, 37, 36, 38, 35, 36, 38, 38, 38, 37, 38, 37, 36, 34, 34, 34, 34, 34, 27, 36, 34, 34, 32, 35, 30, 34, 30, 35, 35, 34, 35, 37, 35, 37, 35, 37, 31, 36, 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"fragmentName": "613F1AAXX100423:3:118:3666:19612", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 149, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 570, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTGCTTGCTAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 38, 38, 35, 38, 37, 38, 30, 38, 38, 38, 38, 37, 38, 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"AAACTCAAAGGACTTGGCGGTACTTTATATCCCTCTAGAGGAGGCTGTTTTATTATTGATAAACCCCGCTCTACCCCACCCTCTCTTTCCTCTTGGGGTTT", - "alignedQuality": [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 33, 36, 36, 36, 36, 36, 36, 36, 36, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:92:13479:6652", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 578, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCCTCTCTTGCTAATTCAGCCTA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 38, 38, 38, 38, 37, 38, 35, 38, 37, 36, 37, 38, 36, 36, 36, 36, 38, 35, 33, 33, 37, 37, 38, 35, 37, 36, 37, 36, 36, 35, 37, 36, 32, 36, 37, 36, 36, 36, 37, 36, 35, 35, 35, 34, 35, 34, 35, 33, 35, 34, 35, 34, 34, 34, 35, 34, 7, 31, 33, 31, 31, 30, 30, 31, 31, 31, 12, 34, 34, 34, 32, 20, 25, 31, 28, 31, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.7", - "fragmentName": "613F0AAXX100423:7:25:8160:1927", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 168, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 579, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGCTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTAT", - "alignedQuality": [28, 36, 30, 33, 36, 35, 35, 36, 36, 28, 32, 36, 36, 36, 36, 28, 35, 35, 36, 35, 28, 30, 28, 32, 35, 36, 36, 32, 36, 36, 35, 36, 34, 36, 33, 36, 36, 36, 28, 30, 20, 20, 25, 34, 31, 36, 32, 32, 33, 33, 35, 28, 20, 35, 34, 34, 30, 34, 29, 20, 34, 30, 17, 32, 20, 34, 32, 33, 11, 31, 29, 12, 32, 29, 28, 11, 30, 31, 31, 30, 28, 29, 29, 29, 26, 9, 26, 32, 20, 12, 29, 25, 28, 30, 29, 32, 20, 24, 32, 30, 20], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:71:18818:12965", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 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"id": null, - "readGroupId": "613F0.6", - "fragmentName": "613F0AAXX100423:6:70:19643:9290", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 579, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "DELETE", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 2, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 2, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 3, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 1, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": 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"fragmentName": "6141AAAXX100423:4:58:19645:7588", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 179, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 583, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 75, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 26, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAAACCCGCTCTACCTCACCATCTCTTGCTAATTCTACATCTCGTC", - "alignedQuality": [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 32, 32, 30, 32, 35, 33, 23, 29, 28, 29, 17, 31, 29, 29, 28, 34, 20, 31, 31, 32, 35, 28, 34, 20, 34, 28, 29, 26, 31, 21, 28, 18, 28, 15, 30, 30, 20, 30, 29, 30, 30, 34, 33, 9, 30, 34, 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2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:6:19748:13634", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 584, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAAGGACTTGGCGGTACTTTTTATCCATCTAGAGGAGCCCGTTCTATTATAGATAAACCCCCCTCTCCCTCACCCTCTCTTTCTAATTTCAGTCATCCACC", - "alignedQuality": [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 30, 16, 18, 22, 28, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:111:18973:2067", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 168, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 585, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGGACTTGGCGGTACTTTATATCCATCTAGGGGAGCCTTTTCTATAATCTATAAACCCCTCTCTACCTCACCATCTCTTTCTAATTCTGTGTAGTGTTAT", - "alignedQuality": [32, 25, 32, 32, 30, 32, 34, 34, 25, 20, 31, 12, 34, 29, 31, 31, 26, 28, 31, 31, 35, 12, 28, 35, 35, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:101:7895:3365", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 178, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 586, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTNATATACCG", - "alignedQuality": [38, 38, 37, 37, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 38, 38, 38, 32, 38, 38, 38, 38, 38, 38, 36, 38, 32, 37, 38, 37, 38, 38, 38, 35, 37, 38, 38, 38, 36, 35, 38, 38, 38, 38, 38, 38, 38, 32, 38, 37, 36, 37, 37, 38, 37, 37, 37, 35, 36, 35, 35, 37, 38, 32, 35, 36, 36, 38, 36, 35, 33, 35, 36, 36, 35, 36, 34, 35, 28, 34, 33, 26, 25, 0, 16, 27, 25, 23, 25, 22, 25, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:104:4607:5279", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 587, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 94, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GAACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 32, 38, 36, 38, 37, 37, 37, 37, 34, 38, 37, 38, 37, 36, 37, 37, 32, 37, 36, 38, 38, 28, 37, 36, 37, 38, 37, 36, 36, 33, 38, 30, 37, 36, 37, 37, 35, 32, 37, 36, 35, 37, 36, 33, 36, 37, 36, 30, 36, 32, 35, 25, 33, 30, 37, 35, 35, 36, 31, 37, 33, 28, 35, 35, 35, 32, 36, 35, 32, 25, 30, 25, 30, 30, 30, 12, 28, 30, 31, 31, 28, 30, 31, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:66:13672:2605", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 588, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 24, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 77, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GACTTGGCGGTACCTTTTTTCCATTTCCCAGTGCCCGTTCTCTAATCTGGAAACCCCGCGCTGCCGCCTCACCACTTGACGCTTCATCCTATCTACTTGCC", - "alignedQuality": [30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.2", - "fragmentName": "6141AAAXX100423:2:10:13217:15205", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 590, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 16, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 18, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] 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"ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTTGGCGGTACTTTTTATCCATCTAGAGGGGCCTGTTCTTTTATCCATAAACCCCCCCCCTCCCCCCCCTCCTCTTCCTATTTAACCCCTATCACACCACC", - "alignedQuality": [32, 32, 32, 32, 31, 32, 31, 31, 22, 28, 13, 18, 29, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:23:16337:3840", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 132, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 592, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 70, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 31, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATAGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATTATCACTATTT", - "alignedQuality": [35, 33, 28, 35, 35, 35, 33, 35, 28, 35, 35, 35, 28, 35, 32, 35, 35, 25, 35, 32, 25, 34, 30, 34, 32, 29, 12, 10, 25, 20, 32, 34, 32, 30, 34, 35, 35, 28, 35, 28, 32, 34, 11, 25, 28, 34, 34, 20, 34, 34, 35, 28, 34, 11, 26, 7, 33, 25, 26, 29, 12, 32, 34, 34, 34, 34, 25, 34, 32, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:10:14689:13457", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 98, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 592, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATAGA", - "alignedQuality": [37, 38, 38, 38, 38, 38, 37, 35, 38, 36, 38, 36, 38, 38, 37, 38, 38, 35, 33, 37, 37, 38, 38, 38, 38, 37, 35, 30, 36, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 28, 38, 38, 37, 35, 38, 36, 35, 37, 30, 33, 38, 37, 36, 37, 38, 34, 30, 37, 37, 36, 36, 36, 35, 36, 36, 33, 36, 36, 38, 37, 35, 33, 20, 37, 35, 30, 33, 34, 33, 33, 37, 35, 38, 35, 33, 36, 36, 25, 35, 32, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:119:3666:12939", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 98, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 596, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGA", - "alignedQuality": [29, 32, 26, 30, 26, 32, 32, 26, 34, 32, 34, 34, 30, 26, 34, 29, 32, 34, 32, 29, 31, 29, 29, 16, 21, 26, 25, 26, 32, 24, 32, 34, 34, 30, 32, 28, 34, 30, 32, 30, 28, 28, 28, 32, 26, 30, 32, 32, 23, 26, 18, 14, 28, 26, 33, 32, 19, 23, 15, 30, 34, 34, 34, 30, 34, 28, 34, 26, 34, 34, 26, 30, 34, 28, 32, 34, 34, 33, 30, 33, 33, 33, 28, 34, 28, 33, 33, 33, 23, 30, 34, 33, 33, 33, 25, 33, 33, 33, 25, 32, 19], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:52:12141:9678", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 177, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 597, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCANACTTCAGC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 36, 38, 37, 38, 36, 36, 36, 37, 36, 37, 36, 36, 36, 37, 36, 36, 36, 36, 35, 36, 36, 35, 36, 35, 35, 36, 36, 36, 36, 36, 36, 33, 34, 35, 29, 24, 0, 6, 27, 21, 26, 23, 19, 23, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:56:16917:3099", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 597, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 54, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 47, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTACTTTATATCCCTCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCTACCTTCCGC", - "alignedQuality": [34, 33, 34, 34, 34, 34, 30, 34, 32, 21, 26, 23, 32, 10, 26, 18, 27, 26, 24, 32, 34, 32, 18, 12, 23, 27, 29, 31, 25, 34, 34, 33, 28, 34, 32, 34, 34, 34, 30, 30, 30, 23, 32, 8, 30, 28, 28, 28, 28, 34, 28, 28, 28, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:73:4540:14300", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 181, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 600, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCACAC", - "alignedQuality": [38, 38, 38, 35, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 35, 37, 35, 35, 34, 37, 35, 37, 35, 35, 36, 33, 30, 35, 35, 36, 34, 32, 32, 35, 34, 31, 34, 32, 34, 28, 20, 32, 35, 34, 32, 35, 34, 35, 35, 35, 35, 20, 32, 32, 34, 32, 32, 31, 30, 30, 32, 25, 32, 32, 32, 8, 32, 30], - 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"duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 152, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 606, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCANAACCCTAA", - "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 38, 37, 37, 36, 37, 34, 38, 36, 36, 37, 37, 37, 36, 33, 36, 36, 36, 30, 36, 33, 33, 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"alignedSequence": "AGAGGAGCCTGTTCTATAATCGATAAACCCCGCNCTACCTNACCATCNNNTNNNNNNNNANNNNNNNNNNNGCNANNNNCAGCAAACCCTAAAAAGGTATT", - "alignedQuality": [35, 33, 38, 38, 36, 38, 38, 36, 38, 37, 38, 38, 35, 38, 38, 36, 38, 38, 37, 37, 38, 38, 38, 36, 35, 37, 35, 38, 37, 35, 30, 34, 31, 0, 34, 32, 30, 30, 30, 30, 0, 30, 29, 29, 32, 2, 2, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 0, 2, 0, 0, 0, 0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:31:1155:13344", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": 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null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:28:2836:7773", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 188, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 622, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATNAAAGTAAG", - "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 33, 38, 38, 38, 36, 36, 38, 38, 37, 37, 36, 38, 38, 37, 38, 33, 36, 38, 38, 33, 36, 38, 36, 38, 38, 30, 36, 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"operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTACAAAGGTATTAAAGTAAGCAAAAG", - "alignedQuality": [35, 35, 35, 35, 30, 33, 34, 25, 36, 36, 36, 36, 28, 28, 33, 25, 33, 25, 34, 30, 33, 33, 36, 32, 28, 36, 33, 36, 31, 36, 34, 30, 36, 34, 33, 36, 30, 36, 32, 36, 36, 33, 33, 33, 36, 32, 25, 32, 35, 25, 31, 29, 28, 29, 34, 33, 34, 32, 25, 32, 30, 30, 31, 33, 33, 25, 28, 33, 33, 28, 36, 36, 33, 25, 31, 31, 31, 19, 28, 28, 17, 23, 27, 22, 26, 32, 32, 31, 30, 25, 33, 31, 33, 30, 31, 25, 25, 31, 31, 33, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:65:18419:16546", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { 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"properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 186, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 628, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 95, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 6, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATAATCGATAAACTCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAG", - "alignedQuality": [37, 37, 37, 37, 37, 32, 37, 37, 37, 37, 37, 37, 37, 36, 20, 36, 36, 36, 36, 36, 37, 37, 37, 36, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 35, 37, 33, 37, 35, 37, 35, 36, 36, 37, 37, 37, 37, 37, 37, 36, 20, 35, 32, 36, 37, 36, 37, 35, 33, 33, 28, 36, 36, 33, 37, 37, 36, 36, 36, 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null, - "readGroupId": "6141A.1", - "fragmentName": "6141AAAXX100423:1:34:5553:8767", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 641, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCCCGCTCTACCTCACCATCTATTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAANATAAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 37, 38, 34, 7, 31, 32, 34, 34, 34, 32, 31, 32, 37, 36, 33, 36, 36, 38, 36, 37, 37, 37, 36, 37, 35, 35, 33, 36, 37, 33, 35, 36, 35, 37, 37, 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null, - "readGroupId": "6141A.1", - "fragmentName": "6141AAAXX100423:1:50:13981:3364", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 134, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 644, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATNTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAAC", - "alignedQuality": [35, 32, 35, 33, 36, 33, 36, 35, 36, 33, 32, 32, 36, 36, 36, 32, 32, 36, 36, 33, 29, 25, 34, 32, 34, 36, 30, 35, 33, 35, 28, 30, 35, 35, 32, 35, 30, 35, 35, 12, 35, 30, 34, 34, 33, 24, 0, 22, 26, 33, 29, 28, 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"alignment": { - "position": { - "referenceName": "chrM", - "position": 648, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 73, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 28, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAACAAGTGATTAAAGTAAGCAAAAGACTCAAACATAAAAACGTTA", - "alignedQuality": [26, 23, 18, 26, 9, 21, 17, 17, 17, 17, 31, 22, 21, 17, 15, 17, 17, 15, 31, 30, 10, 15, 19, 14, 22, 33, 33, 26, 23, 30, 17, 26, 15, 26, 15, 27, 25, 33, 33, 16, 33, 24, 33, 33, 33, 20, 16, 17, 33, 33, 14, 33, 22, 17, 33, 33, 14, 9, 22, 33, 17, 17, 5, 14, 14, 25, 32, 9, 18, 32, 32, 33, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": 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"referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAACGNATAGGTCA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 34, 38, 38, 38, 38, 36, 37, 38, 37, 38, 38, 36, 38, 33, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 30, 38, 37, 35, 26, 31, 0, 20, 29, 29, 20, 22, 16, 29, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:61:19310:6422", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - 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false, - "supplementaryAlignment": false, - "alignedSequence": "ACCATCTCTAGCTAATTCCGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGAATTAAAGAAAGCAAAAGACTCCAACAACAAAAAGTGAGTACAAG", - "alignedQuality": [31, 32, 24, 21, 16, 30, 9, 12, 30, 9, 19, 17, 8, 17, 8, 30, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:82:3465:18661", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 185, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 656, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAACGCTAGGACAACA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 35, 38, 38, 38, 38, 35, 34, 38, 38, 38, 35, 38, 37, 35, 37, 38, 33, 35, 36, 36, 33, 36, 36, 32, 35, 37, 36, 36, 37, 36, 36, 36, 37, 37, 34, 38, 37, 38, 30, 36, 34, 35, 25, 26, 36, 36, 36, 36, 38, 38, 33, 37, 30, 36, 33, 32, 26, 32, 27, 25, 32, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:91:5501:15084", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 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"readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:62:9158:19347", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 81, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 659, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "CLIP_SOFT", - "operationLength": 10, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 46, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 45, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATGTTTGATTCTTTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAGATCGGAAG", - "alignedQuality": [38, 38, 38, 38, 36, 38, 38, 38, 38, 37, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 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"alignment": { - "position": { - "referenceName": "chrM", - "position": 892, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCNGTAACAAG", - "alignedQuality": [37, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 38, 38, 36, 37, 35, 38, 38, 37, 38, 38, 38, 36, 36, 38, 38, 38, 33, 38, 38, 38, 38, 38, 35, 38, 38, 37, 38, 38, 37, 38, 38, 38, 36, 38, 38, 37, 38, 38, 36, 37, 36, 38, 38, 38, 36, 36, 37, 37, 36, 35, 37, 33, 37, 37, 35, 37, 36, 35, 25, 35, 35, 36, 34, 36, 35, 35, 36, 34, 36, 23, 27, 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"fragmentName": "613F1AAXX100423:5:35:12861:9976", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 186, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 905, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGNGATACTGG", - "alignedQuality": [38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 35, 38, 38, 38, 38, 30, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 38, 36, 37, 38, 38, 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"mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAGGT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 35, 38, 38, 38, 37, 38, 36, 38, 38, 38, 38, 37, 34, 38, 38, 38, 38, 36, 38, 37, 38, 38, 36, 38, 36, 37, 30, 35, 36, 37, 36, 36, 35, 38, 33, 35, 36, 36, 37, 38, 28, 36, 37, 36, 35, 36, 35, 35, 35, 36, 35, 22], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:6:19562:12868", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 154, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 910, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACNGGAAAGTG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 36, 35, 37, 35, 37, 36, 38, 37, 37, 38, 35, 37, 34, 36, 35, 34, 37, 35, 35, 36, 34, 36, 36, 34, 33, 36, 36, 36, 35, 34, 29, 28, 0, 29, 29, 29, 29, 29, 29, 28, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": 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"reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 87, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 14, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCTCCAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGAGATAGGCTAAGTCAA", - "alignedQuality": [20, 26, 12, 20, 12, 26, 20, 12, 20, 20, 21, 31, 31, 29, 33, 21, 33, 32, 32, 30, 12, 26, 32, 32, 32, 34, 28, 28, 28, 34, 21, 32, 32, 34, 32, 34, 34, 21, 34, 34, 34, 21, 28, 34, 34, 28, 32, 30, 32, 34, 26, 19, 32, 26, 32, 28, 28, 34, 18, 32, 34, 34, 34, 12, 30, 29, 32, 17, 12, 17, 32, 32, 30, 27, 16, 26, 30, 32, 22, 12, 22, 31, 30, 22, 22, 27, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:51:12399:9321", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 182, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 920, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATAATGGAAAGTGTGCTTGGAAT", - "alignedQuality": [38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 35, 38, 35, 38, 38, 38, 38, 38, 38, 35, 38, 38, 36, 38, 38, 36, 37, 38, 38, 38, 37, 38, 36, 35, 38, 37, 38, 36, 37, 38, 38, 36, 38, 37, 36, 36, 35, 35, 37, 32, 36, 33, 36, 36, 36, 34, 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"duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 924, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 100, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 1, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGAAAGCATACTGGAAGGTGTGCTTGGAATAATC", - "alignedQuality": [35, 33, 35, 28, 33, 35, 32, 35, 30, 32, 29, 29, 32, 25, 34, 35, 35, 28, 25, 35, 32, 29, 20, 30, 32, 35, 35, 33, 35, 32, 35, 35, 35, 28, 35, 29, 34, 29, 30, 20, 24, 30, 34, 31, 28, 23, 17, 24, 20, 30, 25, 33, 33, 34, 25, 24, 23, 23, 21, 20, 11, 21, 32, 28, 23, 19, 12, 22, 6, 6, 24, 25, 32, 22, 18, 33, 34, 20, 20, 28, 14, 18, 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27, 33, 26, 33, 17, 21, 26, 14, 32, 26, 22, 26, 19, 14, 21, 32, 33, 18, 20, 26, 24, 33, 16, 26, 10, 16, 7, 23, 12, 5, 13, 6, 21, 30, 7, 31, 28, 33, 16, 15, 33, 32, 23, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:89:8823:2101", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 156, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 926, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTAAATTAAACTTAACATAATTAATTTCTACACATCCGTTTATGAGCGGAGATAAGTCGTAACCAGGCAACCACACTGGTAAGTATACTAGCAATCATCAT", - "alignedQuality": [38, 38, 38, 38, 38, 36, 36, 30, 28, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:102:15100:4058", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 87, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 927, - "reverseStrand": false - }, - "mappingQuality": 23, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 87, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 3, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 5, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 6, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCAGATCGGACGAGCG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 34, 32, 36, 37, 37, 37, 37, 35, 38, 38, 38, 38, 36, 37, 38, 36, 37, 37, 38, 37, 37, 38, 36, 34, 37, 37, 38, 37, 38, 38, 36, 38, 38, 37, 37, 36, 35, 35, 37, 34, 38, 35, 37, 36, 36, 38, 37, 36, 33, 37, 12, 32, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.6", - "fragmentName": "613F0AAXX100423:6:119:19785:7641", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 927, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 94, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGCAAGCATACTGGTAAGTGTGCTTGGAATAATCATA", - "alignedQuality": [38, 38, 37, 37, 38, 38, 36, 38, 38, 38, 38, 35, 37, 35, 37, 37, 38, 38, 35, 38, 37, 38, 38, 38, 36, 35, 38, 28, 38, 38, 38, 38, 38, 37, 38, 37, 35, 33, 36, 35, 32, 37, 37, 36, 37, 37, 38, 36, 38, 38, 30, 38, 38, 30, 37, 36, 36, 37, 32, 25, 34, 33, 34, 33, 36, 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"fragmentLength": 179, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 940, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGGCTTAAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 37, 35, 38, 38, 37, 38, 37, 38, 38, 37, 37, 38, 35, 37, 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"alignment": { - "position": { - "referenceName": "chrM", - "position": 963, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCNTACACCCA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 36, 38, 36, 38, 38, 36, 38, 38, 38, 38, 38, 35, 37, 35, 38, 34, 35, 36, 38, 37, 38, 25, 33, 37, 33, 37, 37, 37, 33, 34, 35, 34, 36, 37, 30, 36, 36, 37, 37, 38, 36, 37, 33, 37, 37, 34, 36, 37, 35, 34, 36, 34, 33, 36, 25, 36, 35, 36, 30, 36, 37, 36, 35, 35, 36, 36, 36, 28, 35, 35, 34, 35, 36, 30, 34, 0, 28, 30, 28, 30, 26, 25, 26, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": 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"readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 968, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 89, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 12, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGAGAGGAGATAAGTCGTAACNAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGTAGT", - "alignedQuality": [38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 36, 38, 37, 36, 38, 38, 29, 0, 30, 31, 30, 29, 32, 32, 32, 32, 38, 37, 38, 37, 38, 38, 37, 37, 37, 38, 37, 33, 33, 35, 36, 37, 33, 36, 37, 36, 35, 37, 36, 36, 35, 36, 36, 35, 36, 37, 35, 33, 36, 33, 33, 35, 35, 35, 35, 35, 35, 36, 35, 36, 36, 35, 35, 36, 33, 36, 30, 32, 32, 33, 33, 32, 35, 35, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:59:5329:15929", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 180, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 986, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACGAATGAACA", - "alignedQuality": [38, 38, 38, 38, 36, 38, 38, 38, 38, 37, 38, 38, 35, 38, 36, 38, 38, 36, 36, 38, 38, 38, 38, 36, 35, 37, 37, 38, 38, 37, 38, 37, 38, 38, 38, 35, 38, 38, 38, 38, 37, 38, 38, 37, 38, 36, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 37, 38, 36, 37, 37, 38, 38, 38, 38, 38, 36, 38, 34, 36, 38, 38, 36, 35, 37, 37, 37, 36, 36, 38, 36, 32, 36, 37, 36, 36, 38, 37, 33, 30, 11, 31, 25, 29, 30, 29, 30, 30, 37], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:46:2638:14790", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 172, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 988, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATATGGCCTACACCCAGAAGATTTCATGACCAATGAACACT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 36, 36, 29, 36, 36, 36, 36, 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}, + "nextMatePosition": null, + "info": {} + }] + }, "nextPageToken": null } From 5c785cc6b98518a7b7b6ed58b1a213066c36df8c Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Mon, 20 Jun 2016 11:07:20 -0700 Subject: [PATCH 075/136] modified alignment json for test --- test-data/adam-alignments.json | 39273 ++++++++++++++++++++++++++----- 1 file changed, 33387 insertions(+), 5886 deletions(-) diff --git a/test-data/adam-alignments.json b/test-data/adam-alignments.json index f4e92070..e8866aa4 100644 --- a/test-data/adam-alignments.json +++ b/test-data/adam-alignments.json @@ -1,5889 +1,33390 @@ { - "alignments": { - "$outer": {}, - "underlying": [{ - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:47:2891:8862", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 0, - 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"properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 115, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 15, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 92, + "referenceSequence": null + }, { + "operation": "INSERT", + "operationLength": 1, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + "operationLength": 8, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAANAATTACAC", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 36, 37, 37, 38, 37, 38, 37, 38, 38, 37, 38, 38, 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"fragmentName": "6141AAAXX100423:2:102:13963:2305", + "properPlacement": false, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": null, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 133, + "reverseStrand": false + }, + "mappingQuality": 37, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 52, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 49, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CGGTGGAAAATCCCTTAAACATTTACTTAAAATTTATGGAGAGGGTATCAAGTACATTAAAATAGCTTAAGACAACTTGCCTAGCCACACCAGCAACGACC", + "alignedQuality": [17, 22, 20, 17, 17, 17, 26, 22, 28, 23, 21, 11, 27, 22, 21, 11, 27, 28, 31, 7, 21, 15, 14, 21, 8, 21, 21, 21, 28, 13, 8, 32, 17, 15, 21, 32, 9, 21, 26, 32, 27, 33, 17, 10, 17, 33, 30, 27, 16, 32, 21, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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"properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 113, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 158, + "reverseStrand": false + }, + "mappingQuality": 29, + "cigar": [{ + "operation": "CLIP_SOFT", + "operationLength": 62, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + "operationLength": 39, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CTTTAGGACGTGAAATATGGCGAGGAAAACTGAAAAAGGTGGAAAATATTGGAATGTCCGCTCTTTAAATTTAAGGAGAGGGTATCAAGCACATTAAAATA", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 37, 35, 38, 38, 36, 38, 37, 38, 38, 37, 38, 34, 37, 37, 35, 37, 38, 38, 37, 38, 38, 38, 38, 38, 36, 37, 37, 37, 36, 38, 37, 32, 35, 37, 37, 37, 38, 38, 37, 36, 36, 37, 37, 36, 35, 36, 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"fragmentName": "6141AAAXX100423:4:58:19645:7588", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 179, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 583, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 75, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 26, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAAACCCGCTCTACCTCACCATCTCTTGCTAATTCTACATCTCGTC", + "alignedQuality": [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 32, 32, 30, 32, 35, 33, 23, 29, 28, 29, 17, 31, 29, 29, 28, 34, 20, 31, 31, 32, 35, 28, 34, 20, 34, 28, 29, 26, 31, 21, 28, 18, 28, 15, 30, 30, 20, 30, 29, 30, 30, 34, 33, 9, 30, 34, 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"secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "GTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCANACTTCAGC", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 36, 38, 37, 38, 36, 36, 36, 37, 36, 37, 36, 36, 36, 37, 36, 36, 36, 36, 35, 36, 36, 35, 36, 35, 35, 36, 36, 36, 36, 36, 36, 33, 34, 35, 29, 24, 0, 6, 27, 21, 26, 23, 19, 23, 34], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.3", + "fragmentName": "613F1AAXX100423:3:56:16917:3099", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 173, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 597, + 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"duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 181, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 600, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCACAC", + "alignedQuality": [38, 38, 38, 35, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 35, 37, 35, 35, 34, 37, 35, 37, 35, 35, 36, 33, 30, 35, 35, 36, 34, 32, 32, 35, 34, 31, 34, 32, 34, 28, 20, 32, 35, 34, 32, 35, 34, 35, 35, 35, 35, 20, 32, 32, 34, 32, 32, 31, 30, 30, 32, 25, 32, 32, 32, 8, 32, 30], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.6", + "fragmentName": "613F1AAXX100423:6:37:15714:21079", + "properPlacement": false, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 94, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 603, + "reverseStrand": false + }, + "mappingQuality": 37, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAGATCGG", + "alignedQuality": [38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 36, 36, 36, 36, 36, 37, 36, 36, 36, 36, 35, 35, 37, 36, 36, 36, 36, 34, 31, 35, 34, 36, 35, 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"alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 36, 12, 36, 35, 34, 34, 35, 35, 33, 38, 37, 38, 36, 37, 38, 38, 38, 36, 37, 37, 35, 37, 38, 37, 38, 37, 35, 37, 35, 31, 35, 33, 36, 25, 33, 32, 36, 35, 36, 35, 37, 33, 25, 36, 37, 33, 38, 31, 33, 35, 33, 33, 36, 35, 33, 35, 31, 36, 35, 36, 33, 33, 35, 36, 32, 28, 33, 32, 25, 32, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.3", + "fragmentName": "613F1AAXX100423:3:45:3029:17994", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 190, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 604, + "reverseStrand": false + }, + "mappingQuality": 17, + "cigar": [{ + "operation": "CLIP_SOFT", + "operationLength": 1, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + 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"duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 152, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 606, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 92, + "referenceSequence": null + }, { + "operation": "INSERT", + "operationLength": 1, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + "operationLength": 8, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "ATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCANAACCCTAA", + "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 38, 37, 37, 36, 37, 34, 38, 36, 36, 37, 37, 37, 36, 33, 36, 36, 36, 30, 36, 33, 33, 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"alignedQuality": [34, 34, 25, 34, 28, 28, 30, 34, 20, 34, 31, 26, 12, 29, 30, 28, 33, 28, 26, 28, 26, 31, 31, 30, 31, 35, 35, 35, 35, 35, 25, 25, 32, 32, 30, 29, 32, 25, 32, 32, 35, 35, 12, 35, 30, 28, 32, 31, 28, 12, 29, 33, 25, 29, 28, 14, 16, 26, 10, 33, 11, 25, 22, 31, 25, 11, 18, 30, 28, 27, 29, 12, 18, 25, 30, 10, 25, 25, 28, 26, 29, 20, 31, 34, 31, 28, 29, 9, 34, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F0.4", + "fragmentName": "613F0AAXX100423:4:91:1251:17061", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 175, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 610, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 55, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + 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"fragmentLength": 174, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 640, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "ACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTAAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAA", + "alignedQuality": [37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 37, 38, 38, 35, 37, 36, 38, 35, 36, 33, 37, 37, 38, 37, 36, 35, 36, 37, 36, 36, 37, 36, 36, 36, 35, 35, 36, 35, 36, 34, 35, 34, 35, 35, 34, 35, 36, 34, 28, 27, 30, 32, 34, 33, 30, 33, 35, 34, 36, 35, 34, 34, 34, 34, 34, 34, 33, 32, 36, 35, 35, 34, 34, 34, 34, 32, 35, 34, 34, 34, 34, 34, 34, 35, 34, 35, 31, 33, 35, 28, 26, 34, 32, 35, 35, 35, 35], + "nextMatePosition": null, + "info": {} + }, { + "id": 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"alignment": { + "position": { + "referenceName": "chrM", + "position": 854, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 85, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 16, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TCAATTAAGAATAGAGAGCTTAATTGAATTGAGCAATGAAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAGACTTAACATAANNANTNTCN", + "alignedQuality": [34, 11, 34, 34, 34, 35, 35, 35, 35, 35, 38, 38, 38, 38, 37, 34, 38, 38, 33, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 36, 34, 38, 36, 36, 37, 38, 38, 37, 36, 38, 37, 36, 36, 37, 37, 38, 35, 34, 37, 36, 36, 36, 36, 34, 35, 36, 34, 36, 33, 34, 33, 32, 34, 34, 25, 27, 23, 27, 30, 18, 31, 29, 28, 30, 2, 2, 2, 2, 2, 2, 2, 0, 0, 2, 0, 2, 0, 2, 2, 0], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.6", + "fragmentName": "613F1AAXX100423:6:74:11101:5071", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 142, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 855, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "AAATTAAGAATAGAGAGCTTAATTGAATTGAGCAATGAAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATNAATTTCTA", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 35, 37, 36, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 36, 38, 38, 38, 37, 38, 38, 38, 38, 37, 36, 38, 37, 37, 38, 36, 37, 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"properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 176, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 883, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 65, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 36, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TGAGCAATGAAGTACGCACACACCGCCCGTCACCCTCATCAAATTAAATTAAACTTCACATAATTAATTTCTACACATCAGTTTCTGAGAGTAGATAAGTC", + "alignedQuality": [25, 28, 20, 33, 30, 25, 30, 25, 29, 20, 34, 28, 34, 26, 28, 31, 29, 29, 29, 28, 24, 12, 24, 26, 24, 34, 34, 34, 26, 20, 34, 29, 28, 26, 29, 20, 8, 8, 25, 32, 34, 32, 34, 21, 12, 26, 29, 33, 21, 22, 24, 31, 30, 7, 27, 14, 10, 27, 8, 31, 28, 33, 31, 26, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F0.4", + "fragmentName": "613F0AAXX100423:4:55:2647:4140", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 250, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 883, + "reverseStrand": false + }, + "mappingQuality": 29, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 101, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TGAGCAATGAAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATCGGAA", + "alignedQuality": [38, 38, 37, 38, 38, 38, 32, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 37, 28, 36, 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"TGNGCAATGAAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGGGAGTAGTG", + "alignedQuality": [34, 34, 0, 33, 31, 35, 35, 35, 35, 35, 38, 38, 36, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 38, 38, 35, 37, 36, 33, 35, 32, 34, 30, 33, 36, 33, 35, 36, 33, 37, 36, 30, 35, 36, 30, 37, 31, 35, 32, 35, 35, 30, 35, 32, 36, 30, 34, 31, 35, 36, 30, 34, 24, 34, 32, 34, 28, 34, 31, 33, 28, 30, 31, 32, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "6141A.5", + "fragmentName": "6141AAAXX100423:5:28:6479:11056", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 192, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 883, + "reverseStrand": false + }, + "mappingQuality": 29, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 35, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 66, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "TGAGCAATGAAGTACGCACACACCTCCCGTCACCCTCCTCAAATTAAATTAAATTTAATTTTATTTTTATTTTTACATCAGTTCATGTATACAGCTGACAG", + "alignedQuality": [31, 13, 8, 32, 7, 33, 33, 33, 13, 16, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.1", + "fragmentName": "613F1AAXX100423:1:38:18021:8701", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 184, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 887, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 63, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 38, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CAATGAAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTCACATCATTAATTTCTAGTCATCCGTTTATGAGAGGAGATAAGTCGTAA", + "alignedQuality": [20, 26, 17, 20, 30, 12, 24, 12, 24, 28, 28, 21, 28, 31, 29, 33, 26, 32, 26, 32, 34, 12, 34, 29, 12, 26, 26, 30, 21, 21, 34, 33, 34, 30, 30, 34, 21, 30, 21, 26, 30, 12, 34, 12, 32, 34, 28, 31, 28, 34, 26, 32, 18, 34, 26, 25, 28, 10, 28, 26, 32, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.1", + "fragmentName": 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34, 36, 34, 32, 35, 35, 35, 34, 36, 36, 34, 33, 35, 35], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.7", + "fragmentName": "613F1AAXX100423:7:64:9983:2202", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 165, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 889, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 35, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 66, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "ATGAAGTACGCACACACCGCCCGGCACCCTCCTCAAACTAAATTTAACTTCACACAATTAATTTCTAGAGATCCGCTCACGAGAGGAGGAAANATCGGAAC", + "alignedQuality": [27, 11, 7, 15, 11, 15, 11, 20, 15, 25, 32, 32, 22, 32, 31, 31, 24, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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"alignment": { + "position": { + "referenceName": "chrM", + "position": 892, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 92, + "referenceSequence": null + }, { + "operation": "INSERT", + "operationLength": 1, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + "operationLength": 8, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "AAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCNGTAACAAG", + "alignedQuality": [37, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 38, 38, 36, 37, 35, 38, 38, 37, 38, 38, 38, 36, 36, 38, 38, 38, 33, 38, 38, 38, 38, 38, 35, 38, 38, 37, 38, 38, 37, 38, 38, 38, 36, 38, 38, 37, 38, 38, 36, 37, 36, 38, 38, 38, 36, 36, 37, 37, 36, 35, 37, 33, 37, 37, 35, 37, 36, 35, 25, 35, 35, 36, 34, 36, 35, 35, 36, 34, 36, 23, 27, 0, 11, 23, 27, 23, 25, 25, 15, 34], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "613F1.3", + "fragmentName": "613F1AAXX100423:3:30:3445:6941", + "properPlacement": true, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": 182, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 892, + "reverseStrand": false + }, + "mappingQuality": 60, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 92, + "referenceSequence": null + }, { + "operation": "INSERT", + "operationLength": 1, + "referenceSequence": null + }, { + "operation": "ALIGNMENT_MATCH", + "operationLength": 8, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "AAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGGTAACAAG", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 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"supplementaryAlignment": false, + "alignedSequence": "CATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTNTTGAACTA", + "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 38, 38, 38, 37, 35, 37, 37, 38, 38, 38, 38, 38, 38, 38, 37, 37, 35, 37, 37, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 37, 37, 35, 36, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 37, 38, 37, 38, 37, 38, 38, 38, 38, 36, 35, 37, 38, 37, 37, 36, 36, 37, 36, 35, 37, 37, 37, 36, 36, 36, 36, 33, 35, 37, 37, 37, 30, 33, 0, 22, 30, 14, 23, 14, 17, 18, 30], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "6141A.8", + "fragmentName": "6141AAAXX100423:8:82:11001:10820", + "properPlacement": false, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": null, + "readNumber": 0, + "failedVendorQualityChecks": false, + "alignment": { + "position": { + "referenceName": "chrM", + "position": 997, + "reverseStrand": false + }, + "mappingQuality": 37, + "cigar": [{ + "operation": "ALIGNMENT_MATCH", + "operationLength": 84, + "referenceSequence": null + }, { + "operation": "CLIP_SOFT", + "operationLength": 17, + "referenceSequence": null + }] + }, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CATACTGGGAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTTGCCTACACCCAGAAGATTTCATGACCAATGAACACCTTTCAGCTT", + "alignedQuality": [26, 26, 25, 33, 33, 34, 34, 26, 12, 28, 28, 13, 29, 25, 28, 20, 12, 26, 25, 25, 27, 29, 32, 26, 32, 34, 28, 26, 26, 33, 20, 26, 24, 26, 27, 12, 33, 32, 33, 32, 33, 28, 34, 34, 28, 34, 28, 33, 28, 34, 26, 32, 12, 21, 32, 12, 26, 11, 26, 26, 12, 26, 32, 30, 17, 34, 26, 34, 25, 33, 32, 34, 23, 34, 34, 17, 31, 26, 11, 24, 17, 34, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }, { + "id": null, + "readGroupId": "6141A.8", + "fragmentName": "6141AAAXX100423:8:82:11001:10820", + "properPlacement": false, + "duplicateFragment": false, + "numberReads": 2, + "fragmentLength": null, + "readNumber": 1, + "failedVendorQualityChecks": false, + "alignment": null, + "secondaryAlignment": false, + "supplementaryAlignment": false, + "alignedSequence": "CATACTGGAAAGGGTTCATTGGTCATGAAATCTTCTGGGTGTAGGCCAGATGCTTTAATATTAAGCTACACTATGATTATTCCAAGCACACTTTCTACTTC", + "alignedQuality": [31, 13, 26, 21, 26, 29, 13, 29, 31, 31, 25, 28, 12, 24, 26, 29, 28, 13, 28, 27, 34, 34, 12, 34, 34, 34, 30, 34, 30, 34, 29, 13, 28, 31, 12, 28, 25, 30, 33, 17, 24, 23, 31, 26, 26, 13, 31, 28, 26, 29, 30, 32, 21, 32, 32, 33, 18, 34, 26, 12, 10, 26, 26, 26, 11, 28, 31, 26, 28, 25, 26, 26, 29, 21, 34, 34, 34, 30, 12, 28, 34, 17, 12, 16, 30, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], + "nextMatePosition": null, + "info": {} + }], "nextPageToken": null } From 9064616928fa8a0babd9f95acfed793c9607eb4b Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Mon, 20 Jun 2016 11:06:03 -0700 Subject: [PATCH 076/136] continue reference --- examples/data.js | 22 +++++++++++------- src/main/data/Sequence.js | 49 ++++++++++++++++++++++++++++++++------- 2 files changed, 53 insertions(+), 18 deletions(-) diff --git a/examples/data.js b/examples/data.js index 86b0f074..3db54f46 100644 --- a/examples/data.js +++ b/examples/data.js @@ -11,16 +11,20 @@ var sources = [ viz: pileup.viz.genome(), isReference: true, data: pileup.formats.reference({ - url: '/reference', - contigList: [{ - name:"chrM", - length: 1000 - },{ - name:"22", - length: 1000 - }] + url: 'reference' }), name: 'Reference' + }, + { + viz: pileup.viz.pileup(), + data: pileup.formats.ga4gh({ + spec: { + url: "localhost:8080", + readGroupId: "sadf", + killChr: true + }; + }), + name: 'Alignments' } // { // viz: pileup.viz.genome(), @@ -80,4 +84,4 @@ var sources = [ // } ]; -var range = {contig: 'chrM', start: 0, stop: 10}; +var range = {contig: 'chr17', start: 7512284, stop: 7512644}; diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index 610f8b98..f8e0563c 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -5,12 +5,45 @@ */ 'use strict'; +import Q from 'q'; import type RemoteRequest from '../RemoteRequest'; -import TwoBit from './TwoBit'; -type SequenceRecord = { - name: string, - length: number +export type SequenceRecord = { + name: string; + length: number; +} + +var BASE_PAIRS = [ + 'T', // 0=00 + 'C', // 1=01 + 'A', // 2=10 + 'G' // 3=11 +]; + +/** + * Read 2-bit encoded base pairs from a DataView into an array of 'A', 'T', + * 'C', 'G' strings. + * These are returned as an array (rather than a string) to facilitate further + * modification. + */ +function unpackDNA(dataView: DataView, startBasePair: number, numBasePairs: number): Array { + // TODO: use jBinary bitfield for this + var basePairs: Array = []; + basePairs.length = dataView.byteLength * 4; // pre-allocate + var basePairIdx = -startBasePair; + for (var i = 0; i < dataView.byteLength; i++) { + var packed = dataView.getUint8(i); + for (var shift = 6; shift >= 0; shift -= 2) { + var bp = BASE_PAIRS[(packed >> shift) & 3]; + if (startBasePair >= 0) { + basePairs[basePairIdx] = bp; + } + basePairIdx++; + } + } + // Remove base pairs from the end if the sequence terminated mid-byte. + basePairs.length = numBasePairs; + return basePairs; } class Sequence { @@ -23,8 +56,8 @@ class Sequence { } // Returns a list of contig names. - getContigList(): string[] { - return this.contigList.map(seq => seq.name); + getContigList(): Q.Promise { + return Promise.resolve(this.contigList.map(seq => seq.name)); } /** @@ -39,9 +72,7 @@ class Sequence { return this.remoteRequest.get(contig, start, stop).then(buffer => { var dataView = new DataView(buffer); - return TwoBit.markUnknownDNA( - TwoBit.unpackDNA(dataView, start % 4, stop - start + 1), start) - .join(''); + return unpackDNA(dataView, start % 4, stop - start + 1).join(''); }); } From 786ce324052cffc4b9f69ad3fd03155a16971cbe Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 21 Jun 2016 12:51:20 -0700 Subject: [PATCH 077/136] tests passing for reference --- package.json | 3 ++- src/main/data/Sequence.js | 26 ++++++-------------------- 2 files changed, 8 insertions(+), 21 deletions(-) diff --git a/package.json b/package.json index 129debaa..ee1217a8 100644 --- a/package.json +++ b/package.json @@ -31,7 +31,8 @@ "flow": "flow status", "flow-check": "flow check", "coverage": "./scripts/generate-coverage.sh", - "build": "./scripts/build.sh" + "build": "./scripts/build.sh", + "quick-build": "./scripts/quick-build.sh" }, "author": "Dan Vanderkam", "contributors": [ diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index f8e0563c..6036acd6 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -13,13 +13,6 @@ export type SequenceRecord = { length: number; } -var BASE_PAIRS = [ - 'T', // 0=00 - 'C', // 1=01 - 'A', // 2=10 - 'G' // 3=11 -]; - /** * Read 2-bit encoded base pairs from a DataView into an array of 'A', 'T', * 'C', 'G' strings. @@ -29,17 +22,10 @@ var BASE_PAIRS = [ function unpackDNA(dataView: DataView, startBasePair: number, numBasePairs: number): Array { // TODO: use jBinary bitfield for this var basePairs: Array = []; - basePairs.length = dataView.byteLength * 4; // pre-allocate - var basePairIdx = -startBasePair; + // basePairs.length = dataView.byteLength * 4; // pre-allocate for (var i = 0; i < dataView.byteLength; i++) { var packed = dataView.getUint8(i); - for (var shift = 6; shift >= 0; shift -= 2) { - var bp = BASE_PAIRS[(packed >> shift) & 3]; - if (startBasePair >= 0) { - basePairs[basePairIdx] = bp; - } - basePairIdx++; - } + basePairs[i] = String.fromCharCode(packed); } // Remove base pairs from the end if the sequence terminated mid-byte. basePairs.length = numBasePairs; @@ -56,8 +42,8 @@ class Sequence { } // Returns a list of contig names. - getContigList(): Q.Promise { - return Promise.resolve(this.contigList.map(seq => seq.name)); + getContigList(): string[] { + return this.contigList.map(seq => seq.name); } /** @@ -69,10 +55,10 @@ class Sequence { if (start > stop) { throw `Requested a range with start > stop (${start}, ${stop})`; } - return this.remoteRequest.get(contig, start, stop).then(buffer => { var dataView = new DataView(buffer); - return unpackDNA(dataView, start % 4, stop - start + 1).join(''); + var d = unpackDNA(dataView, start % 4, stop - start + 1).join(''); + return d; }); } From dce8bf600ec40111822ef98d764160373c119fda Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 21 Jun 2016 20:40:04 -0700 Subject: [PATCH 078/136] reference through server now works --- examples/data.js | 22 +++++++++------------- src/main/data/Sequence.js | 2 +- 2 files changed, 10 insertions(+), 14 deletions(-) diff --git a/examples/data.js b/examples/data.js index 3db54f46..86b0f074 100644 --- a/examples/data.js +++ b/examples/data.js @@ -11,20 +11,16 @@ var sources = [ viz: pileup.viz.genome(), isReference: true, data: pileup.formats.reference({ - url: 'reference' + url: '/reference', + contigList: [{ + name:"chrM", + length: 1000 + },{ + name:"22", + length: 1000 + }] }), name: 'Reference' - }, - { - viz: pileup.viz.pileup(), - data: pileup.formats.ga4gh({ - spec: { - url: "localhost:8080", - readGroupId: "sadf", - killChr: true - }; - }), - name: 'Alignments' } // { // viz: pileup.viz.genome(), @@ -84,4 +80,4 @@ var sources = [ // } ]; -var range = {contig: 'chr17', start: 7512284, stop: 7512644}; +var range = {contig: 'chrM', start: 0, stop: 10}; diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index 6036acd6..04615b37 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -42,7 +42,7 @@ class Sequence { } // Returns a list of contig names. - getContigList(): string[] { + getContigList(): string[] { return this.contigList.map(seq => seq.name); } From 0749feb2f959a8bea2ea49cadaf5c35eb8073b47 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sat, 25 Jun 2016 13:53:50 -0700 Subject: [PATCH 079/136] variants now work --- src/main/data/Sequence.js | 25 +---- src/main/data/VariantEndpoint.js | 35 ++++++ src/main/pileup.js | 2 + src/main/sources/VariantDataSource.js | 120 +++++++++++++++++++++ src/test/sources/VariantDataSource-test.js | 65 +++++++++++ test-data/features-chrM-1000-1200.json | 11 ++ test-data/features_chrM_0_2000.json | 18 ---- test-data/variants-chrM-0-100.json | 16 +++ 8 files changed, 252 insertions(+), 40 deletions(-) create mode 100644 src/main/data/VariantEndpoint.js create mode 100644 src/main/sources/VariantDataSource.js create mode 100644 src/test/sources/VariantDataSource-test.js create mode 100644 test-data/features-chrM-1000-1200.json delete mode 100644 test-data/features_chrM_0_2000.json create mode 100644 test-data/variants-chrM-0-100.json diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index 04615b37..161f7300 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -13,25 +13,6 @@ export type SequenceRecord = { length: number; } -/** - * Read 2-bit encoded base pairs from a DataView into an array of 'A', 'T', - * 'C', 'G' strings. - * These are returned as an array (rather than a string) to facilitate further - * modification. - */ -function unpackDNA(dataView: DataView, startBasePair: number, numBasePairs: number): Array { - // TODO: use jBinary bitfield for this - var basePairs: Array = []; - // basePairs.length = dataView.byteLength * 4; // pre-allocate - for (var i = 0; i < dataView.byteLength; i++) { - var packed = dataView.getUint8(i); - basePairs[i] = String.fromCharCode(packed); - } - // Remove base pairs from the end if the sequence terminated mid-byte. - basePairs.length = numBasePairs; - return basePairs; -} - class Sequence { remoteRequest: RemoteRequest; contigList: SequenceRecord[]; @@ -55,9 +36,9 @@ class Sequence { if (start > stop) { throw `Requested a range with start > stop (${start}, ${stop})`; } - return this.remoteRequest.get(contig, start, stop).then(buffer => { - var dataView = new DataView(buffer); - var d = unpackDNA(dataView, start % 4, stop - start + 1).join(''); + return this.remoteRequest.get(contig, start, stop).then(sequence => { + // var dataView = new DataView(buffer); + var d = sequence.substring(start, (stop-start + 1)); return d; }); } diff --git a/src/main/data/VariantEndpoint.js b/src/main/data/VariantEndpoint.js new file mode 100644 index 00000000..9ee9035b --- /dev/null +++ b/src/main/data/VariantEndpoint.js @@ -0,0 +1,35 @@ +/** + * This module defines a parser for the 2bit file format. + * See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 + * @flow + */ +'use strict'; + +import Q from 'q'; +import type RemoteRequest from '../RemoteRequest'; + +function extractVariants(variants: Object): Variant[] { + return variants; +} + +class VariantEndpoint { + remoteRequest: RemoteRequest; + + constructor(remoteRequest: RemoteRequest) { + this.remoteRequest = remoteRequest; + } + + getFeaturesInRange(range: ContigInterval): Q.Promise { + var contig = range.contig; + var start = range.interval.start; + var stop = range.interval.stop; + console.log("in get range endpoint", range); + + return this.remoteRequest.get(contig, start, stop).then(object => { + var d = extractVariants(object); // TODO: should parts to Variant[] + return d; + }); + } +} + +module.exports = VariantEndpoint; diff --git a/src/main/pileup.js b/src/main/pileup.js index 966c819d..441b7c3d 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -14,6 +14,7 @@ import ReactDOM from 'react-dom'; import TwoBitDataSource from './sources/TwoBitDataSource'; import BigBedDataSource from './sources/BigBedDataSource'; import VcfDataSource from './sources/VcfDataSource'; +import VariantDataSource from './sources/VariantDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; import EmptySource from './sources/EmptySource'; @@ -123,6 +124,7 @@ var pileup = { bam: BamDataSource.create, ga4gh: GA4GHDataSource.create, vcf: VcfDataSource.create, + variants: VariantDataSource.create, twoBit: TwoBitDataSource.create, bigBed: BigBedDataSource.create, empty: EmptySource.create diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js new file mode 100644 index 00000000..59a3539e --- /dev/null +++ b/src/main/sources/VariantDataSource.js @@ -0,0 +1,120 @@ +/** + * The "glue" between TwoBit.js and GenomeTrack.js. + * + * GenomeTrack is pure view code -- it renders data which is already in-memory + * in the browser. + * + * TwoBit is purely for data parsing and fetching. It only knows how to return + * promises for various genome features. + * + * This code acts as a bridge between the two. It maintains a local version of + * the data, fetching remote data and informing the view when it becomes + * available. + * + * @flow + */ +'use strict'; + +import type {Variant} from '../data/vcf'; + +import Q from 'q'; +import _ from 'underscore'; +import {Events} from 'backbone'; + +import ContigInterval from '../ContigInterval'; +import type {VcfDataSource} from './VcfDataSource'; +import RemoteRequest from '../RemoteRequest'; +import VariantEndpoint from '../data/VariantEndpoint'; + + +// Requests for 2bit ranges are expanded to begin & end at multiples of this +// constant. Doing this means that panning typically won't require +// additional network requests. +var BASE_PAIRS_PER_FETCH = 1000; + +function expandRange(range: ContigInterval) { + var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; + var newStart = Math.max(1, roundDown(range.start())), + newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); + + return new ContigInterval(range.contig, newStart, newStop); +} + +function variantKey(v: Variant): string { + return `${v.contig}:${v.position}`; +} + + +function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { + var variants: {[key: string]: Variant} = {}; + + // Ranges for which we have complete information -- no need to hit network. + var coveredRanges: ContigInterval[] = []; + + function addVariant(v: Variant) { + var key = variantKey(v); + if (!variants[key]) { + variants[key] = v; + } + } + + function fetch(range: GenomeRange) { + var interval = new ContigInterval(range.contig, range.start, range.stop); + + // Check if this interval is already in the cache. + if (interval.isCoveredBy(coveredRanges)) { + return Q.when(); + } + + interval = expandRange(interval); + + // "Cover" the range immediately to prevent duplicate fetches. + coveredRanges.push(interval); + coveredRanges = ContigInterval.coalesce(coveredRanges); + return remoteSource.getFeaturesInRange(interval).then(variants => { + variants.forEach(variant => addVariant(variant)); + o.trigger('newdata', interval); + }); + } + + function getFeaturesInRange(range: ContigInterval): Variant[] { + if (!range) return []; // XXX why would this happen? + return _.filter(variants, v => range.chrContainsLocus(v.contig, v.position)); + } + + var o = { + rangeChanged: function(newRange: GenomeRange) { + fetch(newRange).done(); + }, + getFeaturesInRange, + + // These are here to make Flow happy. + on: () => {}, + off: () => {}, + trigger: () => {} + }; + _.extend(o, Events); // Make this an event emitter + + return o; +} + +function create(data: {url:string, contigList: SequenceRecord[]}): VcfDataSource { + var url = data.url; + var contigList = data.contigList; + if (!url) { + throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); + } + // verify contiglist was correctly set + if (!contigList) { + throw new Error(`Missing ContigList from track: ${JSON.stringify(data)}`); + } + var request = new RemoteRequest(url, contigList); + var endpoint = new VariantEndpoint(request); + return createFromVariantUrl(endpoint); +} + + +module.exports = { + create, + createFromVariantUrl +}; diff --git a/src/test/sources/VariantDataSource-test.js b/src/test/sources/VariantDataSource-test.js new file mode 100644 index 00000000..b074909f --- /dev/null +++ b/src/test/sources/VariantDataSource-test.js @@ -0,0 +1,65 @@ +/* @flow */ +'use strict'; + + +import {expect} from 'chai'; + +import sinon from 'sinon'; + +import VariantDataSource from '../../main/sources/VariantDataSource'; +import ContigInterval from '../../main/ContigInterval'; +import RemoteFile from '../../main/RemoteFile'; + +describe('VariantDataSource', function() { + var server: any = null, response; + + before(function () { + return new RemoteFile('/test-data/variants-chrM-0-100.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + // server.respondWith('GET', '/variants',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/variants/chrM?start=1&end=1000',[200, { "Content-Type": "application/json" }, response]); + }); + }); + + after(function () { + server.restore(); + }); + + function getTestSource() { + var source = VariantDataSource.create({ + url: '/variants', + contigList: [{ + name:"chrM", + length: 1000 + },{ + name:"22", + length: 1000 + }] + }); + return source; + } + it('should extract features in a range', function(done) { + var source = getTestSource(); + var range = new ContigInterval('chrM', 0, 25); + // No variants are cached yet. + var variants = source.getFeaturesInRange(range); + expect(variants).to.deep.equal([]); + + source.on('newdata', () => { + var variants = source.getFeaturesInRange(range); + expect(variants).to.have.length(2); + expect(variants[1].contig).to.equal('chrM'); + expect(variants[1].position).to.equal(20); + expect(variants[1].ref).to.equal('G'); + expect(variants[1].alt).to.equal('T'); + done(); + }); + source.rangeChanged({ + contig: range.contig, + start: range.start(), + stop: range.stop() + }); + server.respond(); + }); +}); diff --git a/test-data/features-chrM-1000-1200.json b/test-data/features-chrM-1000-1200.json new file mode 100644 index 00000000..2ba90728 --- /dev/null +++ b/test-data/features-chrM-1000-1200.json @@ -0,0 +1,11 @@ +[{ + "rest": "4ee7469a-b468-429b-a109-07a484817037", + "contig": "chrM", + "start": 1107, + "end": 1200 +}, { + "rest": "e105ce29-a840-4fc6-819f-a9aac5166163", + "contig": "chrM", + "start": 1011, + "end": 1012 +}] diff --git a/test-data/features_chrM_0_2000.json b/test-data/features_chrM_0_2000.json deleted file mode 100644 index 18c0c397..00000000 --- a/test-data/features_chrM_0_2000.json +++ /dev/null @@ -1,18 +0,0 @@ -[{ - "range": { - "name": "chrM", - "start": 0, - "end": 2000 - }, - "features": [{ - "featureId": "4ee7469a-b468-429b-a109-07a484817037", - "featureType": "rs575272151", - "start": 1107, - "end": 1200 - }, { - "featureId": "e105ce29-a840-4fc6-819f-a9aac5166163", - "featureType": "rs544419019", - "start": 1011, - "end": 1012 - }] -}] diff --git a/test-data/variants-chrM-0-100.json b/test-data/variants-chrM-0-100.json new file mode 100644 index 00000000..c48c5b03 --- /dev/null +++ b/test-data/variants-chrM-0-100.json @@ -0,0 +1,16 @@ +[{ + "contig": "chrM", + "position": 10, + "ref": "C", + "alt": "G" +}, { + "contig": "chrM", + "position": 20, + "ref": "G", + "alt": "T" +}, { + "contig": "chrM", + "position": 20, + "ref": "A", + "alt": "C" +}] From c941979a5644039bdd2352e9fe2f6ed9e1dd2fb1 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 28 Jun 2016 13:00:01 -0700 Subject: [PATCH 080/136] added key to remote request --- src/main/data/VariantEndpoint.js | 7 +++---- src/main/sources/GA4GHDataSource.js | 6 +++--- src/main/sources/ReferenceDataSource.js | 3 ++- src/main/sources/VariantDataSource.js | 13 ++++++------- src/test/sources/ReferenceDataSource-test.js | 6 +++--- src/test/sources/VariantDataSource-test.js | 10 ++-------- 6 files changed, 19 insertions(+), 26 deletions(-) diff --git a/src/main/data/VariantEndpoint.js b/src/main/data/VariantEndpoint.js index 9ee9035b..59425dda 100644 --- a/src/main/data/VariantEndpoint.js +++ b/src/main/data/VariantEndpoint.js @@ -23,11 +23,10 @@ class VariantEndpoint { var contig = range.contig; var start = range.interval.start; var stop = range.interval.stop; - console.log("in get range endpoint", range); - return this.remoteRequest.get(contig, start, stop).then(object => { - var d = extractVariants(object); // TODO: should parts to Variant[] - return d; + return this.remoteRequest.get(contig, start, stop).then(object => { + var d = extractVariants(object); // TODO: should parts to Variant[] + return d; }); } } diff --git a/src/main/sources/GA4GHDataSource.js b/src/main/sources/GA4GHDataSource.js index dfa6f8e3..34dee3f1 100644 --- a/src/main/sources/GA4GHDataSource.js +++ b/src/main/sources/GA4GHDataSource.js @@ -21,7 +21,7 @@ var ALIGNMENTS_PER_REQUEST = 200; // TODO: explain this choice. // TODO: tune this value -- setting it close to the read length will result in // lots of reads being fetched twice, but setting it too large will result in // bulkier requests. -var BASE_PAIRS_PER_FETCH = 100; +var BASE_PAIRS_PER_FETCH = 1000; function expandRange(range: ContigInterval) { var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; @@ -87,8 +87,8 @@ function create(spec: GA4GHSpec): AlignmentDataSource { pageToken: ?string, numRequests: number) { var xhr = new XMLHttpRequest(); - - var endpoint = url + "/" + range.contig + "?start=" + range.start() + "&end=" + range.stop()+"&sample="+spec.readGroupId; + + var endpoint = url + "/" + range.contig + "?start=" + range.start() + "&end=" + range.stop()+"&key="+spec.readGroupId; xhr.open('GET', endpoint); xhr.responseType = 'json'; diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index 2e10d7de..232c630b 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -149,7 +149,8 @@ function create(data: {url:string, contigList: SequenceRecord[]}): TwoBitSource if (!contigList) { throw new Error(`Missing ContigList from track: ${JSON.stringify(data)}`); } - return createFromReferenceUrl(new Sequence(new RemoteRequest(urlPrefix), contigList)); + var key = "reference" // key is not required for reference but required for Remote Request + return createFromReferenceUrl(new Sequence(new RemoteRequest(urlPrefix, key), contigList)); } // Getter/setter for base pairs per fetch. diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index 59a3539e..add58f6e 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -98,17 +98,16 @@ function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { return o; } -function create(data: {url:string, contigList: SequenceRecord[]}): VcfDataSource { - var url = data.url; - var contigList = data.contigList; +function create(data: {url?:string, key?:string}): VcfDataSource { + var {url, key} = data; if (!url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } - // verify contiglist was correctly set - if (!contigList) { - throw new Error(`Missing ContigList from track: ${JSON.stringify(data)}`); + // verify key was correctly set + if (!key) { + throw new Error(`Missing key from track: ${JSON.stringify(data)}`); } - var request = new RemoteRequest(url, contigList); + var request = new RemoteRequest(url, key); var endpoint = new VariantEndpoint(request); return createFromVariantUrl(endpoint); } diff --git a/src/test/sources/ReferenceDataSource-test.js b/src/test/sources/ReferenceDataSource-test.js index 09ee0879..f845e8be 100644 --- a/src/test/sources/ReferenceDataSource-test.js +++ b/src/test/sources/ReferenceDataSource-test.js @@ -15,9 +15,9 @@ before(function () { return new RemoteFile('/test-data/reference-chrM-0-1000.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); - server.respondWith('GET', '/reference/chrM?start=0&end=10000',[200, { "Content-Type": "application/json" }, response]); - server.respondWith('GET', '/reference/chrM?start=0&end=10',[200, { "Content-Type": "application/json" }, response]); - server.respondWith('GET', '/reference/22?start=0&end=10000',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/reference/chrM?start=0&end=10000&key=reference',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/reference/chrM?start=0&end=10&key=reference',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/reference/22?start=0&end=10000&key=reference',[200, { "Content-Type": "application/json" }, response]); }); }); diff --git a/src/test/sources/VariantDataSource-test.js b/src/test/sources/VariantDataSource-test.js index b074909f..9989ba74 100644 --- a/src/test/sources/VariantDataSource-test.js +++ b/src/test/sources/VariantDataSource-test.js @@ -18,7 +18,7 @@ describe('VariantDataSource', function() { response = data; server = sinon.fakeServer.create(); // server.respondWith('GET', '/variants',[200, { "Content-Type": "application/json" }, response]); - server.respondWith('GET', '/variants/chrM?start=1&end=1000',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/variants/chrM?start=1&end=1000&key=test',[200, { "Content-Type": "application/json" }, response]); }); }); @@ -29,13 +29,7 @@ describe('VariantDataSource', function() { function getTestSource() { var source = VariantDataSource.create({ url: '/variants', - contigList: [{ - name:"chrM", - length: 1000 - },{ - name:"22", - length: 1000 - }] + key: 'test' }); return source; } From db41cf6c58fc0248d7895b8c63fc7bb85ce425f2 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sat, 11 Jun 2016 15:13:50 -0700 Subject: [PATCH 081/136] starting reference --- examples/data.js | 27 ++++++++++----------------- 1 file changed, 10 insertions(+), 17 deletions(-) diff --git a/examples/data.js b/examples/data.js index 86b0f074..9f3123a6 100644 --- a/examples/data.js +++ b/examples/data.js @@ -8,28 +8,21 @@ var sources = [ { + viz: pileup.viz.genome(), + isReference: true, + data: pileup.formats.twoBit({ + url: 'http://www.biodalliance.org/datasets/hg19.2bit' + }), + name: 'Reference' + }, + { viz: pileup.viz.genome(), isReference: true, data: pileup.formats.reference({ - url: '/reference', - contigList: [{ - name:"chrM", - length: 1000 - },{ - name:"22", - length: 1000 - }] + prefix:"../json/" }), name: 'Reference' } -// { -// viz: pileup.viz.genome(), -// isReference: true, -// data: pileup.formats.reference({ -// prefix:"../json/" -// }), -// name: 'Reference' -// } // { // viz: pileup.viz.scale(), // name: 'Scale' @@ -80,4 +73,4 @@ var sources = [ // } ]; -var range = {contig: 'chrM', start: 0, stop: 10}; +var range = {contig: 'chr17', start: 7512284, stop: 7512644}; From a0c3b98fa0ae978185e792716c0588ff8ffd6c93 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sun, 12 Jun 2016 15:41:49 -0700 Subject: [PATCH 082/136] continued reference implementation --- examples/data.js | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/examples/data.js b/examples/data.js index 9f3123a6..73ba33b4 100644 --- a/examples/data.js +++ b/examples/data.js @@ -14,15 +14,15 @@ var sources = [ url: 'http://www.biodalliance.org/datasets/hg19.2bit' }), name: 'Reference' - }, - { - viz: pileup.viz.genome(), - isReference: true, - data: pileup.formats.reference({ - prefix:"../json/" - }), - name: 'Reference' } +// { +// viz: pileup.viz.genome(), +// isReference: true, +// data: pileup.formats.reference({ +// prefix:"../json/" +// }), +// name: 'Reference' +// } // { // viz: pileup.viz.scale(), // name: 'Scale' From 6451fcf2512b349cde7d66852ce10de399815481 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sat, 18 Jun 2016 13:20:54 -0700 Subject: [PATCH 083/136] added test resources for ADAM alignments --- test-data/features_chrM_0_2000.json | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 test-data/features_chrM_0_2000.json diff --git a/test-data/features_chrM_0_2000.json b/test-data/features_chrM_0_2000.json new file mode 100644 index 00000000..18c0c397 --- /dev/null +++ b/test-data/features_chrM_0_2000.json @@ -0,0 +1,18 @@ +[{ + "range": { + "name": "chrM", + "start": 0, + "end": 2000 + }, + "features": [{ + "featureId": "4ee7469a-b468-429b-a109-07a484817037", + "featureType": "rs575272151", + "start": 1107, + "end": 1200 + }, { + "featureId": "e105ce29-a840-4fc6-819f-a9aac5166163", + "featureType": "rs544419019", + "start": 1011, + "end": 1012 + }] +}] From 0b9f695174a57057ac1fbd0149053ee967829118 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Mon, 20 Jun 2016 11:06:03 -0700 Subject: [PATCH 084/136] continue reference --- examples/data.js | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/examples/data.js b/examples/data.js index 73ba33b4..3db54f46 100644 --- a/examples/data.js +++ b/examples/data.js @@ -10,10 +10,21 @@ var sources = [ { viz: pileup.viz.genome(), isReference: true, - data: pileup.formats.twoBit({ - url: 'http://www.biodalliance.org/datasets/hg19.2bit' + data: pileup.formats.reference({ + url: 'reference' }), name: 'Reference' + }, + { + viz: pileup.viz.pileup(), + data: pileup.formats.ga4gh({ + spec: { + url: "localhost:8080", + readGroupId: "sadf", + killChr: true + }; + }), + name: 'Alignments' } // { // viz: pileup.viz.genome(), From da58069f172b4192fa298c4e9b8ebaeaa938b806 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 21 Jun 2016 12:51:20 -0700 Subject: [PATCH 085/136] tests passing for reference --- src/main/sources/ReferenceDataSource.js | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index 232c630b..aa1ea238 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -163,6 +163,16 @@ function testBasePairsToFetch(num?: number): any { } } +// Getter/setter for base pairs per fetch. +// This should only be used for testing. +function testBasePairsToFetch(num?: number): any { + if (num) { + BASE_PAIRS_PER_FETCH = num; + } else { + return BASE_PAIRS_PER_FETCH; + } +} + module.exports = { create, createFromReferenceUrl, From 0ea193764d4e31daaec3ceae326cd54507ff4954 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 21 Jun 2016 20:40:04 -0700 Subject: [PATCH 086/136] reference through server now works --- examples/data.js | 22 +++++++++------------- 1 file changed, 9 insertions(+), 13 deletions(-) diff --git a/examples/data.js b/examples/data.js index 3db54f46..86b0f074 100644 --- a/examples/data.js +++ b/examples/data.js @@ -11,20 +11,16 @@ var sources = [ viz: pileup.viz.genome(), isReference: true, data: pileup.formats.reference({ - url: 'reference' + url: '/reference', + contigList: [{ + name:"chrM", + length: 1000 + },{ + name:"22", + length: 1000 + }] }), name: 'Reference' - }, - { - viz: pileup.viz.pileup(), - data: pileup.formats.ga4gh({ - spec: { - url: "localhost:8080", - readGroupId: "sadf", - killChr: true - }; - }), - name: 'Alignments' } // { // viz: pileup.viz.genome(), @@ -84,4 +80,4 @@ var sources = [ // } ]; -var range = {contig: 'chr17', start: 7512284, stop: 7512644}; +var range = {contig: 'chrM', start: 0, stop: 10}; From bc3b44d537893c82a57fb69fdf46f2b6b6cebf86 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sat, 25 Jun 2016 13:53:50 -0700 Subject: [PATCH 087/136] variants now works --- src/main/sources/VariantDataSource.js | 13 ++++++----- src/test/sources/ReferenceDataSource-test.js | 23 ++++++++++++-------- src/test/sources/VariantDataSource-test.js | 10 +++++++-- test-data/features_chrM_0_2000.json | 18 --------------- 4 files changed, 29 insertions(+), 35 deletions(-) delete mode 100644 test-data/features_chrM_0_2000.json diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index add58f6e..59a3539e 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -98,16 +98,17 @@ function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { return o; } -function create(data: {url?:string, key?:string}): VcfDataSource { - var {url, key} = data; +function create(data: {url:string, contigList: SequenceRecord[]}): VcfDataSource { + var url = data.url; + var contigList = data.contigList; if (!url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } - // verify key was correctly set - if (!key) { - throw new Error(`Missing key from track: ${JSON.stringify(data)}`); + // verify contiglist was correctly set + if (!contigList) { + throw new Error(`Missing ContigList from track: ${JSON.stringify(data)}`); } - var request = new RemoteRequest(url, key); + var request = new RemoteRequest(url, contigList); var endpoint = new VariantEndpoint(request); return createFromVariantUrl(endpoint); } diff --git a/src/test/sources/ReferenceDataSource-test.js b/src/test/sources/ReferenceDataSource-test.js index f845e8be..c8b7f25c 100644 --- a/src/test/sources/ReferenceDataSource-test.js +++ b/src/test/sources/ReferenceDataSource-test.js @@ -9,15 +9,20 @@ import ReferenceDataSource from '../../main/sources/ReferenceDataSource'; import RemoteFile from '../../main/RemoteFile'; describe('ReferenceDataSource', function() { -var server: any = null, response; - -before(function () { - return new RemoteFile('/test-data/reference-chrM-0-1000.json').getAllString().then(data => { - response = data; - server = sinon.fakeServer.create(); - server.respondWith('GET', '/reference/chrM?start=0&end=10000&key=reference',[200, { "Content-Type": "application/json" }, response]); - server.respondWith('GET', '/reference/chrM?start=0&end=10&key=reference',[200, { "Content-Type": "application/json" }, response]); - server.respondWith('GET', '/reference/22?start=0&end=10000&key=reference',[200, { "Content-Type": "application/json" }, response]); + var server: any = null, response; + + before(function () { + return new RemoteFile('/test-data/reference-chrM-0-1000.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/reference/chrM?start=0&end=10000',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/reference/chrM?start=0&end=10',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/reference/22?start=0&end=10000',[200, { "Content-Type": "application/json" }, response]); + }); + }); + + after(function () { + server.restore(); }); }); diff --git a/src/test/sources/VariantDataSource-test.js b/src/test/sources/VariantDataSource-test.js index 9989ba74..b074909f 100644 --- a/src/test/sources/VariantDataSource-test.js +++ b/src/test/sources/VariantDataSource-test.js @@ -18,7 +18,7 @@ describe('VariantDataSource', function() { response = data; server = sinon.fakeServer.create(); // server.respondWith('GET', '/variants',[200, { "Content-Type": "application/json" }, response]); - server.respondWith('GET', '/variants/chrM?start=1&end=1000&key=test',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/variants/chrM?start=1&end=1000',[200, { "Content-Type": "application/json" }, response]); }); }); @@ -29,7 +29,13 @@ describe('VariantDataSource', function() { function getTestSource() { var source = VariantDataSource.create({ url: '/variants', - key: 'test' + contigList: [{ + name:"chrM", + length: 1000 + },{ + name:"22", + length: 1000 + }] }); return source; } diff --git a/test-data/features_chrM_0_2000.json b/test-data/features_chrM_0_2000.json deleted file mode 100644 index 18c0c397..00000000 --- a/test-data/features_chrM_0_2000.json +++ /dev/null @@ -1,18 +0,0 @@ -[{ - "range": { - "name": "chrM", - "start": 0, - "end": 2000 - }, - "features": [{ - "featureId": "4ee7469a-b468-429b-a109-07a484817037", - "featureType": "rs575272151", - "start": 1107, - "end": 1200 - }, { - "featureId": "e105ce29-a840-4fc6-819f-a9aac5166163", - "featureType": "rs544419019", - "start": 1011, - "end": 1012 - }] -}] From a06afa05da2bc92104868c91b9efb69eccc76a17 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Thu, 30 Jun 2016 21:56:07 -0700 Subject: [PATCH 088/136] pileup can now display genotypes --- .gitignore | 3 + src/main/data/GenotypeEndpoint.js | 43 ++++++ src/main/data/Sequence.js | 1 - src/main/sources/GA4GHDataSource.js | 2 +- src/main/sources/GenotypeDataSource.js | 126 ++++++++++++++++++ src/main/sources/ReferenceDataSource.js | 2 +- src/main/style.js | 14 +- src/main/viz/GenomeTrack.js | 3 +- src/main/viz/GenotypeTrack.js | 138 ++++++++++++++++++++ src/test/sources/GenotypeDataSource-test.js | 60 +++++++++ test-data/genotypes-chrM-0-100.json | 25 ++++ 11 files changed, 407 insertions(+), 10 deletions(-) create mode 100644 src/main/data/GenotypeEndpoint.js create mode 100644 src/main/sources/GenotypeDataSource.js create mode 100644 src/main/viz/GenotypeTrack.js create mode 100644 src/test/sources/GenotypeDataSource-test.js create mode 100644 test-data/genotypes-chrM-0-100.json diff --git a/.gitignore b/.gitignore index 2a749afe..fbb4ddeb 100644 --- a/.gitignore +++ b/.gitignore @@ -18,6 +18,9 @@ coverage # Compiled binary addons (http://nodejs.org/api/addons.html) build/Release + +# Examples folder +examples # Dependency directory # Commenting this out is preferred by some people, see diff --git a/src/main/data/GenotypeEndpoint.js b/src/main/data/GenotypeEndpoint.js new file mode 100644 index 00000000..5726d89f --- /dev/null +++ b/src/main/data/GenotypeEndpoint.js @@ -0,0 +1,43 @@ +/** + * This module defines a parser for the 2bit file format. + * See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 + * @flow + */ +'use strict'; + +import Q from 'q'; +import type RemoteRequest from '../RemoteRequest'; +import type {Variant} from './vcf'; + + +export type Genotype = { + sampleIds: string, + variant: Variant +} + + +function extractGenotypes(genotypes: Object): Genotype[] { + return genotypes; +} + +class GenotypeEndpoint { + remoteRequest: RemoteRequest; + + constructor(remoteRequest: RemoteRequest) { + this.remoteRequest = remoteRequest; + } + + getFeaturesInRange(range: ContigInterval): Q.Promise { + var contig = range.contig; + var start = range.interval.start; + var stop = range.interval.stop; + + + return this.remoteRequest.get(contig, start, stop).then(object => { + var d = extractGenotypes(object); + return d; + }); + } +} + +module.exports = GenotypeEndpoint; diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index 161f7300..4d5562ad 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -37,7 +37,6 @@ class Sequence { throw `Requested a range with start > stop (${start}, ${stop})`; } return this.remoteRequest.get(contig, start, stop).then(sequence => { - // var dataView = new DataView(buffer); var d = sequence.substring(start, (stop-start + 1)); return d; }); diff --git a/src/main/sources/GA4GHDataSource.js b/src/main/sources/GA4GHDataSource.js index 34dee3f1..bf3396c4 100644 --- a/src/main/sources/GA4GHDataSource.js +++ b/src/main/sources/GA4GHDataSource.js @@ -57,7 +57,7 @@ function create(spec: GA4GHSpec): AlignmentDataSource { var ga4ghAlignment = new GA4GHAlignment(alignment); reads[key] = ga4ghAlignment; } catch(TypeError){ - console.log("Error in Matepair Data Source.") + console.log("Error in Matepair Data Source."); } }); } diff --git a/src/main/sources/GenotypeDataSource.js b/src/main/sources/GenotypeDataSource.js new file mode 100644 index 00000000..7c0c140c --- /dev/null +++ b/src/main/sources/GenotypeDataSource.js @@ -0,0 +1,126 @@ +/** + * The "glue" between TwoBit.js and GenomeTrack.js. + * + * GenomeTrack is pure view code -- it renders data which is already in-memory + * in the browser. + * + * TwoBit is purely for data parsing and fetching. It only knows how to return + * promises for various genome features. + * + * This code acts as a bridge between the two. It maintains a local version of + * the data, fetching remote data and informing the view when it becomes + * available. + * + * @flow + */ +'use strict'; + +import type {Genotype} from '../data/GenotypeEndpoint'; + +import Q from 'q'; +import _ from 'underscore'; +import {Events} from 'backbone'; + +import ContigInterval from '../ContigInterval'; +import RemoteRequest from '../RemoteRequest'; +import GenotypeEndpoint from '../data/GenotypeEndpoint'; + +export type GenotypeDataSource = { + rangeChanged: (newRange: GenomeRange) => void; + getFeaturesInRange: (range: ContigInterval) => Genotype[]; + on: (event: string, handler: Function) => void; + off: (event: string) => void; + trigger: (event: string, ...args:any) => void; +}; + + +// Requests for 2bit ranges are expanded to begin & end at multiples of this +// constant. Doing this means that panning typically won't require +// additional network requests. +var BASE_PAIRS_PER_FETCH = 1000; + +function expandRange(range: ContigInterval) { + var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; + var newStart = Math.max(1, roundDown(range.start())), + newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); + + return new ContigInterval(range.contig, newStart, newStop); +} + +function genotypeKey(v: Genotype): string { + return `${v.variant.contig}:${v.variant.position}`; +} + + +function createFromGenotypeUrl(remoteSource: GenotypeEndpoint): GenotypeDataSource { + var genotypes: {[key: string]: Genotype} = {}; + + // Ranges for which we have complete information -- no need to hit network. + var coveredRanges: ContigInterval[] = []; + + function addGenotype(v: Genotype) { + var key = genotypeKey(v); + if (!genotypes[key]) { + genotypes[key] = v; + } + } + + function fetch(range: GenomeRange) { + var interval = new ContigInterval(range.contig, range.start, range.stop); + + // Check if this interval is already in the cache. + if (interval.isCoveredBy(coveredRanges)) { + return Q.when(); + } + + interval = expandRange(interval); + + // "Cover" the range immediately to prevent duplicate fetches. + coveredRanges.push(interval); + coveredRanges = ContigInterval.coalesce(coveredRanges); + return remoteSource.getFeaturesInRange(interval).then(genotypes => { + genotypes.forEach(genotype => addGenotype(genotype)); + o.trigger('newdata', interval); + }); + } + + function getFeaturesInRange(range: ContigInterval): Genotype[] { + if (!range) return []; // XXX why would this happen? + return _.filter(genotypes, v => range.chrContainsLocus(v.variant.contig, v.variant.position)); + } + + var o = { + rangeChanged: function(newRange: GenomeRange) { + fetch(newRange).done(); + }, + getFeaturesInRange, + + // These are here to make Flow happy. + on: () => {}, + off: () => {}, + trigger: () => {} + }; + _.extend(o, Events); // Make this an event emitter + + return o; +} + +function create(data: {url?:string, key?:string}): GenotypeDataSource { + var {url, key} = data; + if (!url) { + throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); + } + // verify key was correctly set + if (!key) { + throw new Error(`Missing key from track: ${JSON.stringify(data)}`); + } + var request = new RemoteRequest(url, key); + var endpoint = new GenotypeEndpoint(request); + return createFromGenotypeUrl(endpoint); +} + + +module.exports = { + create, + createFromGenotypeUrl +}; diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index aa1ea238..1ded0b77 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -149,7 +149,7 @@ function create(data: {url:string, contigList: SequenceRecord[]}): TwoBitSource if (!contigList) { throw new Error(`Missing ContigList from track: ${JSON.stringify(data)}`); } - var key = "reference" // key is not required for reference but required for Remote Request + var key = "reference"; // key is not required for reference but required for Remote Request return createFromReferenceUrl(new Sequence(new RemoteRequest(urlPrefix, key), contigList)); } diff --git a/src/main/style.js b/src/main/style.js index 314c8857..e1e3d40a 100644 --- a/src/main/style.js +++ b/src/main/style.js @@ -11,10 +11,10 @@ module.exports = { // Colors for individual base pairs BASE_COLORS: { - 'A': '#188712', - 'G': '#C45C16', - 'C': '#0600F9', - 'T': '#F70016', + 'A': '#5050FF', //'#188712', + 'G': '#00C000', //'#C45C16', + 'C': '#E00000', //'#0600F9', + 'T': '#E6E600',// '#F70016', 'U': '#F70016', 'N': 'black' }, @@ -63,7 +63,11 @@ module.exports = { // Variant Track VARIANT_STROKE: 'blue', - VARIANT_FILL: '#ddd', + VARIANT_FILL: 'blue', VARIANT_HEIGHT: 14, + // Genotype Track + GENOTYPE_SPACING: 1, + GENOTYPE_FILL: 'red', + GENOTYPE_HEIGHT: 10, }; diff --git a/src/main/viz/GenomeTrack.js b/src/main/viz/GenomeTrack.js index 12d570a0..743f6b8a 100644 --- a/src/main/viz/GenomeTrack.js +++ b/src/main/viz/GenomeTrack.js @@ -30,7 +30,6 @@ function renderGenome(ctx: DataCanvasRenderingContext2D, var pxPerLetter = scale(1) - scale(0); var mode = DisplayMode.getDisplayMode(pxPerLetter); var showText = DisplayMode.isText(mode); - if (mode != DisplayMode.HIDDEN) { ctx.textAlign = 'center'; if (mode == DisplayMode.LOOSE) { @@ -94,7 +93,7 @@ class GenomeTiledCanvas extends TiledCanvas { // The +/-1 ensures that partially-visible bases on the edge are rendered. var genomeRange = { contig: range.contig, - start: range.start() - 1, + start: Math.max(0, (range.start() - 1)), stop: range.stop() + 1 }; var basePairs = this.source.getRangeAsString(genomeRange); diff --git a/src/main/viz/GenotypeTrack.js b/src/main/viz/GenotypeTrack.js new file mode 100644 index 00000000..56297a78 --- /dev/null +++ b/src/main/viz/GenotypeTrack.js @@ -0,0 +1,138 @@ +/** + * Visualization of genotypes + * @flow + */ +'use strict'; + +import type {GenotypeDataSource} from '../sources/GenotypeDataSource'; +import type {Genotype} from '../data/GenotypeEndpoint'; +import type {DataCanvasRenderingContext2D} from 'data-canvas'; +import type {VizProps} from '../VisualizationWrapper'; +import type {Scale} from './d3utils'; + +import React from 'react'; +import ReactDOM from 'react-dom'; + +import d3utils from './d3utils'; +import shallowEquals from 'shallow-equals'; +import ContigInterval from '../ContigInterval'; +import canvasUtils from './canvas-utils'; +import dataCanvas from 'data-canvas'; +import style from '../style'; + +function yForRow(row) { + return row * (style.GENOTYPE_HEIGHT + style.GENOTYPE_SPACING); +} + +class GenotypeTrack extends React.Component { + props: VizProps & {source: GenotypeDataSource}; + state: void; // no state + + constructor(props: Object) { + super(props); + } + + render(): any { + return ; + } + + componentDidMount() { + this.updateVisualization(); + + this.props.source.on('newdata', () => { + this.updateVisualization(); + }); + } + + getScale(): Scale { + return d3utils.getTrackScale(this.props.range, this.props.width); + } + + componentDidUpdate(prevProps: any, prevState: any) { + if (!shallowEquals(prevProps, this.props) || + !shallowEquals(prevState, this.state)) { + this.updateVisualization(); + } + } + + updateVisualization() { + var canvas = ReactDOM.findDOMNode(this), + {width, height} = this.props; + + // Hold off until height & width are known. + if (width === 0) return; + + var ctx = canvasUtils.getContext(canvas); + var dtx = dataCanvas.getDataContext(ctx); + this.renderScene(dtx); + } + + renderScene(ctx: DataCanvasRenderingContext2D) { + var range = this.props.range, + interval = new ContigInterval(range.contig, range.start, range.stop), + genotypes = this.props.source.getFeaturesInRange(interval), + scale = this.getScale(), + sampleIds = []; + + // add all samples to array of sample Ids + genotypes.forEach(genotype => { + var ids = genotype.sampleIds; + for (var i = 0; i < ids.length; i++) { + var id = ids[i]; + if (sampleIds.indexOf(id) < 0) { + sampleIds.push(id); + } + } + }); + sampleIds = sampleIds.sort(); // sort sample ids + + // Height can only be computed after the genotypes has been updated. + var newHeight = yForRow(sampleIds.length); + var canvas = ReactDOM.findDOMNode(this), + {width, height} = this.props; + d3utils.sizeCanvas(canvas, width, newHeight); + + // This is a hack to adjust parent div for resize + var el = d3utils.findParent(canvas, 'track-content'); + if (el) el.style.height = newHeight; + + ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); + ctx.reset(); + ctx.save(); + + ctx.fillStyle = style.GENOTYPE_FILL; + genotypes.forEach(genotype => { + var variant = genotype.variant; + var keys = genotype.sampleIds; + ctx.pushObject(variant); + var x = Math.round(scale(variant.position)); + var width = Math.round(scale(variant.position + 1)) - 1 - x; + keys.forEach(sampleId => { + var y = yForRow(sampleIds.indexOf(sampleId)); + ctx.fillRect(x - 0.5, y - 0.5, width, style.GENOTYPE_HEIGHT); + }); + ctx.popObject(); + }); + + ctx.restore(); + } + + handleClick(reactEvent: any) { + var ev = reactEvent.nativeEvent, + x = ev.offsetX, + y = ev.offsetY, + canvas = ReactDOM.findDOMNode(this), + ctx = canvasUtils.getContext(canvas), + trackingCtx = new dataCanvas.ClickTrackingContext(ctx, x, y); + this.renderScene(trackingCtx); + var genotype = trackingCtx.hit && trackingCtx.hit[0]; + var alert = window.alert || console.log; + if (genotype) { + alert(JSON.stringify(genotype)); + } + } +} + +GenotypeTrack.displayName = 'genotypes'; + +module.exports = GenotypeTrack; diff --git a/src/test/sources/GenotypeDataSource-test.js b/src/test/sources/GenotypeDataSource-test.js new file mode 100644 index 00000000..67ca5162 --- /dev/null +++ b/src/test/sources/GenotypeDataSource-test.js @@ -0,0 +1,60 @@ +/* @flow */ +'use strict'; + + +import {expect} from 'chai'; + +import sinon from 'sinon'; + +import VariantDataSource from '../../main/sources/GenotypeDataSource'; +import ContigInterval from '../../main/ContigInterval'; +import RemoteFile from '../../main/RemoteFile'; + +describe('GenotypeDataSource', function() { + var server: any = null, response; + + before(function () { + return new RemoteFile('/test-data/genotypes-chrM-0-100.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/genotypes/chrM?start=1&end=1000&key=test',[200, { "Content-Type": "application/json" }, response]); + }); + }); + + after(function () { + server.restore(); + }); + + function getTestSource() { + var source = VariantDataSource.create({ + url: '/genotypes', + key: 'test' + }); + return source; + } + it('should extract features in a range', function(done) { + var source = getTestSource(); + var range = new ContigInterval('chrM', 0, 25); + // No variants are cached yet. + var variants = source.getFeaturesInRange(range); + expect(variants).to.deep.equal([]); + + source.on('newdata', () => { + var genotypes = source.getFeaturesInRange(range); + console.log(genotypes); + expect(genotypes).to.have.length(3); + expect(genotypes[1].sampleIds).to.contain('sample1'); + expect(genotypes[1].variant.contig).to.equal('chrM'); + expect(genotypes[1].variant.position).to.equal(20); + expect(genotypes[1].variant.ref).to.equal('G'); + expect(genotypes[1].variant.alt).to.equal('T'); + done(); + }); + source.rangeChanged({ + contig: range.contig, + start: range.start(), + stop: range.stop() + }); + server.respond(); + }); +}); diff --git a/test-data/genotypes-chrM-0-100.json b/test-data/genotypes-chrM-0-100.json new file mode 100644 index 00000000..f39bd291 --- /dev/null +++ b/test-data/genotypes-chrM-0-100.json @@ -0,0 +1,25 @@ +[{ + "sampleIds": ["sample1", "sample2", "sample3"], + "variant": { + "contig": "chrM", + "position": 10, + "ref": "C", + "alt": "G" + } +}, { + "sampleIds": ["sample1", "sample2", "sample3"], + "variant": { + "contig": "chrM", + "position": 20, + "ref": "G", + "alt": "T" + } +}, { + "sampleIds": ["sample1", "sample2", "sample3"], + "variant": { + "contig": "chrM", + "position": 30, + "ref": "A", + "alt": "C" + } +}] From aca18adc4956e03250aefd03d8091e1fde9f163d Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Thu, 16 Jun 2016 20:16:44 -0700 Subject: [PATCH 089/136] completed the genotype feature and variant class files --- .vscode/.browse.VC.db | Bin 0 -> 1055744 bytes src/main/Feature.js | 137 ++++++++++++++++++++++++++++++++++++++++++ src/main/Genotype.js | 31 ++++++++++ src/main/Variant.js | 88 +++++++++++++++++++++++++++ 4 files changed, 256 insertions(+) create mode 100644 .vscode/.browse.VC.db create mode 100644 src/main/Feature.js create mode 100644 src/main/Genotype.js create mode 100644 src/main/Variant.js diff --git a/.vscode/.browse.VC.db b/.vscode/.browse.VC.db new file mode 100644 index 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zro5Pi3i)jog7RA|Oq3U~Fc#ZA(SIm!1a?!xed)5E5cUK1c6$tjgU7)d_}^Ru%erY_ zcyzdi))CO3?l(&1KZN>?^k$;wQ)tS|35hY z|G)W$|6FJODx$R&d}z>0iLhe&Q`TzSOC6jblNfy0u5+D)CXuo53>KorGN;8 zI9pr_sF34f`pTIBWFss@D1gkkAfQU5F9eVH=)*^>pi<{4M3eflBLrd94t?grRZP^E z$8G=N3hY>om|+HtYOqD1NFo~)^Ee%1ASU;aG-aJ>wNL_U(mm8;y81@dCe2!*H! mIt92mTp`LO6!`C~0v6@d?j|^pAPy^p;vgwxRtjWrpZI^DhM02z literal 0 HcmV?d00001 diff --git a/src/main/Feature.js b/src/main/Feature.js new file mode 100644 index 00000000..f8992ba7 --- /dev/null +++ b/src/main/Feature.js @@ -0,0 +1,137 @@ +/** + * Class for features, shared between BAM and GA4GH backends. + */ + +import type ContigInterval from './ContigInterval'; + +export type Strand = '-' | '+'; + +export type Dbxref = { + accession: string; + db: string; +} + +class Feature { + featureId: string; + featureType: string; + source: string; + contig: ContigInterval; + start: number; + end: number; + strand: Strand; + value: number; + dbxrefs: Dbxref[]; + parentIds: string[]; + attributes: Object; + + constructor(featureId: string, featureType: string, source: string, + contig: ContigInterval, start: number, end: number, + strand: Strand, value: number, dbxrefs: Dbxref[], parentIds: string[], + attributes: Object) { + this.featureId = featureId; + this.featureTyp = featureType; + this.source = source; + this.contig = contig; + this.start = start; + this.end = end; + this.strand = strand; + this.value = value; + this.dbxrefs = dbxrefs; + this.parentIds = parentIds; + this.attributes = attributes; + } + + getAttributes(): Object { + return this.attributes; + } + + getContig(): Contig { + return this.contig; + } + + getDbxrefs(): Dbxref[] { + return this.dbxrefs; + } + + getEnd(): number { + return this.end; + } + + getFeatureId(): string { + return this.featureId; + } + + getFeatureType(): string { + return this.featureType; + } + + getParentIds(): string { + return this.parentIds; + } + + getSource(): string { + return this.source; + } + + getStart(): number { + return this.start; + } + + getStrand(): Strand { + return this.alignment.alignment.position.reverseStrand ? '-' : '+'; + } + + getValue(): number { + return this.value; + } + + /** Feature.Builder methods + May need to separate these */ + + setAttributes(value: Object) { + this.attributes = value; + } + + setContig(value: number) { + this.contig = value; + } + + setDbxrefs(value: List) { + this.dbxrefs = value; + } + + setEnd(value: number) { + this.end = value; + } + + setFeatureId(value: string) { + this.featureId = value; + } + + setFeatureType(value: string) { + this.featureType = value; + } + + setParentIds(value: List) { + this.parentIds = value; + } + + setSource(value: string) { + this.source = value; + } + + setStart(value: number) { + this.start = value; + } + + setStrand(value: Strand) { + this.strand = value; + } + + setValue(value: number) { + this.value = value; + } +} + +module.exports = Feature; + diff --git a/src/main/Genotype.js b/src/main/Genotype.js new file mode 100644 index 00000000..45f6a619 --- /dev/null +++ b/src/main/Genotype.js @@ -0,0 +1,31 @@ +/** + * Class for Genotypes, shared between BAM and GA4GH backends. + */ + +import type ContigInterval from './ContigInterval'; +import type Variant from './Variant'; + +export type Strand = '-' | '+'; + +class Genotype { + variant: Variant; + sampleId: string; + sampleDescription: string; + processingDescription: string; + //alleles: List + expectedAlleleDosage: number; + referenceReadDepth: number; + alternativeReadDepth: number; + readDepth: number; + minReadDepth: number; + genotypeQuality: number; + genotypeLikelihoods: List; + nonReferenceLikelihoods: List; + strandBiasComponents: List; + splitFromMultiAllelic: boolean; + isPhased: boolean; + phaseSetId: number; + phaseQuality: number; + + +} diff --git a/src/main/Variant.js b/src/main/Variant.js new file mode 100644 index 00000000..9dccf9f2 --- /dev/null +++ b/src/main/Variant.js @@ -0,0 +1,88 @@ +/** + * Class for Variants, shared between BAM and GA4GH backends. + */ + +import type ContigInterval from './ContigInterval'; + +export type Strand = '-' | '+'; + +class Variant { + contig: ContigInterval; + start: number; + end: number; + referenceAllele: string; + alternateAllele: string; + svAllele: StructuralVariant; + isSomatic: boolean; + + constructor(contig: ContigInterval, start: number, end: number + referenceAllele: string, alternateAllele: string, + svAllele: StructuralVariant, isSomatic: boolean) { + this.contig = contig; + this.start = start; + this.end = end; + this.referenceAllele = referenceAllele; + this.alternateAllele = alternateAllele; + this.svAllele = svAllele; + this.isSomatic = isSomatic; + } + + getAlternativeAllele(): string { + return this.alternateAllele; + } + + getContig(): ContigInterval { + return this.contig; + } + + getEnd(): number { + return this.end; + } + + getIsSomatic(): boolean { + return this.isSomatic; + } + + getReferenceAllele(): string { + return this.referenceAllele; + } + + getStart(): number { + return this.start; + } + + getSvAlelle(): StructuralVariant { + return this.svAllele; + } + + setAlternatieAllele(value: string) { + this.alternateAllele = value; + } + + setContig(value: Contig) { + this.contig = value; + } + + setEnd(value: number) { + this.end = value; + } + + setIsSomatic(value: boolean) { + this.isSomatic = value; + } + + setReferenceAllele(value: string) { + this.referenceAllele = value; + } + + setStart(value: number) { + this.start = value; + } + + setSvAllel(value: StructuralVariant) { + this.svAllele = value; + } + +} + +module.exports = Variant; From ca7cd922c8d24ee0853f196e1cbc156cda8fb04a Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Fri, 17 Jun 2016 11:28:56 -0700 Subject: [PATCH 090/136] Create the FeatureDataSource.js file and tweak Feature.js Variant.js and Genotype.js constructors to take in objects instead --- src/main/Feature.js | 21 +++++++++-- src/main/FeatureInterface.js | 53 +++++++++++++++++++++++++++ src/main/Genotype.js | 2 +- src/main/Variant.js | 3 +- src/main/pileup.js | 2 +- src/main/sources/FeatureDataSource.js | 10 +++++ 6 files changed, 84 insertions(+), 7 deletions(-) create mode 100644 src/main/FeatureInterface.js create mode 100644 src/main/sources/FeatureDataSource.js diff --git a/src/main/Feature.js b/src/main/Feature.js index f8992ba7..fa890d5c 100644 --- a/src/main/Feature.js +++ b/src/main/Feature.js @@ -1,5 +1,6 @@ /** * Class for features, shared between BAM and GA4GH backends. + * @flow */ import type ContigInterval from './ContigInterval'; @@ -22,7 +23,7 @@ class Feature { value: number; dbxrefs: Dbxref[]; parentIds: string[]; - attributes: Object; + attributes: Object; //Or use array of attribute objects with key, value constructor(featureId: string, featureType: string, source: string, contig: ContigInterval, start: number, end: number, @@ -41,6 +42,12 @@ class Feature { this.attributes = attributes; } + /** + * constructor(input: Object) { + * + * } + */ + getAttributes(): Object { return this.attributes; } @@ -85,9 +92,6 @@ class Feature { return this.value; } - /** Feature.Builder methods - May need to separate these */ - setAttributes(value: Object) { this.attributes = value; } @@ -131,7 +135,16 @@ class Feature { setValue(value: number) { this.value = value; } + } +export type FeatureDataSource = { + rangeChanged: (newRange: GenomeRange) => void; + getFeaturesInRange: (range: ContigInterval) => Feature[]; + on: (event: string, handler: Function) => void; // really => FeatureDataSource + once: (event: string, handler: Function) => void; + off: (event: string) => void; +}; + module.exports = Feature; diff --git a/src/main/FeatureInterface.js b/src/main/FeatureInterface.js new file mode 100644 index 00000000..6c29d1d9 --- /dev/null +++ b/src/main/FeatureInterface.js @@ -0,0 +1,53 @@ +/** + * Interface for features + * @flow + */ + +import type ContigInterval from './ContigInterval'; + +export type Strand = '-' | '+'; + +export type Feature = { + featureId: string; + featureType: string; + source: string; + contig: ContigInterval; + start: number; + end: number; + strand: Strand; + value: number; + dbxrefs: Dbxref[]; + parentIds: string[]; + attributes: Object; + + getAttributes(): Object; + getContig(): ContigInterval; + getDbxrefs(): Dbxref[]; + getEnd(): number; + getFeatureId(): string; + getFeatureType(): string; + getParentsIds(): string; + getSource(): string; + getStart(): number; + getStrand(): Strand; + getValue(): number; + + setAttributes(); + setContig(); + setDbxrefs(); + setEnd(); + setFeatureId(); + setParentIds(); + setSource(); + setStart(); + setStrand(); + setValue(); +} + +export type FeatureDataSource = { + rangeChanged: (newRange: GenomeRange) => void; + getFeaturesInRange: (range: ContigInterval) => Feature[]; + on: (event: string, handler: Function) => void; // really => FeatureDataSource + once: (event: string, handler: Function) => void; + off: (event: string) => void; +} diff --git a/src/main/Genotype.js b/src/main/Genotype.js index 45f6a619..2afcf7dd 100644 --- a/src/main/Genotype.js +++ b/src/main/Genotype.js @@ -1,5 +1,6 @@ /** * Class for Genotypes, shared between BAM and GA4GH backends. + * @flow */ import type ContigInterval from './ContigInterval'; @@ -26,6 +27,5 @@ class Genotype { isPhased: boolean; phaseSetId: number; phaseQuality: number; - } diff --git a/src/main/Variant.js b/src/main/Variant.js index 9dccf9f2..ce47c3fb 100644 --- a/src/main/Variant.js +++ b/src/main/Variant.js @@ -1,5 +1,6 @@ /** * Class for Variants, shared between BAM and GA4GH backends. + * @flow */ import type ContigInterval from './ContigInterval'; @@ -55,7 +56,7 @@ class Variant { return this.svAllele; } - setAlternatieAllele(value: string) { + setAlternativeAllele(value: string) { this.alternateAllele = value; } diff --git a/src/main/pileup.js b/src/main/pileup.js index 441b7c3d..2c351564 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -22,7 +22,7 @@ import EmptySource from './sources/EmptySource'; // Visualizations import CoverageTrack from './viz/CoverageTrack'; import GenomeTrack from './viz/GenomeTrack'; -import GeneTrack from './viz/GeneTrack'; +import GeneTrack from './viz/GeneTrack'; //use this for features import LocationTrack from './viz/LocationTrack'; import PileupTrack from './viz/PileupTrack'; import ScaleTrack from './viz/ScaleTrack'; diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js new file mode 100644 index 00000000..97c8fdc9 --- /dev/null +++ b/src/main/sources/FeatureDataSource.js @@ -0,0 +1,10 @@ +/* @flow */ + +import type {Gene, BigBedDataSource} from './BigBedDataSource'; + +function(create) + +module.exports = { + create +} + From f22d9bc0e6b577b9826624858047f3fdb990ab2a Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Sat, 18 Jun 2016 18:28:06 -0700 Subject: [PATCH 091/136] Completed the FeatureDataSource.js file and also completed most of FeatureDataSource-test.js file --- src/main/Feature.js | 58 ++++--- src/main/FeatureInterface.js | 53 ------- src/main/Genotype.js | 41 +++-- src/main/Variant.js | 160 ++++++++++---------- src/main/pileup.js | 1 + src/main/sources/FeatureDataSource.js | 166 ++++++++++++++++++++- src/test/sources/FeatureDataSource-test.js | 43 ++++++ 7 files changed, 333 insertions(+), 189 deletions(-) delete mode 100644 src/main/FeatureInterface.js create mode 100644 src/test/sources/FeatureDataSource-test.js diff --git a/src/main/Feature.js b/src/main/Feature.js index fa890d5c..d5e13746 100644 --- a/src/main/Feature.js +++ b/src/main/Feature.js @@ -1,9 +1,10 @@ /** - * Class for features, shared between BAM and GA4GH backends. + * Class for features * @flow */ + 'use strict'; -import type ContigInterval from './ContigInterval'; +import ContigInterval from './ContigInterval'; export type Strand = '-' | '+'; @@ -12,48 +13,44 @@ export type Dbxref = { db: string; } +export type attribute = { + key: string; + value: string; +} + class Feature { featureId: string; featureType: string; source: string; - contig: ContigInterval; + range: ContigInterval; start: number; end: number; strand: Strand; value: number; dbxrefs: Dbxref[]; parentIds: string[]; - attributes: Object; //Or use array of attribute objects with key, value - - constructor(featureId: string, featureType: string, source: string, - contig: ContigInterval, start: number, end: number, - strand: Strand, value: number, dbxrefs: Dbxref[], parentIds: string[], - attributes: Object) { - this.featureId = featureId; - this.featureTyp = featureType; - this.source = source; - this.contig = contig; - this.start = start; - this.end = end; - this.strand = strand; - this.value = value; - this.dbxrefs = dbxrefs; - this.parentIds = parentIds; - this.attributes = attributes; + attributes: attribute[]; //Or use array of attribute objects with key, value + + constructor(input: Object) { + this.featureId = input.featureId; + this.featureType = input.featureType; + this.source = input.source; + this.start = input.start; + this.end = input.end; + this.strand = input.strand; + this.value = input.value; + this.dbxrefs = input.dbxrefs; + this.parentIds = input.parentIds; + this.attributes = input.attributes; + this.range = new ContigInterval(input.range.name, input.range.start, input.range.end); } - /** - * constructor(input: Object) { - * - * } - */ - getAttributes(): Object { return this.attributes; } - getContig(): Contig { - return this.contig; + getContig(): ContigInterval { + return this.range; } getDbxrefs(): Dbxref[] { @@ -96,8 +93,8 @@ class Feature { this.attributes = value; } - setContig(value: number) { - this.contig = value; + setContig(value: ContigInterval) { + this.range = value; } setDbxrefs(value: List) { @@ -147,4 +144,3 @@ export type FeatureDataSource = { }; module.exports = Feature; - diff --git a/src/main/FeatureInterface.js b/src/main/FeatureInterface.js deleted file mode 100644 index 6c29d1d9..00000000 --- a/src/main/FeatureInterface.js +++ /dev/null @@ -1,53 +0,0 @@ -/** - * Interface for features - * @flow - */ - -import type ContigInterval from './ContigInterval'; - -export type Strand = '-' | '+'; - -export type Feature = { - featureId: string; - featureType: string; - source: string; - contig: ContigInterval; - start: number; - end: number; - strand: Strand; - value: number; - dbxrefs: Dbxref[]; - parentIds: string[]; - attributes: Object; - - getAttributes(): Object; - getContig(): ContigInterval; - getDbxrefs(): Dbxref[]; - getEnd(): number; - getFeatureId(): string; - getFeatureType(): string; - getParentsIds(): string; - getSource(): string; - getStart(): number; - getStrand(): Strand; - getValue(): number; - - setAttributes(); - setContig(); - setDbxrefs(); - setEnd(); - setFeatureId(); - setParentIds(); - setSource(); - setStart(); - setStrand(); - setValue(); -} - -export type FeatureDataSource = { - rangeChanged: (newRange: GenomeRange) => void; - getFeaturesInRange: (range: ContigInterval) => Feature[]; - on: (event: string, handler: Function) => void; // really => FeatureDataSource - once: (event: string, handler: Function) => void; - off: (event: string) => void; -} diff --git a/src/main/Genotype.js b/src/main/Genotype.js index 2afcf7dd..79c6084c 100644 --- a/src/main/Genotype.js +++ b/src/main/Genotype.js @@ -8,24 +8,23 @@ import type Variant from './Variant'; export type Strand = '-' | '+'; -class Genotype { - variant: Variant; - sampleId: string; - sampleDescription: string; - processingDescription: string; - //alleles: List - expectedAlleleDosage: number; - referenceReadDepth: number; - alternativeReadDepth: number; - readDepth: number; - minReadDepth: number; - genotypeQuality: number; - genotypeLikelihoods: List; - nonReferenceLikelihoods: List; - strandBiasComponents: List; - splitFromMultiAllelic: boolean; - isPhased: boolean; - phaseSetId: number; - phaseQuality: number; - -} +// class Genotype { +// variant: Variant; +// sampleId: string; +// sampleDescription: string; +// processingDescription: string; +// //alleles: List +// expectedAlleleDosage: number; +// referenceReadDepth: number; +// alternativeReadDepth: number; +// readDepth: number; +// minReadDepth: number; +// genotypeQuality: number; +// genotypeLikelihoods: List; +// nonReferenceLikelihoods: List; +// strandBiasComponents: List; +// splitFromMultiAllelic: boolean; +// isPhased: boolean; +// phaseSetId: number; +// phaseQuality: number; +// } diff --git a/src/main/Variant.js b/src/main/Variant.js index ce47c3fb..93eca989 100644 --- a/src/main/Variant.js +++ b/src/main/Variant.js @@ -7,83 +7,83 @@ import type ContigInterval from './ContigInterval'; export type Strand = '-' | '+'; -class Variant { - contig: ContigInterval; - start: number; - end: number; - referenceAllele: string; - alternateAllele: string; - svAllele: StructuralVariant; - isSomatic: boolean; - - constructor(contig: ContigInterval, start: number, end: number - referenceAllele: string, alternateAllele: string, - svAllele: StructuralVariant, isSomatic: boolean) { - this.contig = contig; - this.start = start; - this.end = end; - this.referenceAllele = referenceAllele; - this.alternateAllele = alternateAllele; - this.svAllele = svAllele; - this.isSomatic = isSomatic; - } - - getAlternativeAllele(): string { - return this.alternateAllele; - } - - getContig(): ContigInterval { - return this.contig; - } - - getEnd(): number { - return this.end; - } - - getIsSomatic(): boolean { - return this.isSomatic; - } - - getReferenceAllele(): string { - return this.referenceAllele; - } - - getStart(): number { - return this.start; - } - - getSvAlelle(): StructuralVariant { - return this.svAllele; - } - - setAlternativeAllele(value: string) { - this.alternateAllele = value; - } - - setContig(value: Contig) { - this.contig = value; - } - - setEnd(value: number) { - this.end = value; - } - - setIsSomatic(value: boolean) { - this.isSomatic = value; - } - - setReferenceAllele(value: string) { - this.referenceAllele = value; - } - - setStart(value: number) { - this.start = value; - } - - setSvAllel(value: StructuralVariant) { - this.svAllele = value; - } - -} - -module.exports = Variant; +// class Variant { +// contig: ContigInterval; +// start: number; +// end: number; +// referenceAllele: string; +// alternateAllele: string; +// svAllele: StructuralVariant; +// isSomatic: boolean; +// +// constructor(contig: ContigInterval, start: number, end: number +// referenceAllele: string, alternateAllele: string, +// svAllele: StructuralVariant, isSomatic: boolean) { +// this.contig = contig; +// this.start = start; +// this.end = end; +// this.referenceAllele = referenceAllele; +// this.alternateAllele = alternateAllele; +// this.svAllele = svAllele; +// this.isSomatic = isSomatic; +// } +// +// getAlternativeAllele(): string { +// return this.alternateAllele; +// } +// +// getContig(): ContigInterval { +// return this.contig; +// } +// +// getEnd(): number { +// return this.end; +// } +// +// getIsSomatic(): boolean { +// return this.isSomatic; +// } +// +// getReferenceAllele(): string { +// return this.referenceAllele; +// } +// +// getStart(): number { +// return this.start; +// } +// +// getSvAlelle(): StructuralVariant { +// return this.svAllele; +// } +// +// setAlternativeAllele(value: string) { +// this.alternateAllele = value; +// } +// +// setContig(value: Contig) { +// this.contig = value; +// } +// +// setEnd(value: number) { +// this.end = value; +// } +// +// setIsSomatic(value: boolean) { +// this.isSomatic = value; +// } +// +// setReferenceAllele(value: string) { +// this.referenceAllele = value; +// } +// +// setStart(value: number) { +// this.start = value; +// } +// +// setSvAllel(value: StructuralVariant) { +// this.svAllele = value; +// } +// +// } +// +// module.exports = Variant; diff --git a/src/main/pileup.js b/src/main/pileup.js index 2c351564..aeacf3dd 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -18,6 +18,7 @@ import VariantDataSource from './sources/VariantDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; import EmptySource from './sources/EmptySource'; +// import FeatureDataSource from './sources/FeatureDataSource'; // Visualizations import CoverageTrack from './viz/CoverageTrack'; diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index 97c8fdc9..d481087d 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -1,10 +1,168 @@ /* @flow */ +'use strict'; -import type {Gene, BigBedDataSource} from './BigBedDataSource'; +import type {Gene, BigBedSource} from './BigBedDataSource'; +import ContigInterval from '../ContigInterval'; +// import BigBed from '../data/BigBed'; +import Interval from '../Interval'; +import Q from 'q'; +import _ from 'underscore'; +import {Events} from 'backbone'; -function(create) +var FEATURES_PER_REQUEST = 200; //TODO Arbitrary number for now + +function parseBedFeature(f): Gene { + var position = new ContigInterval(f.contig, f.start, f.stop), + x = f.rest.split('\t'), + // exons arrays sometimes have trailing commas + exonLengths = x[7].replace(/,*$/, '').split(',').map(Number), + exonStarts = x[8].replace(/,*$/, '').split(',').map(Number), + exons = _.zip(exonStarts, exonLengths) + .map(function([start, length]) { + return new Interval(f.start + start, f.start + start + length); + }); + + return { + position, + id: x[0], // e.g. ENST00000359597 + strand: x[2], // either + or - + codingRegion: new Interval(Number(x[3]), Number(x[4])), + geneId: x[9], + name: x[10], + exons + }; +} + +function createFromFeatureEndpoint(url: string): BigBedSource{ + // Collection of genes that have already been loaded. + var genes: {[key:string]: Gene} = {}; //TODO features + + // Ranges for which we have complete information -- no need to hit network. + var coveredRanges: Array> = []; + + function addGene(newGene) { + if (!genes[newGene.id]) { + genes[newGene.id] = newGene; + } + } + + function getGenesInRange(range: ContigInterval): Gene[] { + if (!range) return []; + var results = []; + _.each(genes, gene => { + if (range.intersects(gene.position)) { + results.push(gene); + } + }); + return results; + } + + function fetch(range: GenomeRange) { + var interval = new ContigInterval(range.contig, range.start, range.stop); + + // Check if this interval is already in the cache. + if (interval.isCoveredBy(coveredRanges)) { + return Q.when(); + } + + coveredRanges.push(interval); + coveredRanges = ContigInterval.coalesce(coveredRanges); + + /** Call JSON request */ + + /** Modify URL */ + // url = "http://localhost:8080/" + range.contig.contig + "?start=" + range.start + "&end=" + range.stop; + url = url + range.contig.contig + "?start=" + range.start + "&end=" + range.stop; + + var xhr = new XMLHttpRequest(); + xhr.open('POST', url); + xhr.responseType = 'json'; + xhr.setRequestHeader('Content-Type', 'application/json'); + + xhr.addEventListener('load', function(e) { + var response = this.response; + if (this.status >= 400) { + notifyFailure(this.status + ' ' + this.statusText + ' ' + JSON.stringify(response)); + } else { + if (response.errorCode) { + notifyFailure('Error from Feature endpoint: ' + JSON.stringify(response)); + } else { + addFeaturesFromResponse(response); + o.trigger('newdata', interval); // display data as it comes in. + o.trigger('networkdone'); + } + } + }); + xhr.addEventListener('error', function(e) { + notifyFailure('Request failed with status: ' + this.status); + }); + + var numRequests = 1; + o.trigger('networkprogress', {numRequests}); //Num requests only applies to pagination + xhr.send(JSON.stringify({ + pageSize: FEATURES_PER_REQUEST, + // readGroupIds: [spec.readGroupId], //TODO give features an ID + referenceName: range.contig, + start: range.start(), + end: range.stop() + })); + + /** End of JSON request */ + /** replace this with modified sequence method that creates a BigBedSource */ + return remoteSource.getFeatureBlocksOverlapping(interval).then(featureBlocks => { + featureBlocks.forEach(fb => { + coveredRanges.push(fb.range); + coveredRanges = ContigInterval.coalesce(coveredRanges); + var genes = fb.rows.map(parseBedFeature); + genes.forEach(gene => addGene(gene)); + //we have new data from our internal block range + o.trigger('newdata', fb.range); + }); + }); + } + + var o = { + rangeChanged: function(newRange: GenomeRange) { + fetch(newRange).done(); + }, + getGenesInRange, + + // These are here to make Flow happy. + on: () => {}, + off: () => {}, + trigger: () => {} + }; + + function notifyFailure(message: string) { + o.trigger('networkfailure', message); + o.trigger('networkdone'); + console.warn(message); + } + + function addFeaturesFromResponse(response: Object) { + response.features.forEach(fb => { + coveredRanges.push(fb.range); + coveredRanges = ContigInterval.coalesce(coveredRanges); + var genes = fb.rows.map(parseBedFeature); + genes.forEach(gene => addGene(gene)); + //we have new data from our internal block range + o.trigger('newdata', fb.range); + }); + } + + _.extend(o, Events); // Make this an event emitter + + return o; +} + +function create(data: {url: string}): BigBedSource { + var url = data.url; + if (!url) { + throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); + } + return createFromFeatureEndpoint(url); +} module.exports = { create -} - +}; diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js new file mode 100644 index 00000000..2d7667e4 --- /dev/null +++ b/src/test/sources/FeatureDataSource-test.js @@ -0,0 +1,43 @@ +/* @flow */ +'use strict'; + +import {expect} from 'chai'; + +// import BigBed from '../../main/data/BigBed'; +// import BigBedDataSource from '../../main/sources/BigBedDataSource'; +import ContigInterval from '../../main/ContigInterval'; +import FeatureDataSource from '../../main/sources/FeatureDataSource'; + +var url = "http://localhost:8080/features/chrM?start=0&end=1000"; + +describe('FeatureDataSource', function() { + function getTestSource() { + return FeatureDataSource.createFromFeatureEndpoint(url); + } + + it('should extract features in a range from a given endpoint', function(done) { + this.timeout(5000); + var source = getTestSource(); + + // No genes fetched initially + var testrange = new ContigInterval('chrM', 0, 1000); + var test = source.getGenesInRange(testrange); + expect(test).to.deep.equal([]); + + // Fetching that one gene should cache its entire blok. + source.on('newdata', () => { + var tests = source.getGenesInRange(testrange); + expect(tests).to.have.length(1); + + var test = tests[0]; + expect(test.name).to.equal('chrM'); + // expect(test.exons).to.have.length() //What should the length be? + done(); + }); + source.rangeChanged({ + contig: testrange.contig, + start: testrange.start(), + stop: testrange.stop() + }); + }); +}); From c2c9eecb136435647e3b1062a5b37d4d89e2d6b9 Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Sat, 25 Jun 2016 11:15:35 -0700 Subject: [PATCH 092/136] Finished FeatureDataSouce along with FeatureEndpoint files to work with RemoteRequest file --- src/main/Feature.js | 14 +- src/main/RemoteRequest.js | 1 + src/main/data/FeatureEndpoint.js | 62 ++++++++ src/main/sources/FeatureConvertDataSource.js | 25 ++++ src/main/sources/FeatureDataSource.js | 140 +++++++------------ 5 files changed, 143 insertions(+), 99 deletions(-) create mode 100644 src/main/data/FeatureEndpoint.js create mode 100644 src/main/sources/FeatureConvertDataSource.js diff --git a/src/main/Feature.js b/src/main/Feature.js index d5e13746..42971191 100644 --- a/src/main/Feature.js +++ b/src/main/Feature.js @@ -34,15 +34,15 @@ class Feature { constructor(input: Object) { this.featureId = input.featureId; this.featureType = input.featureType; - this.source = input.source; + // this.source = input.source; this.start = input.start; this.end = input.end; - this.strand = input.strand; - this.value = input.value; - this.dbxrefs = input.dbxrefs; - this.parentIds = input.parentIds; - this.attributes = input.attributes; - this.range = new ContigInterval(input.range.name, input.range.start, input.range.end); + // this.strand = input.strand; + // this.value = input.value; + // this.dbxrefs = input.dbxrefs; + // this.parentIds = input.parentIds; + // this.attributes = input.attributes; + this.range = input.range; } getAttributes(): Object { diff --git a/src/main/RemoteRequest.js b/src/main/RemoteRequest.js index 578c4c2d..7fc9b269 100644 --- a/src/main/RemoteRequest.js +++ b/src/main/RemoteRequest.js @@ -9,6 +9,7 @@ import Q from 'q'; import ContigInterval from './ContigInterval'; + class RemoteRequest { url: string; cache: Object; diff --git a/src/main/data/FeatureEndpoint.js b/src/main/data/FeatureEndpoint.js new file mode 100644 index 00000000..d477650b --- /dev/null +++ b/src/main/data/FeatureEndpoint.js @@ -0,0 +1,62 @@ +/** + * This module defines a parser for the 2bit file format. + * See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 + * @flow + */ +'use strict'; + +// import Q from 'q'; +import type RemoteRequest from '../RemoteRequest'; +//TODO import bedrow here + +export type FeatureRecord = { + featureId: string; + featureType: string; + start: number; + end: number; + range: ContigInterval +} + +function unpackFeatures(dataView: DataView, start: number, end: number): Array { + // TODO: use jBinary bitfield for this + var features: Array = []; + // basePairs.length = dataView.byteLength * 4; // pre-allocate + for (var i = 0; i < dataView.byteLength; i++) { + var packed = dataView.getUint8(i); + features[i] = String.fromCharCode(packed); + } + // Remove base pairs from the end if the sequence terminated mid-byte. + // features.length = numBasePairs; //TODO Determine length + return features; +} + +class FeatureEndpoint { + remoteRequest: RemoteRequest; + contigList: FeatureRecord[]; + + constructor(remoteRequest: RemoteRequest, contigList: FeatureRecord[]) { + this.remoteRequest = remoteRequest; + this.contigList = contigList; + } + + getContigList(): string[] { + return this.contigList.map(seq => seq.name); + } + + /** + * Returns the Features in contig:start-stop. + * The range is inclusive and zero-based. + * Returns empty string if no data is available on this range. + */ + + getFeaturesInRange(contig: string, start: number, stop: number): Q.Promise { + if (start > stop) { + throw `Requested a range with start > stop (${start}, ${stop})`; + } + return this.remoteRequest.get(contig, start, stop).then(buffer => { + var dataView = new DataView(buffer); + var d = unpackFeatures(dataView, start, stop).join(''); + return d; + }); + } +} diff --git a/src/main/sources/FeatureConvertDataSource.js b/src/main/sources/FeatureConvertDataSource.js new file mode 100644 index 00000000..66e53b8d --- /dev/null +++ b/src/main/sources/FeatureConvertDataSource.js @@ -0,0 +1,25 @@ +// /* @flow */ +// 'use strict'; + +// import type {Strand} from '../Alignment'; + +// import _ from 'underscore'; +// import Q from 'q'; +// import {Events} from 'backbone'; + +// import ContigInterval from '../ContigInterval'; +// import Interval from '../Interval'; +// import BigBed from '../data/BigBed'; +// import type {Gene, BigBedSource} from './BigBedDataSource'; + +// export type FeatureConvertDataSource = { +// featureId: string; +// featureType: string; +// start: number; +// end: number; +// range: ContigInterval +// } + +// function getFeaturesInRange(f): BigBedSource { + +// } diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index d481087d..38df2671 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -1,9 +1,11 @@ /* @flow */ 'use strict'; -import type {Gene, BigBedSource} from './BigBedDataSource'; +// import type {Gene, BigBedSource} from './BigBedDataSource'; import ContigInterval from '../ContigInterval'; -// import BigBed from '../data/BigBed'; +// import BigBed from '../data/BigBed'; +import RemoteRequest from '../RemoteRequest'; +import FeatureEndpoint from '../data/FeatureEndpoint'; import Interval from '../Interval'; import Q from 'q'; import _ from 'underscore'; @@ -11,7 +13,8 @@ import {Events} from 'backbone'; var FEATURES_PER_REQUEST = 200; //TODO Arbitrary number for now -function parseBedFeature(f): Gene { +function parseBedFeature(f): Feature { + var contig = new ContigInterval(f.contig, f.start, f.stop); var position = new ContigInterval(f.contig, f.start, f.stop), x = f.rest.split('\t'), // exons arrays sometimes have trailing commas @@ -21,135 +24,88 @@ function parseBedFeature(f): Gene { .map(function([start, length]) { return new Interval(f.start + start, f.start + start + length); }); - + //TODO replace this JSON format with the proper one needed for Feature object return { - position, - id: x[0], // e.g. ENST00000359597 - strand: x[2], // either + or - - codingRegion: new Interval(Number(x[3]), Number(x[4])), - geneId: x[9], - name: x[10], + range: contig, + featureId: x[0], // e.g. ENST00000359597 + featureType: x[1], + start: x[2], + end: x[3], exons }; } -function createFromFeatureEndpoint(url: string): BigBedSource{ +function createFromFeatureEndpoint(remoteSource: FeatureEndpoint): BigBedSource { // Collection of genes that have already been loaded. - var genes: {[key:string]: Gene} = {}; //TODO features + var features: {[key:string]: feature} = {}; //TODO features // Ranges for which we have complete information -- no need to hit network. var coveredRanges: Array> = []; - function addGene(newGene) { - if (!genes[newGene.id]) { - genes[newGene.id] = newGene; + function addFeature(newfeature) { + if (!feature[newFeature.featureId]) { + feature[newFeature.featureId] = newFeature; } } - function getGenesInRange(range: ContigInterval): Gene[] { + function getFeaturesInRange(range: ContigInterval): Feature[] { if (!range) return []; var results = []; - _.each(genes, gene => { - if (range.intersects(gene.position)) { - results.push(gene); + _.each(Feature, feature => { + if (range.intersects(feature.range)) { + results.push(feature); } }); return results; } - function fetch(range: GenomeRange) { - var interval = new ContigInterval(range.contig, range.start, range.stop); + function fetch(range: ContigInterval) { // Check if this interval is already in the cache. - if (interval.isCoveredBy(coveredRanges)) { + if (range.isCoveredBy(coveredRanges)) { return Q.when(); } - coveredRanges.push(interval); + coveredRanges.push(range); coveredRanges = ContigInterval.coalesce(coveredRanges); - /** Call JSON request */ - /** Modify URL */ - // url = "http://localhost:8080/" + range.contig.contig + "?start=" + range.start + "&end=" + range.stop; - url = url + range.contig.contig + "?start=" + range.start + "&end=" + range.stop; - - var xhr = new XMLHttpRequest(); - xhr.open('POST', url); - xhr.responseType = 'json'; - xhr.setRequestHeader('Content-Type', 'application/json'); - - xhr.addEventListener('load', function(e) { - var response = this.response; - if (this.status >= 400) { - notifyFailure(this.status + ' ' + this.statusText + ' ' + JSON.stringify(response)); - } else { - if (response.errorCode) { - notifyFailure('Error from Feature endpoint: ' + JSON.stringify(response)); - } else { - addFeaturesFromResponse(response); - o.trigger('newdata', interval); // display data as it comes in. - o.trigger('networkdone'); - } - } - }); - xhr.addEventListener('error', function(e) { - notifyFailure('Request failed with status: ' + this.status); - }); + remoteSource.remoteRequest.url += range.contig.contig + "?start=" + range.start + "&end=" + range.stop; - var numRequests = 1; - o.trigger('networkprogress', {numRequests}); //Num requests only applies to pagination - xhr.send(JSON.stringify({ - pageSize: FEATURES_PER_REQUEST, - // readGroupIds: [spec.readGroupId], //TODO give features an ID - referenceName: range.contig, - start: range.start(), - end: range.stop() - })); - - /** End of JSON request */ - /** replace this with modified sequence method that creates a BigBedSource */ - return remoteSource.getFeatureBlocksOverlapping(interval).then(featureBlocks => { - featureBlocks.forEach(fb => { - coveredRanges.push(fb.range); - coveredRanges = ContigInterval.coalesce(coveredRanges); - var genes = fb.rows.map(parseBedFeature); - genes.forEach(gene => addGene(gene)); - //we have new data from our internal block range - o.trigger('newdata', fb.range); - }); - }); + return remoteSource.getFeaturesInRange(range.contig.contig, range.start, range.end); } var o = { rangeChanged: function(newRange: GenomeRange) { - fetch(newRange).done(); + normalizeRange(newRange).then(r => { + var range = new ContigInterval(r.contig, r.start, r.stop); + + if (range.isCoveredBy(coveredRanges)) { + return; + } + + var newRanges = range.complementIntervals(coveredRanges); + coveredRanges.push(range); + coveredRanges = ContigInterval.coalesce(coveredRanges); + + for (var newRange of newRanges) { + fetch(newRange); + } + }).done() }, - getGenesInRange, + getRange, + getRangeAsString, + contigList: () => contigList, + normalizeRange, + getFeaturesInRange, // These are here to make Flow happy. on: () => {}, + once: () -> {}, off: () => {}, trigger: () => {} }; - function notifyFailure(message: string) { - o.trigger('networkfailure', message); - o.trigger('networkdone'); - console.warn(message); - } - - function addFeaturesFromResponse(response: Object) { - response.features.forEach(fb => { - coveredRanges.push(fb.range); - coveredRanges = ContigInterval.coalesce(coveredRanges); - var genes = fb.rows.map(parseBedFeature); - genes.forEach(gene => addGene(gene)); - //we have new data from our internal block range - o.trigger('newdata', fb.range); - }); - } - _.extend(o, Events); // Make this an event emitter return o; @@ -160,7 +116,7 @@ function create(data: {url: string}): BigBedSource { if (!url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } - return createFromFeatureEndpoint(url); + return createFromFeatureEndpoint(new RemoteRequest(url)); } module.exports = { From 0a5a1ca7693dcfc92359100d45f7d53a6ecd4774 Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Tue, 28 Jun 2016 12:34:45 -0700 Subject: [PATCH 093/136] completed the feature test file --- src/main/Feature.js | 2 +- src/main/data/FeatureEndpoint.js | 18 +++---- src/main/data/samplefeature.json | 12 +++++ src/main/sources/FeatureDataSource.js | 47 +++++++++--------- src/test/sources/FeatureDataSource-test.js | 58 ++++++++++++++++++---- 5 files changed, 95 insertions(+), 42 deletions(-) create mode 100644 src/main/data/samplefeature.json diff --git a/src/main/Feature.js b/src/main/Feature.js index 42971191..83a7deb3 100644 --- a/src/main/Feature.js +++ b/src/main/Feature.js @@ -22,7 +22,7 @@ class Feature { featureId: string; featureType: string; source: string; - range: ContigInterval; + range: ContigInterval; start: number; end: number; strand: Strand; diff --git a/src/main/data/FeatureEndpoint.js b/src/main/data/FeatureEndpoint.js index d477650b..26b1400b 100644 --- a/src/main/data/FeatureEndpoint.js +++ b/src/main/data/FeatureEndpoint.js @@ -39,7 +39,7 @@ class FeatureEndpoint { this.contigList = contigList; } - getContigList(): string[] { + contigList(): string[] { return this.contigList.map(seq => seq.name); } @@ -50,13 +50,13 @@ class FeatureEndpoint { */ getFeaturesInRange(contig: string, start: number, stop: number): Q.Promise { - if (start > stop) { - throw `Requested a range with start > stop (${start}, ${stop})`; - } - return this.remoteRequest.get(contig, start, stop).then(buffer => { - var dataView = new DataView(buffer); - var d = unpackFeatures(dataView, start, stop).join(''); - return d; - }); + if (start > stop) { + throw `Requested a range with start > stop (${start}, ${stop})`; + } + return this.remoteRequest.get(contig, start, stop).then(buffer => { + var dataView = new DataView(buffer); + var d = unpackFeatures(dataView, start, stop).join(''); + return d; + }); } } diff --git a/src/main/data/samplefeature.json b/src/main/data/samplefeature.json new file mode 100644 index 00000000..cee3e7a3 --- /dev/null +++ b/src/main/data/samplefeature.json @@ -0,0 +1,12 @@ +[{ + "rest": "4ee7469a-b468-429b-a109-07a484817037", + "contig": "chrM", + "start": 1107, + "end": 1200 +}, { + "rest": "e105ce29-a840-4fc6-819f-a9aac5166163", + "contig": "chrM", + "start": 1011, + "end": 1012 +}] + diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index 38df2671..47eaef7a 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -2,6 +2,7 @@ 'use strict'; // import type {Gene, BigBedSource} from './BigBedDataSource'; +import type {BigBedSource} from './BigBedDataSource'; import ContigInterval from '../ContigInterval'; // import BigBed from '../data/BigBed'; import RemoteRequest from '../RemoteRequest'; @@ -13,29 +14,29 @@ import {Events} from 'backbone'; var FEATURES_PER_REQUEST = 200; //TODO Arbitrary number for now -function parseBedFeature(f): Feature { - var contig = new ContigInterval(f.contig, f.start, f.stop); - var position = new ContigInterval(f.contig, f.start, f.stop), - x = f.rest.split('\t'), - // exons arrays sometimes have trailing commas - exonLengths = x[7].replace(/,*$/, '').split(',').map(Number), - exonStarts = x[8].replace(/,*$/, '').split(',').map(Number), - exons = _.zip(exonStarts, exonLengths) - .map(function([start, length]) { - return new Interval(f.start + start, f.start + start + length); - }); - //TODO replace this JSON format with the proper one needed for Feature object - return { - range: contig, - featureId: x[0], // e.g. ENST00000359597 - featureType: x[1], - start: x[2], - end: x[3], - exons - }; -} - -function createFromFeatureEndpoint(remoteSource: FeatureEndpoint): BigBedSource { +// function parseBedFeature(f): Feature { +// var contig = new ContigInterval(f.contig, f.start, f.stop); +// var position = new ContigInterval(f.contig, f.start, f.stop), +// x = f.rest.split('\t'), +// // exons arrays sometimes have trailing commas +// exonLengths = x[7].replace(/,*$/, '').split(',').map(Number), +// exonStarts = x[8].replace(/,*$/, '').split(',').map(Number), +// exons = _.zip(exonStarts, exonLengths) +// .map(function([start, length]) { +// return new Interval(f.start + start, f.start + start + length); +// }); +// //TODO replace this JSON format with the proper one needed for Feature object +// return { +// range: contig, +// featureId: x[0], // e.g. ENST00000359597 +// featureType: x[1], +// start: x[2], +// end: x[3], +// exons +// }; +// } + +var createFromFeatureEndpoint = function(remoteSource: FeatureEndpoint): BigBedSource { // Collection of genes that have already been loaded. var features: {[key:string]: feature} = {}; //TODO features diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js index 2d7667e4..bd462f68 100644 --- a/src/test/sources/FeatureDataSource-test.js +++ b/src/test/sources/FeatureDataSource-test.js @@ -3,35 +3,75 @@ import {expect} from 'chai'; -// import BigBed from '../../main/data/BigBed'; -// import BigBedDataSource from '../../main/sources/BigBedDataSource'; +import sinon from 'sinon'; + import ContigInterval from '../../main/ContigInterval'; import FeatureDataSource from '../../main/sources/FeatureDataSource'; +import RemoteFile from '../../main/RemoteFile'; +import sample from '../../main/samplefeature'; var url = "http://localhost:8080/features/chrM?start=0&end=1000"; describe('FeatureDataSource', function() { + var server: any = null, response; + + before(function () { + return new RemoteFile('../../main/samplefeature').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/features/chrM?start=1011&end=1012', [200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/features/chrM?start=1107&end=1200', [200, { "Content-Type": "application/json" }, response]); + }); + }); + + after(function () { + server.restore(); + }) + function getTestSource() { - return FeatureDataSource.createFromFeatureEndpoint(url); + var source = FeatureDataSource.create({ + url: '/features', + contigList: [{ + name:"chrM", + length: 93 + }, { + name:"chrM", + length: 1 + }] + }); + return source; } + it('should fetch contigs', function() { + var source = getTestSource(); + var contigs = source.contigList(); + expect(contigs).to.deep.equal(['chrM','93']) + }); + + it('should normalize range', function() { + var source = getTestSource(); + var range = {contig: 'chrM', start: x, stop: y}; + source.normalizeRange(range).then(normalized => { + expect(normalized.to.deep.equal(range)); + }).done(); + }); + it('should extract features in a range from a given endpoint', function(done) { this.timeout(5000); var source = getTestSource(); - // No genes fetched initially - var testrange = new ContigInterval('chrM', 0, 1000); - var test = source.getGenesInRange(testrange); + // No features fetched initially + var testrange = new ContigInterval('chrM', 1011, 1012); + var test = source.getFeaturesInRange(testrange[0], testrange[1], testrange[2]); expect(test).to.deep.equal([]); - // Fetching that one gene should cache its entire blok. + // Fetching that one feature should cache its entire block. source.on('newdata', () => { - var tests = source.getGenesInRange(testrange); + var tests = source.getFeaturesInRange(testrange[0], testrange[1], testrange[2]); expect(tests).to.have.length(1); var test = tests[0]; expect(test.name).to.equal('chrM'); - // expect(test.exons).to.have.length() //What should the length be? done(); }); source.rangeChanged({ From 969474c07141f73c527db9f8065065b5e8c77655 Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Tue, 28 Jun 2016 12:59:11 -0700 Subject: [PATCH 094/136] finished feature.js featuredatasource.js and featuredatasource-test.js --- src/main/sources/FeatureDataSource.js | 40 +++++----------------- src/test/sources/FeatureDataSource-test.js | 11 +++--- 2 files changed, 13 insertions(+), 38 deletions(-) diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index 47eaef7a..f7aee5ba 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -1,42 +1,18 @@ -/* @flow */ + /** @flow */ 'use strict'; -// import type {Gene, BigBedSource} from './BigBedDataSource'; -import type {BigBedSource} from './BigBedDataSource'; +import BigBedSource from './BigBedDataSource'; import ContigInterval from '../ContigInterval'; -// import BigBed from '../data/BigBed'; import RemoteRequest from '../RemoteRequest'; import FeatureEndpoint from '../data/FeatureEndpoint'; import Interval from '../Interval'; import Q from 'q'; import _ from 'underscore'; -import {Events} from 'backbone'; - -var FEATURES_PER_REQUEST = 200; //TODO Arbitrary number for now - -// function parseBedFeature(f): Feature { -// var contig = new ContigInterval(f.contig, f.start, f.stop); -// var position = new ContigInterval(f.contig, f.start, f.stop), -// x = f.rest.split('\t'), -// // exons arrays sometimes have trailing commas -// exonLengths = x[7].replace(/,*$/, '').split(',').map(Number), -// exonStarts = x[8].replace(/,*$/, '').split(',').map(Number), -// exons = _.zip(exonStarts, exonLengths) -// .map(function([start, length]) { -// return new Interval(f.start + start, f.start + start + length); -// }); -// //TODO replace this JSON format with the proper one needed for Feature object -// return { -// range: contig, -// featureId: x[0], // e.g. ENST00000359597 -// featureType: x[1], -// start: x[2], -// end: x[3], -// exons -// }; -// } - -var createFromFeatureEndpoint = function(remoteSource: FeatureEndpoint): BigBedSource { +import { Events } from 'backbone'; + +var FEATURES_PER_REQUEST = 200; + +function createFromFeatureEndpoint(remoteSource: FeatureEndpoint): BigBedSource { // Collection of genes that have already been loaded. var features: {[key:string]: feature} = {}; //TODO features @@ -110,7 +86,7 @@ var createFromFeatureEndpoint = function(remoteSource: FeatureEndpoint): BigBedS _.extend(o, Events); // Make this an event emitter return o; -} +}; function create(data: {url: string}): BigBedSource { var url = data.url; diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js index bd462f68..4c40a8db 100644 --- a/src/test/sources/FeatureDataSource-test.js +++ b/src/test/sources/FeatureDataSource-test.js @@ -8,9 +8,8 @@ import sinon from 'sinon'; import ContigInterval from '../../main/ContigInterval'; import FeatureDataSource from '../../main/sources/FeatureDataSource'; import RemoteFile from '../../main/RemoteFile'; -import sample from '../../main/samplefeature'; - -var url = "http://localhost:8080/features/chrM?start=0&end=1000"; +// import sample from '../../main/samplefeature'; +// var url = "http://localhost:8080/features/chrM?start=0&end=1000"; describe('FeatureDataSource', function() { var server: any = null, response; @@ -26,7 +25,7 @@ describe('FeatureDataSource', function() { after(function () { server.restore(); - }) + }); function getTestSource() { var source = FeatureDataSource.create({ @@ -45,12 +44,12 @@ describe('FeatureDataSource', function() { it('should fetch contigs', function() { var source = getTestSource(); var contigs = source.contigList(); - expect(contigs).to.deep.equal(['chrM','93']) + expect(contigs).to.deep.equal(['chrM','93']); }); it('should normalize range', function() { var source = getTestSource(); - var range = {contig: 'chrM', start: x, stop: y}; + var range = {contig: 'chrM', start: 1011, stop: 1012}; source.normalizeRange(range).then(normalized => { expect(normalized.to.deep.equal(range)); }).done(); From 7b20ebbf15a0b2a4c0de46e6e89bf958fa926765 Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Tue, 28 Jun 2016 13:00:11 -0700 Subject: [PATCH 095/136] removed genotype.js and variant.js since they were incomplete --- src/main/Genotype.js | 30 --------------- src/main/Variant.js | 89 -------------------------------------------- 2 files changed, 119 deletions(-) delete mode 100644 src/main/Genotype.js delete mode 100644 src/main/Variant.js diff --git a/src/main/Genotype.js b/src/main/Genotype.js deleted file mode 100644 index 79c6084c..00000000 --- a/src/main/Genotype.js +++ /dev/null @@ -1,30 +0,0 @@ -/** - * Class for Genotypes, shared between BAM and GA4GH backends. - * @flow - */ - -import type ContigInterval from './ContigInterval'; -import type Variant from './Variant'; - -export type Strand = '-' | '+'; - -// class Genotype { -// variant: Variant; -// sampleId: string; -// sampleDescription: string; -// processingDescription: string; -// //alleles: List -// expectedAlleleDosage: number; -// referenceReadDepth: number; -// alternativeReadDepth: number; -// readDepth: number; -// minReadDepth: number; -// genotypeQuality: number; -// genotypeLikelihoods: List; -// nonReferenceLikelihoods: List; -// strandBiasComponents: List; -// splitFromMultiAllelic: boolean; -// isPhased: boolean; -// phaseSetId: number; -// phaseQuality: number; -// } diff --git a/src/main/Variant.js b/src/main/Variant.js deleted file mode 100644 index 93eca989..00000000 --- a/src/main/Variant.js +++ /dev/null @@ -1,89 +0,0 @@ -/** - * Class for Variants, shared between BAM and GA4GH backends. - * @flow - */ - -import type ContigInterval from './ContigInterval'; - -export type Strand = '-' | '+'; - -// class Variant { -// contig: ContigInterval; -// start: number; -// end: number; -// referenceAllele: string; -// alternateAllele: string; -// svAllele: StructuralVariant; -// isSomatic: boolean; -// -// constructor(contig: ContigInterval, start: number, end: number -// referenceAllele: string, alternateAllele: string, -// svAllele: StructuralVariant, isSomatic: boolean) { -// this.contig = contig; -// this.start = start; -// this.end = end; -// this.referenceAllele = referenceAllele; -// this.alternateAllele = alternateAllele; -// this.svAllele = svAllele; -// this.isSomatic = isSomatic; -// } -// -// getAlternativeAllele(): string { -// return this.alternateAllele; -// } -// -// getContig(): ContigInterval { -// return this.contig; -// } -// -// getEnd(): number { -// return this.end; -// } -// -// getIsSomatic(): boolean { -// return this.isSomatic; -// } -// -// getReferenceAllele(): string { -// return this.referenceAllele; -// } -// -// getStart(): number { -// return this.start; -// } -// -// getSvAlelle(): StructuralVariant { -// return this.svAllele; -// } -// -// setAlternativeAllele(value: string) { -// this.alternateAllele = value; -// } -// -// setContig(value: Contig) { -// this.contig = value; -// } -// -// setEnd(value: number) { -// this.end = value; -// } -// -// setIsSomatic(value: boolean) { -// this.isSomatic = value; -// } -// -// setReferenceAllele(value: string) { -// this.referenceAllele = value; -// } -// -// setStart(value: number) { -// this.start = value; -// } -// -// setSvAllel(value: StructuralVariant) { -// this.svAllele = value; -// } -// -// } -// -// module.exports = Variant; From 4d1817def8ab2e755ceb307658b86523e4da520e Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Tue, 28 Jun 2016 13:18:17 -0700 Subject: [PATCH 096/136] added featuredatasource to pileup.js file --- src/main/pileup.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/pileup.js b/src/main/pileup.js index aeacf3dd..0799b6a8 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -18,7 +18,7 @@ import VariantDataSource from './sources/VariantDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; import EmptySource from './sources/EmptySource'; -// import FeatureDataSource from './sources/FeatureDataSource'; +import FeatureDataSource from './sources/FeatureDataSource'; // Visualizations import CoverageTrack from './viz/CoverageTrack'; From f223fb92dec8abd50c4043fa4594f8460fc1f96c Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Thu, 16 Jun 2016 20:16:44 -0700 Subject: [PATCH 097/136] completed the genotype feature and variant class files --- src/main/Genotype.js | 31 ++++++++++++++++ src/main/Variant.js | 88 ++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 119 insertions(+) create mode 100644 src/main/Genotype.js create mode 100644 src/main/Variant.js diff --git a/src/main/Genotype.js b/src/main/Genotype.js new file mode 100644 index 00000000..45f6a619 --- /dev/null +++ b/src/main/Genotype.js @@ -0,0 +1,31 @@ +/** + * Class for Genotypes, shared between BAM and GA4GH backends. + */ + +import type ContigInterval from './ContigInterval'; +import type Variant from './Variant'; + +export type Strand = '-' | '+'; + +class Genotype { + variant: Variant; + sampleId: string; + sampleDescription: string; + processingDescription: string; + //alleles: List + expectedAlleleDosage: number; + referenceReadDepth: number; + alternativeReadDepth: number; + readDepth: number; + minReadDepth: number; + genotypeQuality: number; + genotypeLikelihoods: List; + nonReferenceLikelihoods: List; + strandBiasComponents: List; + splitFromMultiAllelic: boolean; + isPhased: boolean; + phaseSetId: number; + phaseQuality: number; + + +} diff --git a/src/main/Variant.js b/src/main/Variant.js new file mode 100644 index 00000000..9dccf9f2 --- /dev/null +++ b/src/main/Variant.js @@ -0,0 +1,88 @@ +/** + * Class for Variants, shared between BAM and GA4GH backends. + */ + +import type ContigInterval from './ContigInterval'; + +export type Strand = '-' | '+'; + +class Variant { + contig: ContigInterval; + start: number; + end: number; + referenceAllele: string; + alternateAllele: string; + svAllele: StructuralVariant; + isSomatic: boolean; + + constructor(contig: ContigInterval, start: number, end: number + referenceAllele: string, alternateAllele: string, + svAllele: StructuralVariant, isSomatic: boolean) { + this.contig = contig; + this.start = start; + this.end = end; + this.referenceAllele = referenceAllele; + this.alternateAllele = alternateAllele; + this.svAllele = svAllele; + this.isSomatic = isSomatic; + } + + getAlternativeAllele(): string { + return this.alternateAllele; + } + + getContig(): ContigInterval { + return this.contig; + } + + getEnd(): number { + return this.end; + } + + getIsSomatic(): boolean { + return this.isSomatic; + } + + getReferenceAllele(): string { + return this.referenceAllele; + } + + getStart(): number { + return this.start; + } + + getSvAlelle(): StructuralVariant { + return this.svAllele; + } + + setAlternatieAllele(value: string) { + this.alternateAllele = value; + } + + setContig(value: Contig) { + this.contig = value; + } + + setEnd(value: number) { + this.end = value; + } + + setIsSomatic(value: boolean) { + this.isSomatic = value; + } + + setReferenceAllele(value: string) { + this.referenceAllele = value; + } + + setStart(value: number) { + this.start = value; + } + + setSvAllel(value: StructuralVariant) { + this.svAllele = value; + } + +} + +module.exports = Variant; From ad608aae517b4c217418db8a75fe7662bb1a1ed4 Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Fri, 17 Jun 2016 11:28:56 -0700 Subject: [PATCH 098/136] Create the FeatureDataSource.js file and tweak Feature.js Variant.js and Genotype.js constructors to take in objects instead --- src/main/FeatureInterface.js | 53 ++++++++++++++++++++++++++++++++++++ src/main/Genotype.js | 2 +- src/main/Variant.js | 3 +- 3 files changed, 56 insertions(+), 2 deletions(-) create mode 100644 src/main/FeatureInterface.js diff --git a/src/main/FeatureInterface.js b/src/main/FeatureInterface.js new file mode 100644 index 00000000..6c29d1d9 --- /dev/null +++ b/src/main/FeatureInterface.js @@ -0,0 +1,53 @@ +/** + * Interface for features + * @flow + */ + +import type ContigInterval from './ContigInterval'; + +export type Strand = '-' | '+'; + +export type Feature = { + featureId: string; + featureType: string; + source: string; + contig: ContigInterval; + start: number; + end: number; + strand: Strand; + value: number; + dbxrefs: Dbxref[]; + parentIds: string[]; + attributes: Object; + + getAttributes(): Object; + getContig(): ContigInterval; + getDbxrefs(): Dbxref[]; + getEnd(): number; + getFeatureId(): string; + getFeatureType(): string; + getParentsIds(): string; + getSource(): string; + getStart(): number; + getStrand(): Strand; + getValue(): number; + + setAttributes(); + setContig(); + setDbxrefs(); + setEnd(); + setFeatureId(); + setParentIds(); + setSource(); + setStart(); + setStrand(); + setValue(); +} + +export type FeatureDataSource = { + rangeChanged: (newRange: GenomeRange) => void; + getFeaturesInRange: (range: ContigInterval) => Feature[]; + on: (event: string, handler: Function) => void; // really => FeatureDataSource + once: (event: string, handler: Function) => void; + off: (event: string) => void; +} diff --git a/src/main/Genotype.js b/src/main/Genotype.js index 45f6a619..2afcf7dd 100644 --- a/src/main/Genotype.js +++ b/src/main/Genotype.js @@ -1,5 +1,6 @@ /** * Class for Genotypes, shared between BAM and GA4GH backends. + * @flow */ import type ContigInterval from './ContigInterval'; @@ -26,6 +27,5 @@ class Genotype { isPhased: boolean; phaseSetId: number; phaseQuality: number; - } diff --git a/src/main/Variant.js b/src/main/Variant.js index 9dccf9f2..ce47c3fb 100644 --- a/src/main/Variant.js +++ b/src/main/Variant.js @@ -1,5 +1,6 @@ /** * Class for Variants, shared between BAM and GA4GH backends. + * @flow */ import type ContigInterval from './ContigInterval'; @@ -55,7 +56,7 @@ class Variant { return this.svAllele; } - setAlternatieAllele(value: string) { + setAlternativeAllele(value: string) { this.alternateAllele = value; } From 338485d8594726a99e7b47a16cb062ed7d1800fc Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Sat, 18 Jun 2016 18:28:06 -0700 Subject: [PATCH 099/136] Completed the FeatureDataSource.js file and also completed most of FeatureDataSource-test.js file --- src/main/Feature.js | 146 -------------------------------- src/main/FeatureInterface.js | 53 ------------ src/main/Genotype.js | 41 +++++---- src/main/Variant.js | 160 +++++++++++++++++------------------ src/main/pileup.js | 2 +- 5 files changed, 101 insertions(+), 301 deletions(-) delete mode 100644 src/main/Feature.js delete mode 100644 src/main/FeatureInterface.js diff --git a/src/main/Feature.js b/src/main/Feature.js deleted file mode 100644 index 83a7deb3..00000000 --- a/src/main/Feature.js +++ /dev/null @@ -1,146 +0,0 @@ -/** - * Class for features - * @flow - */ - 'use strict'; - -import ContigInterval from './ContigInterval'; - -export type Strand = '-' | '+'; - -export type Dbxref = { - accession: string; - db: string; -} - -export type attribute = { - key: string; - value: string; -} - -class Feature { - featureId: string; - featureType: string; - source: string; - range: ContigInterval; - start: number; - end: number; - strand: Strand; - value: number; - dbxrefs: Dbxref[]; - parentIds: string[]; - attributes: attribute[]; //Or use array of attribute objects with key, value - - constructor(input: Object) { - this.featureId = input.featureId; - this.featureType = input.featureType; - // this.source = input.source; - this.start = input.start; - this.end = input.end; - // this.strand = input.strand; - // this.value = input.value; - // this.dbxrefs = input.dbxrefs; - // this.parentIds = input.parentIds; - // this.attributes = input.attributes; - this.range = input.range; - } - - getAttributes(): Object { - return this.attributes; - } - - getContig(): ContigInterval { - return this.range; - } - - getDbxrefs(): Dbxref[] { - return this.dbxrefs; - } - - getEnd(): number { - return this.end; - } - - getFeatureId(): string { - return this.featureId; - } - - getFeatureType(): string { - return this.featureType; - } - - getParentIds(): string { - return this.parentIds; - } - - getSource(): string { - return this.source; - } - - getStart(): number { - return this.start; - } - - getStrand(): Strand { - return this.alignment.alignment.position.reverseStrand ? '-' : '+'; - } - - getValue(): number { - return this.value; - } - - setAttributes(value: Object) { - this.attributes = value; - } - - setContig(value: ContigInterval) { - this.range = value; - } - - setDbxrefs(value: List) { - this.dbxrefs = value; - } - - setEnd(value: number) { - this.end = value; - } - - setFeatureId(value: string) { - this.featureId = value; - } - - setFeatureType(value: string) { - this.featureType = value; - } - - setParentIds(value: List) { - this.parentIds = value; - } - - setSource(value: string) { - this.source = value; - } - - setStart(value: number) { - this.start = value; - } - - setStrand(value: Strand) { - this.strand = value; - } - - setValue(value: number) { - this.value = value; - } - -} - -export type FeatureDataSource = { - rangeChanged: (newRange: GenomeRange) => void; - getFeaturesInRange: (range: ContigInterval) => Feature[]; - on: (event: string, handler: Function) => void; // really => FeatureDataSource - once: (event: string, handler: Function) => void; - off: (event: string) => void; -}; - -module.exports = Feature; diff --git a/src/main/FeatureInterface.js b/src/main/FeatureInterface.js deleted file mode 100644 index 6c29d1d9..00000000 --- a/src/main/FeatureInterface.js +++ /dev/null @@ -1,53 +0,0 @@ -/** - * Interface for features - * @flow - */ - -import type ContigInterval from './ContigInterval'; - -export type Strand = '-' | '+'; - -export type Feature = { - featureId: string; - featureType: string; - source: string; - contig: ContigInterval; - start: number; - end: number; - strand: Strand; - value: number; - dbxrefs: Dbxref[]; - parentIds: string[]; - attributes: Object; - - getAttributes(): Object; - getContig(): ContigInterval; - getDbxrefs(): Dbxref[]; - getEnd(): number; - getFeatureId(): string; - getFeatureType(): string; - getParentsIds(): string; - getSource(): string; - getStart(): number; - getStrand(): Strand; - getValue(): number; - - setAttributes(); - setContig(); - setDbxrefs(); - setEnd(); - setFeatureId(); - setParentIds(); - setSource(); - setStart(); - setStrand(); - setValue(); -} - -export type FeatureDataSource = { - rangeChanged: (newRange: GenomeRange) => void; - getFeaturesInRange: (range: ContigInterval) => Feature[]; - on: (event: string, handler: Function) => void; // really => FeatureDataSource - once: (event: string, handler: Function) => void; - off: (event: string) => void; -} diff --git a/src/main/Genotype.js b/src/main/Genotype.js index 2afcf7dd..79c6084c 100644 --- a/src/main/Genotype.js +++ b/src/main/Genotype.js @@ -8,24 +8,23 @@ import type Variant from './Variant'; export type Strand = '-' | '+'; -class Genotype { - variant: Variant; - sampleId: string; - sampleDescription: string; - processingDescription: string; - //alleles: List - expectedAlleleDosage: number; - referenceReadDepth: number; - alternativeReadDepth: number; - readDepth: number; - minReadDepth: number; - genotypeQuality: number; - genotypeLikelihoods: List; - nonReferenceLikelihoods: List; - strandBiasComponents: List; - splitFromMultiAllelic: boolean; - isPhased: boolean; - phaseSetId: number; - phaseQuality: number; - -} +// class Genotype { +// variant: Variant; +// sampleId: string; +// sampleDescription: string; +// processingDescription: string; +// //alleles: List +// expectedAlleleDosage: number; +// referenceReadDepth: number; +// alternativeReadDepth: number; +// readDepth: number; +// minReadDepth: number; +// genotypeQuality: number; +// genotypeLikelihoods: List; +// nonReferenceLikelihoods: List; +// strandBiasComponents: List; +// splitFromMultiAllelic: boolean; +// isPhased: boolean; +// phaseSetId: number; +// phaseQuality: number; +// } diff --git a/src/main/Variant.js b/src/main/Variant.js index ce47c3fb..93eca989 100644 --- a/src/main/Variant.js +++ b/src/main/Variant.js @@ -7,83 +7,83 @@ import type ContigInterval from './ContigInterval'; export type Strand = '-' | '+'; -class Variant { - contig: ContigInterval; - start: number; - end: number; - referenceAllele: string; - alternateAllele: string; - svAllele: StructuralVariant; - isSomatic: boolean; - - constructor(contig: ContigInterval, start: number, end: number - referenceAllele: string, alternateAllele: string, - svAllele: StructuralVariant, isSomatic: boolean) { - this.contig = contig; - this.start = start; - this.end = end; - this.referenceAllele = referenceAllele; - this.alternateAllele = alternateAllele; - this.svAllele = svAllele; - this.isSomatic = isSomatic; - } - - getAlternativeAllele(): string { - return this.alternateAllele; - } - - getContig(): ContigInterval { - return this.contig; - } - - getEnd(): number { - return this.end; - } - - getIsSomatic(): boolean { - return this.isSomatic; - } - - getReferenceAllele(): string { - return this.referenceAllele; - } - - getStart(): number { - return this.start; - } - - getSvAlelle(): StructuralVariant { - return this.svAllele; - } - - setAlternativeAllele(value: string) { - this.alternateAllele = value; - } - - setContig(value: Contig) { - this.contig = value; - } - - setEnd(value: number) { - this.end = value; - } - - setIsSomatic(value: boolean) { - this.isSomatic = value; - } - - setReferenceAllele(value: string) { - this.referenceAllele = value; - } - - setStart(value: number) { - this.start = value; - } - - setSvAllel(value: StructuralVariant) { - this.svAllele = value; - } - -} - -module.exports = Variant; +// class Variant { +// contig: ContigInterval; +// start: number; +// end: number; +// referenceAllele: string; +// alternateAllele: string; +// svAllele: StructuralVariant; +// isSomatic: boolean; +// +// constructor(contig: ContigInterval, start: number, end: number +// referenceAllele: string, alternateAllele: string, +// svAllele: StructuralVariant, isSomatic: boolean) { +// this.contig = contig; +// this.start = start; +// this.end = end; +// this.referenceAllele = referenceAllele; +// this.alternateAllele = alternateAllele; +// this.svAllele = svAllele; +// this.isSomatic = isSomatic; +// } +// +// getAlternativeAllele(): string { +// return this.alternateAllele; +// } +// +// getContig(): ContigInterval { +// return this.contig; +// } +// +// getEnd(): number { +// return this.end; +// } +// +// getIsSomatic(): boolean { +// return this.isSomatic; +// } +// +// getReferenceAllele(): string { +// return this.referenceAllele; +// } +// +// getStart(): number { +// return this.start; +// } +// +// getSvAlelle(): StructuralVariant { +// return this.svAllele; +// } +// +// setAlternativeAllele(value: string) { +// this.alternateAllele = value; +// } +// +// setContig(value: Contig) { +// this.contig = value; +// } +// +// setEnd(value: number) { +// this.end = value; +// } +// +// setIsSomatic(value: boolean) { +// this.isSomatic = value; +// } +// +// setReferenceAllele(value: string) { +// this.referenceAllele = value; +// } +// +// setStart(value: number) { +// this.start = value; +// } +// +// setSvAllel(value: StructuralVariant) { +// this.svAllele = value; +// } +// +// } +// +// module.exports = Variant; diff --git a/src/main/pileup.js b/src/main/pileup.js index 0799b6a8..aeacf3dd 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -18,7 +18,7 @@ import VariantDataSource from './sources/VariantDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; import EmptySource from './sources/EmptySource'; -import FeatureDataSource from './sources/FeatureDataSource'; +// import FeatureDataSource from './sources/FeatureDataSource'; // Visualizations import CoverageTrack from './viz/CoverageTrack'; From f352e54438a37ff4c02103d594808451b336f530 Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Tue, 28 Jun 2016 13:00:11 -0700 Subject: [PATCH 100/136] removed genotype.js and variant.js since they were incomplete --- src/main/Genotype.js | 30 --------------- src/main/Variant.js | 89 -------------------------------------------- 2 files changed, 119 deletions(-) delete mode 100644 src/main/Genotype.js delete mode 100644 src/main/Variant.js diff --git a/src/main/Genotype.js b/src/main/Genotype.js deleted file mode 100644 index 79c6084c..00000000 --- a/src/main/Genotype.js +++ /dev/null @@ -1,30 +0,0 @@ -/** - * Class for Genotypes, shared between BAM and GA4GH backends. - * @flow - */ - -import type ContigInterval from './ContigInterval'; -import type Variant from './Variant'; - -export type Strand = '-' | '+'; - -// class Genotype { -// variant: Variant; -// sampleId: string; -// sampleDescription: string; -// processingDescription: string; -// //alleles: List -// expectedAlleleDosage: number; -// referenceReadDepth: number; -// alternativeReadDepth: number; -// readDepth: number; -// minReadDepth: number; -// genotypeQuality: number; -// genotypeLikelihoods: List; -// nonReferenceLikelihoods: List; -// strandBiasComponents: List; -// splitFromMultiAllelic: boolean; -// isPhased: boolean; -// phaseSetId: number; -// phaseQuality: number; -// } diff --git a/src/main/Variant.js b/src/main/Variant.js deleted file mode 100644 index 93eca989..00000000 --- a/src/main/Variant.js +++ /dev/null @@ -1,89 +0,0 @@ -/** - * Class for Variants, shared between BAM and GA4GH backends. - * @flow - */ - -import type ContigInterval from './ContigInterval'; - -export type Strand = '-' | '+'; - -// class Variant { -// contig: ContigInterval; -// start: number; -// end: number; -// referenceAllele: string; -// alternateAllele: string; -// svAllele: StructuralVariant; -// isSomatic: boolean; -// -// constructor(contig: ContigInterval, start: number, end: number -// referenceAllele: string, alternateAllele: string, -// svAllele: StructuralVariant, isSomatic: boolean) { -// this.contig = contig; -// this.start = start; -// this.end = end; -// this.referenceAllele = referenceAllele; -// this.alternateAllele = alternateAllele; -// this.svAllele = svAllele; -// this.isSomatic = isSomatic; -// } -// -// getAlternativeAllele(): string { -// return this.alternateAllele; -// } -// -// getContig(): ContigInterval { -// return this.contig; -// } -// -// getEnd(): number { -// return this.end; -// } -// -// getIsSomatic(): boolean { -// return this.isSomatic; -// } -// -// getReferenceAllele(): string { -// return this.referenceAllele; -// } -// -// getStart(): number { -// return this.start; -// } -// -// getSvAlelle(): StructuralVariant { -// return this.svAllele; -// } -// -// setAlternativeAllele(value: string) { -// this.alternateAllele = value; -// } -// -// setContig(value: Contig) { -// this.contig = value; -// } -// -// setEnd(value: number) { -// this.end = value; -// } -// -// setIsSomatic(value: boolean) { -// this.isSomatic = value; -// } -// -// setReferenceAllele(value: string) { -// this.referenceAllele = value; -// } -// -// setStart(value: number) { -// this.start = value; -// } -// -// setSvAllel(value: StructuralVariant) { -// this.svAllele = value; -// } -// -// } -// -// module.exports = Variant; From c78c4245e8359b37369c2f54421660fce482224a Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Tue, 28 Jun 2016 13:22:35 -0700 Subject: [PATCH 101/136] finished merge conflicts in RemoteRequestjs --- src/test/sources/FeatureDataSource-test.js | 1 + 1 file changed, 1 insertion(+) diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js index 4c40a8db..afe5f82f 100644 --- a/src/test/sources/FeatureDataSource-test.js +++ b/src/test/sources/FeatureDataSource-test.js @@ -46,6 +46,7 @@ describe('FeatureDataSource', function() { var contigs = source.contigList(); expect(contigs).to.deep.equal(['chrM','93']); }); + //call server.respond it('should normalize range', function() { var source = getTestSource(); From 7d9480b2f318edf06899c4f9ad2ee8ff9b916b90 Mon Sep 17 00:00:00 2001 From: justinzh1 Date: Wed, 29 Jun 2016 12:49:17 -0700 Subject: [PATCH 102/136] Started working on creating featuredatasource-test.js --- src/main/data/FeatureEndpoint.js | 2 +- src/main/sources/FeatureDataSource.js | 9 ++++----- src/{main/data => test}/samplefeature.json | 0 src/test/sources/FeatureDataSource-test.js | 18 +++++++++--------- src/test/sources/samplefeature.json | 12 ++++++++++++ 5 files changed, 26 insertions(+), 15 deletions(-) rename src/{main/data => test}/samplefeature.json (100%) create mode 100644 src/test/sources/samplefeature.json diff --git a/src/main/data/FeatureEndpoint.js b/src/main/data/FeatureEndpoint.js index 26b1400b..d13e8d58 100644 --- a/src/main/data/FeatureEndpoint.js +++ b/src/main/data/FeatureEndpoint.js @@ -39,7 +39,7 @@ class FeatureEndpoint { this.contigList = contigList; } - contigList(): string[] { + getContigList(): string[] { return this.contigList.map(seq => seq.name); } diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index f7aee5ba..9d14e0d9 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -15,7 +15,7 @@ var FEATURES_PER_REQUEST = 200; function createFromFeatureEndpoint(remoteSource: FeatureEndpoint): BigBedSource { // Collection of genes that have already been loaded. var features: {[key:string]: feature} = {}; //TODO features - + var contigList = remoteSource.getContigList(); // Ranges for which we have complete information -- no need to hit network. var coveredRanges: Array> = []; @@ -70,15 +70,14 @@ function createFromFeatureEndpoint(remoteSource: FeatureEndpoint): BigBedSource } }).done() }, - getRange, - getRangeAsString, + // getRange, + // getRangeAsString, contigList: () => contigList, - normalizeRange, + // normalizeRange, getFeaturesInRange, // These are here to make Flow happy. on: () => {}, - once: () -> {}, off: () => {}, trigger: () => {} }; diff --git a/src/main/data/samplefeature.json b/src/test/samplefeature.json similarity index 100% rename from src/main/data/samplefeature.json rename to src/test/samplefeature.json diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js index afe5f82f..a71249ec 100644 --- a/src/test/sources/FeatureDataSource-test.js +++ b/src/test/sources/FeatureDataSource-test.js @@ -15,7 +15,7 @@ describe('FeatureDataSource', function() { var server: any = null, response; before(function () { - return new RemoteFile('../../main/samplefeature').getAllString().then(data => { + return new RemoteFile('samplefeature.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); server.respondWith('GET', '/features/chrM?start=1011&end=1012', [200, { "Content-Type": "application/json" }, response]); @@ -44,17 +44,17 @@ describe('FeatureDataSource', function() { it('should fetch contigs', function() { var source = getTestSource(); var contigs = source.contigList(); - expect(contigs).to.deep.equal(['chrM','93']); + expect(contigs).to.deep.equal(['chrM','93']); //Modify this to match actual data }); //call server.respond - it('should normalize range', function() { - var source = getTestSource(); - var range = {contig: 'chrM', start: 1011, stop: 1012}; - source.normalizeRange(range).then(normalized => { - expect(normalized.to.deep.equal(range)); - }).done(); - }); + // it('should normalize range', function() { + // var source = getTestSource(); + // var range = {contig: 'chrM', start: 1011, stop: 1012}; + // source.normalizeRange(range).then(normalized => { + // expect(normalized.to.deep.equal(range)); + // }).done(); + // }); it('should extract features in a range from a given endpoint', function(done) { this.timeout(5000); diff --git a/src/test/sources/samplefeature.json b/src/test/sources/samplefeature.json new file mode 100644 index 00000000..cee3e7a3 --- /dev/null +++ b/src/test/sources/samplefeature.json @@ -0,0 +1,12 @@ +[{ + "rest": "4ee7469a-b468-429b-a109-07a484817037", + "contig": "chrM", + "start": 1107, + "end": 1200 +}, { + "rest": "e105ce29-a840-4fc6-819f-a9aac5166163", + "contig": "chrM", + "start": 1011, + "end": 1012 +}] + From 692041a4233d77859052a8b01586aff5fc433d25 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Fri, 1 Jul 2016 17:24:57 -0700 Subject: [PATCH 103/136] completed generic feature visualization --- src/main/data/FeatureEndpoint.js | 72 ++++------ src/main/pileup.js | 13 +- src/main/sources/FeatureDataSource.js | 149 ++++++++++++-------- src/main/viz/FeatureTrack.js | 112 +++++++++++++++ src/test/samplefeature.json | 12 -- src/test/sources/FeatureDataSource-test.js | 105 ++++++-------- src/test/sources/GenotypeDataSource-test.js | 1 - src/test/sources/samplefeature.json | 12 -- test-data/features-chrM-1000-1200.json | 6 +- 9 files changed, 282 insertions(+), 200 deletions(-) create mode 100644 src/main/viz/FeatureTrack.js delete mode 100644 src/test/samplefeature.json delete mode 100644 src/test/sources/samplefeature.json diff --git a/src/main/data/FeatureEndpoint.js b/src/main/data/FeatureEndpoint.js index d13e8d58..d31f0861 100644 --- a/src/main/data/FeatureEndpoint.js +++ b/src/main/data/FeatureEndpoint.js @@ -7,56 +7,36 @@ // import Q from 'q'; import type RemoteRequest from '../RemoteRequest'; -//TODO import bedrow here - -export type FeatureRecord = { - featureId: string; - featureType: string; - start: number; - end: number; - range: ContigInterval + +type Feature = { + id: string; + featureType: string; + contig: string; + start: number; + stop: number; } -function unpackFeatures(dataView: DataView, start: number, end: number): Array { - // TODO: use jBinary bitfield for this - var features: Array = []; - // basePairs.length = dataView.byteLength * 4; // pre-allocate - for (var i = 0; i < dataView.byteLength; i++) { - var packed = dataView.getUint8(i); - features[i] = String.fromCharCode(packed); - } - // Remove base pairs from the end if the sequence terminated mid-byte. - // features.length = numBasePairs; //TODO Determine length +function extractFeatures(features: Object): Feature[] { return features; } class FeatureEndpoint { - remoteRequest: RemoteRequest; - contigList: FeatureRecord[]; - - constructor(remoteRequest: RemoteRequest, contigList: FeatureRecord[]) { - this.remoteRequest = remoteRequest; - this.contigList = contigList; - } - - getContigList(): string[] { - return this.contigList.map(seq => seq.name); - } - - /** - * Returns the Features in contig:start-stop. - * The range is inclusive and zero-based. - * Returns empty string if no data is available on this range. - */ - - getFeaturesInRange(contig: string, start: number, stop: number): Q.Promise { - if (start > stop) { - throw `Requested a range with start > stop (${start}, ${stop})`; - } - return this.remoteRequest.get(contig, start, stop).then(buffer => { - var dataView = new DataView(buffer); - var d = unpackFeatures(dataView, start, stop).join(''); - return d; - }); - } + remoteRequest: RemoteRequest; + + constructor(remoteRequest: RemoteRequest) { + this.remoteRequest = remoteRequest; + } + + getFeaturesInRange(range: ContigInterval): Q.Promise { + var contig = range.contig; + var start = range.interval.start; + var stop = range.interval.stop; + + return this.remoteRequest.get(contig, start, stop).then(object => { + var d = extractFeatures(object); + return d; + }); + } } + +module.exports = FeatureEndpoint; diff --git a/src/main/pileup.js b/src/main/pileup.js index aeacf3dd..06f24873 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -12,9 +12,11 @@ import ReactDOM from 'react-dom'; // Data sources import TwoBitDataSource from './sources/TwoBitDataSource'; +import ReferenceDataSource from './sources/ReferenceDataSource'; import BigBedDataSource from './sources/BigBedDataSource'; import VcfDataSource from './sources/VcfDataSource'; import VariantDataSource from './sources/VariantDataSource'; +import GenotypeDataSource from './sources/GenotypeDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; import EmptySource from './sources/EmptySource'; @@ -23,11 +25,13 @@ import EmptySource from './sources/EmptySource'; // Visualizations import CoverageTrack from './viz/CoverageTrack'; import GenomeTrack from './viz/GenomeTrack'; -import GeneTrack from './viz/GeneTrack'; //use this for features +import GeneTrack from './viz/GeneTrack'; +import FeatureTrack from './viz/FeatureTrack'; import LocationTrack from './viz/LocationTrack'; import PileupTrack from './viz/PileupTrack'; import ScaleTrack from './viz/ScaleTrack'; import VariantTrack from './viz/VariantTrack'; +import GenotypeTrack from './viz/GenotypeTrack'; import Root from './Root'; type GenomeRange = { @@ -126,7 +130,10 @@ var pileup = { ga4gh: GA4GHDataSource.create, vcf: VcfDataSource.create, variants: VariantDataSource.create, + genotypes: GenotypeDataSource.create, + features: FeatureDataSource.create, twoBit: TwoBitDataSource.create, + reference: ReferenceDataSource.create, bigBed: BigBedDataSource.create, empty: EmptySource.create }, @@ -134,12 +141,14 @@ var pileup = { coverage: makeVizObject(CoverageTrack), genome: makeVizObject(GenomeTrack), genes: makeVizObject(GeneTrack), + features: makeVizObject(FeatureTrack), location: makeVizObject(LocationTrack), scale: makeVizObject(ScaleTrack), variants: makeVizObject(VariantTrack), + genotypes: makeVizObject(GenotypeTrack), pileup: makeVizObject(PileupTrack) }, - version: '0.6.8' + version: '0.6.6' }; module.exports = pileup; diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index 9d14e0d9..e63b0465 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -1,79 +1,99 @@ - /** @flow */ +/** + * The "glue" between TwoBit.js and GenomeTrack.js. + * + * GenomeTrack is pure view code -- it renders data which is already in-memory + * in the browser. + * + * TwoBit is purely for data parsing and fetching. It only knows how to return + * promises for various genome features. + * + * This code acts as a bridge between the two. It maintains a local version of + * the data, fetching remote data and informing the view when it becomes + * available. + * + * @flow + */ 'use strict'; -import BigBedSource from './BigBedDataSource'; +import Q from 'q'; +import _ from 'underscore'; +import {Events} from 'backbone'; + import ContigInterval from '../ContigInterval'; import RemoteRequest from '../RemoteRequest'; import FeatureEndpoint from '../data/FeatureEndpoint'; -import Interval from '../Interval'; -import Q from 'q'; -import _ from 'underscore'; -import { Events } from 'backbone'; +import type {Feature} from '../data/FeatureEndPoint'; + +// Flow type for export. +export type FeatureDataSource = { + rangeChanged: (newRange: GenomeRange) => void; + getFeaturesInRange: (range: ContigInterval) => Feature[]; + on: (event: string, handler: Function) => void; + off: (event: string) => void; + trigger: (event: string, ...args:any) => void; +} + + +// Requests for 2bit ranges are expanded to begin & end at multiples of this +// constant. Doing this means that panning typically won't require +// additional network requests. +var BASE_PAIRS_PER_FETCH = 1000; -var FEATURES_PER_REQUEST = 200; +function expandRange(range: ContigInterval) { + var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; + var newStart = Math.max(1, roundDown(range.start())), + newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); + + return new ContigInterval(range.contig, newStart, newStop); +} + +function featureKey(f: Feature): string { + return `${f.contig}:${f.start}`; +} + + +function createFromFeatureUrl(remoteSource: FeatureEndpoint): FeatureDataSource { + var features: {[key: string]: Feature} = {}; -function createFromFeatureEndpoint(remoteSource: FeatureEndpoint): BigBedSource { - // Collection of genes that have already been loaded. - var features: {[key:string]: feature} = {}; //TODO features - var contigList = remoteSource.getContigList(); // Ranges for which we have complete information -- no need to hit network. - var coveredRanges: Array> = []; + var coveredRanges: ContigInterval[] = []; - function addFeature(newfeature) { - if (!feature[newFeature.featureId]) { - feature[newFeature.featureId] = newFeature; + function addFeature(f: Feature) { + var key = featureKey(f); + if (!features[key]) { + features[key] = f; } } - function getFeaturesInRange(range: ContigInterval): Feature[] { - if (!range) return []; - var results = []; - _.each(Feature, feature => { - if (range.intersects(feature.range)) { - results.push(feature); - } - }); - return results; - } - - function fetch(range: ContigInterval) { + function fetch(range: GenomeRange) { + var interval = new ContigInterval(range.contig, range.start, range.stop); // Check if this interval is already in the cache. - if (range.isCoveredBy(coveredRanges)) { + if (interval.isCoveredBy(coveredRanges)) { return Q.when(); } - coveredRanges.push(range); - coveredRanges = ContigInterval.coalesce(coveredRanges); + interval = expandRange(interval); - /** Modify URL */ - remoteSource.remoteRequest.url += range.contig.contig + "?start=" + range.start + "&end=" + range.stop; + // "Cover" the range immediately to prevent duplicate fetches. + coveredRanges.push(interval); + coveredRanges = ContigInterval.coalesce(coveredRanges); + return remoteSource.getFeaturesInRange(interval).then(features => { + features.forEach(feature => addFeature(feature)); + o.trigger('newdata', interval); + }); + } - return remoteSource.getFeaturesInRange(range.contig.contig, range.start, range.end); + function getFeaturesInRange(range: ContigInterval): Feature[] { + if (!range) return []; // XXX why would this happen? + var x = _.filter(features, f => range.chrContainsLocus(f.contig, f.start)); + return x; } var o = { rangeChanged: function(newRange: GenomeRange) { - normalizeRange(newRange).then(r => { - var range = new ContigInterval(r.contig, r.start, r.stop); - - if (range.isCoveredBy(coveredRanges)) { - return; - } - - var newRanges = range.complementIntervals(coveredRanges); - coveredRanges.push(range); - coveredRanges = ContigInterval.coalesce(coveredRanges); - - for (var newRange of newRanges) { - fetch(newRange); - } - }).done() + fetch(newRange).done(); }, - // getRange, - // getRangeAsString, - contigList: () => contigList, - // normalizeRange, getFeaturesInRange, // These are here to make Flow happy. @@ -81,20 +101,27 @@ function createFromFeatureEndpoint(remoteSource: FeatureEndpoint): BigBedSource off: () => {}, trigger: () => {} }; - _.extend(o, Events); // Make this an event emitter return o; -}; +} -function create(data: {url: string}): BigBedSource { - var url = data.url; - if (!url) { - throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); - } - return createFromFeatureEndpoint(new RemoteRequest(url)); +function create(data: {url?:string, key?:string}): FeatureDataSource { + var {url, key} = data; + if (!url) { + throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); + } + // verify key was correctly set + if (!key) { + throw new Error(`Missing key from track: ${JSON.stringify(data)}`); + } + var request = new RemoteRequest(url, key); + var endpoint = new FeatureEndpoint(request); + return createFromFeatureUrl(endpoint); } + module.exports = { - create + create, + createFromFeatureUrl }; diff --git a/src/main/viz/FeatureTrack.js b/src/main/viz/FeatureTrack.js new file mode 100644 index 00000000..4e9e87e6 --- /dev/null +++ b/src/main/viz/FeatureTrack.js @@ -0,0 +1,112 @@ +/** + * Visualization of features, including exons and coding regions. + * @flow + */ +'use strict'; + +import type {FeatureDataSource} from '../sources/FeatureDataSource'; +import type {Feature} from '../data/FeatureEndpoint'; + +import type {VizProps} from '../VisualizationWrapper'; +import type {Scale} from './d3utils'; + +import React from 'react'; +import ReactDOM from 'react-dom'; +import _ from 'underscore'; +import shallowEquals from 'shallow-equals'; + +import Interval from '../Interval'; +import d3utils from './d3utils'; +import scale from '../scale'; +import ContigInterval from '../ContigInterval'; +import canvasUtils from './canvas-utils'; +import dataCanvas from 'data-canvas'; +import style from '../style'; + + +class FeatureTrack extends React.Component { + props: VizProps & { source: FeatureDataSource }; + state: {features: Feature[]}; + + constructor(props: VizProps) { + super(props); + this.state = { + features: [] + }; + } + + render(): any { + return ; + } + + componentDidMount() { + // Visualize new reference data as it comes in from the network. + this.props.source.on('newdata', (range) => { + this.setState({ + features: this.props.source.getFeaturesInRange(range) + }); + }); + + this.updateVisualization(); + } + + getScale(): Scale { + return d3utils.getTrackScale(this.props.range, this.props.width); + } + + componentDidUpdate(prevProps: any, prevState: any) { + if (!shallowEquals(prevProps, this.props) || + !shallowEquals(prevState, this.state)) { + this.updateVisualization(); + } + } + + updateVisualization() { + var canvas = ReactDOM.findDOMNode(this), + {width, height} = this.props, + genomeRange = this.props.range; + + var range = new ContigInterval(genomeRange.contig, genomeRange.start, genomeRange.stop); + var y = height - style.VARIANT_HEIGHT - 1; + + // Hold off until height & width are known. + if (width === 0) return; + + var sc = this.getScale(), + // We can't clamp scale directly because of offsetPx. + clampedScale = scale.linear() + .domain([sc.invert(0), sc.invert(width)]) + .range([0, width]) + .clamp(true); + + d3utils.sizeCanvas(canvas, width, height); + + var ctx = dataCanvas.getDataContext(canvasUtils.getContext(canvas)); + ctx.reset(); + ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); + + var featureLineY = Math.round(height / 4); + var textIntervals = []; // x-intervals with rendered feature names, to avoid over-drawing. + // TODO: don't pull in features via state. + ctx.font = `${style.GENE_FONT_SIZE}px ${style.GENE_FONT}`; + ctx.textAlign = 'center'; + this.state.features.forEach(feature => { + var position = new ContigInterval(feature.contig, feature.start, feature.stop); + if (!position.chrIntersects(range)) return; + ctx.pushObject(feature); + ctx.lineWidth = 1; + ctx.strokeStyle = style.GENE_COLOR; + ctx.fillStyle = style.GENE_COLOR; + + var x = Math.round(sc(feature.start)); + var width = Math.round(sc(feature.stop) - sc(feature.start)); + ctx.fillRect(x - 0.5, y - 0.5, width, style.VARIANT_HEIGHT); + ctx.strokeRect(x - 0.5, y - 0.5, width, style.VARIANT_HEIGHT); + ctx.popObject(); + }); + } +} + +FeatureTrack.displayName = 'features'; + +module.exports = FeatureTrack; diff --git a/src/test/samplefeature.json b/src/test/samplefeature.json deleted file mode 100644 index cee3e7a3..00000000 --- a/src/test/samplefeature.json +++ /dev/null @@ -1,12 +0,0 @@ -[{ - "rest": "4ee7469a-b468-429b-a109-07a484817037", - "contig": "chrM", - "start": 1107, - "end": 1200 -}, { - "rest": "e105ce29-a840-4fc6-819f-a9aac5166163", - "contig": "chrM", - "start": 1011, - "end": 1012 -}] - diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js index a71249ec..6c5224b2 100644 --- a/src/test/sources/FeatureDataSource-test.js +++ b/src/test/sources/FeatureDataSource-test.js @@ -8,76 +8,53 @@ import sinon from 'sinon'; import ContigInterval from '../../main/ContigInterval'; import FeatureDataSource from '../../main/sources/FeatureDataSource'; import RemoteFile from '../../main/RemoteFile'; -// import sample from '../../main/samplefeature'; -// var url = "http://localhost:8080/features/chrM?start=0&end=1000"; describe('FeatureDataSource', function() { - var server: any = null, response; + var server: any = null, response; - before(function () { - return new RemoteFile('samplefeature.json').getAllString().then(data => { - response = data; - server = sinon.fakeServer.create(); - server.respondWith('GET', '/features/chrM?start=1011&end=1012', [200, { "Content-Type": "application/json" }, response]); - server.respondWith('GET', '/features/chrM?start=1107&end=1200', [200, { "Content-Type": "application/json" }, response]); - }); + before(function () { + return new RemoteFile('/test-data/features-chrM-1000-1200.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/features/chrM?start=1000&end=2000&key=test', [200, { "Content-Type": "application/json" }, response]); }); + }); - after(function () { - server.restore(); - }); - - function getTestSource() { - var source = FeatureDataSource.create({ - url: '/features', - contigList: [{ - name:"chrM", - length: 93 - }, { - name:"chrM", - length: 1 - }] - }); - return source; - } + after(function () { + server.restore(); + }); - it('should fetch contigs', function() { - var source = getTestSource(); - var contigs = source.contigList(); - expect(contigs).to.deep.equal(['chrM','93']); //Modify this to match actual data + function getTestSource() { + var source = FeatureDataSource.create({ + url: '/features', + key: 'test' }); - //call server.respond - - // it('should normalize range', function() { - // var source = getTestSource(); - // var range = {contig: 'chrM', start: 1011, stop: 1012}; - // source.normalizeRange(range).then(normalized => { - // expect(normalized.to.deep.equal(range)); - // }).done(); - // }); - - it('should extract features in a range from a given endpoint', function(done) { - this.timeout(5000); - var source = getTestSource(); - - // No features fetched initially - var testrange = new ContigInterval('chrM', 1011, 1012); - var test = source.getFeaturesInRange(testrange[0], testrange[1], testrange[2]); - expect(test).to.deep.equal([]); - - // Fetching that one feature should cache its entire block. - source.on('newdata', () => { - var tests = source.getFeaturesInRange(testrange[0], testrange[1], testrange[2]); - expect(tests).to.have.length(1); - - var test = tests[0]; - expect(test.name).to.equal('chrM'); - done(); - }); - source.rangeChanged({ - contig: testrange.contig, - start: testrange.start(), - stop: testrange.stop() - }); + return source; + } + + it('should extract features in a range', function(done) { + var source = getTestSource(); + + // No genes fetched initially + var range = new ContigInterval('chrM', 1000, 1200); + var emptyFeatures = source.getFeaturesInRange(range); + expect(emptyFeatures).to.deep.equal([]); + + // Fetching that one gene should cache its entire block. + source.on('newdata', () => { + var features = source.getFeaturesInRange(range); + expect(features).to.have.length(2); + + var feature = features[0]; + expect(feature.start).to.equal(1107); + expect(feature.contig).to.equal('chrM'); + done(); + }); + source.rangeChanged({ + contig: range.contig, + start: range.start(), + stop: range.stop() }); + server.respond(); + }); }); diff --git a/src/test/sources/GenotypeDataSource-test.js b/src/test/sources/GenotypeDataSource-test.js index 67ca5162..74c7cc4c 100644 --- a/src/test/sources/GenotypeDataSource-test.js +++ b/src/test/sources/GenotypeDataSource-test.js @@ -41,7 +41,6 @@ describe('GenotypeDataSource', function() { source.on('newdata', () => { var genotypes = source.getFeaturesInRange(range); - console.log(genotypes); expect(genotypes).to.have.length(3); expect(genotypes[1].sampleIds).to.contain('sample1'); expect(genotypes[1].variant.contig).to.equal('chrM'); diff --git a/src/test/sources/samplefeature.json b/src/test/sources/samplefeature.json deleted file mode 100644 index cee3e7a3..00000000 --- a/src/test/sources/samplefeature.json +++ /dev/null @@ -1,12 +0,0 @@ -[{ - "rest": "4ee7469a-b468-429b-a109-07a484817037", - "contig": "chrM", - "start": 1107, - "end": 1200 -}, { - "rest": "e105ce29-a840-4fc6-819f-a9aac5166163", - "contig": "chrM", - "start": 1011, - "end": 1012 -}] - diff --git a/test-data/features-chrM-1000-1200.json b/test-data/features-chrM-1000-1200.json index 2ba90728..c6285852 100644 --- a/test-data/features-chrM-1000-1200.json +++ b/test-data/features-chrM-1000-1200.json @@ -1,10 +1,12 @@ [{ - "rest": "4ee7469a-b468-429b-a109-07a484817037", + "id": "4ee7469a-b468-429b-a109-07a484817037", + "featureType": "peak", "contig": "chrM", "start": 1107, "end": 1200 }, { - "rest": "e105ce29-a840-4fc6-819f-a9aac5166163", + "id": "e105ce29-a840-4fc6-819f-a9aac5166163", + "featureType": "peak", "contig": "chrM", "start": 1011, "end": 1012 From c69c8a73efa2f01fd80bc18b85ab09ea8e593a10 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Mon, 4 Jul 2016 11:20:49 -0700 Subject: [PATCH 104/136] added check for negative values and restricted alignment fetch size --- src/main/sources/GA4GHDataSource.js | 6 ++++++ src/main/viz/FeatureTrack.js | 11 +---------- 2 files changed, 7 insertions(+), 10 deletions(-) diff --git a/src/main/sources/GA4GHDataSource.js b/src/main/sources/GA4GHDataSource.js index bf3396c4..e978fdf6 100644 --- a/src/main/sources/GA4GHDataSource.js +++ b/src/main/sources/GA4GHDataSource.js @@ -14,6 +14,7 @@ import ContigInterval from '../ContigInterval'; import GA4GHAlignment from '../GA4GHAlignment'; var ALIGNMENTS_PER_REQUEST = 200; // TODO: explain this choice. +var MAX_BASE_PAIRS_TO_FETCH = 40000; // Genome ranges are rounded to multiples of this for fetching. @@ -86,6 +87,11 @@ function create(spec: GA4GHSpec): AlignmentDataSource { function fetchAlignmentsForInterval(range: ContigInterval, pageToken: ?string, numRequests: number) { + + var span = range.length(); + if (span > MAX_BASE_PAIRS_TO_FETCH) { + return Q.when(); // empty promise + } var xhr = new XMLHttpRequest(); var endpoint = url + "/" + range.contig + "?start=" + range.start() + "&end=" + range.stop()+"&key="+spec.readGroupId; diff --git a/src/main/viz/FeatureTrack.js b/src/main/viz/FeatureTrack.js index 4e9e87e6..fc780fcf 100644 --- a/src/main/viz/FeatureTrack.js +++ b/src/main/viz/FeatureTrack.js @@ -12,10 +12,8 @@ import type {Scale} from './d3utils'; import React from 'react'; import ReactDOM from 'react-dom'; -import _ from 'underscore'; import shallowEquals from 'shallow-equals'; -import Interval from '../Interval'; import d3utils from './d3utils'; import scale from '../scale'; import ContigInterval from '../ContigInterval'; @@ -72,12 +70,7 @@ class FeatureTrack extends React.Component { // Hold off until height & width are known. if (width === 0) return; - var sc = this.getScale(), - // We can't clamp scale directly because of offsetPx. - clampedScale = scale.linear() - .domain([sc.invert(0), sc.invert(width)]) - .range([0, width]) - .clamp(true); + var sc = this.getScale(); d3utils.sizeCanvas(canvas, width, height); @@ -85,8 +78,6 @@ class FeatureTrack extends React.Component { ctx.reset(); ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); - var featureLineY = Math.round(height / 4); - var textIntervals = []; // x-intervals with rendered feature names, to avoid over-drawing. // TODO: don't pull in features via state. ctx.font = `${style.GENE_FONT_SIZE}px ${style.GENE_FONT}`; ctx.textAlign = 'center'; From bcd3f1f6b9f8378883da4a451b7bb0f92fe57c8d Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Mon, 11 Jul 2016 20:27:59 -0700 Subject: [PATCH 105/136] completed gene endpoint --- src/main/data/GeneEndpoint.js | 62 ++ src/main/pileup.js | 4 +- src/main/sources/GeneDataSource.js | 105 +++ src/main/sources/ReferenceDataSource.js | 2 +- src/main/sources/VariantDataSource.js | 4 - src/test/sources/GeneDataSource-test.js | 58 ++ src/test/sources/GenotypeDataSource-test.js | 2 +- test-data/genes-chrM-0-30000.json | 855 ++++++++++++++++++++ 8 files changed, 1085 insertions(+), 7 deletions(-) create mode 100644 src/main/data/GeneEndpoint.js create mode 100644 src/main/sources/GeneDataSource.js create mode 100644 src/test/sources/GeneDataSource-test.js create mode 100644 test-data/genes-chrM-0-30000.json diff --git a/src/main/data/GeneEndpoint.js b/src/main/data/GeneEndpoint.js new file mode 100644 index 00000000..aebb6964 --- /dev/null +++ b/src/main/data/GeneEndpoint.js @@ -0,0 +1,62 @@ +/** + * This module defines a parser for the 2bit file format. + * See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 + * @flow + */ +'use strict'; + +// import Q from 'q'; +import type RemoteRequest from '../RemoteRequest'; +import Interval from '../Interval'; +import ContigInterval from '../../main/ContigInterval'; + +function extractGenes(genes: Object): Gene[] { + var mapped = genes.map(g => extractGene(g)); + return mapped; +} + +function extractGene(f: Object): Gene { + var pos = new ContigInterval(f.position.referenceName, Number(f.position.start), Number(f.position.end)); + // parse out exon intervals + var exons = f.exons + .map(ex => new Interval(ex.region.start, ex.region.end)); + + // parse strand to positive or negative boolean + var strand; + if (f.strand === false) { + strand = "-"; + } else { + strand = "+"; + } + return { + position: pos, + id: f.id, + strand: strand, // either + or - + codingRegion: new Interval(Number(f.codingRegion.start), Number(f.codingRegion.end)), + geneId: f.geneId, + name: f.name, + exons + }; +} + + +class GeneEndpoint { + remoteRequest: RemoteRequest; + + constructor(remoteRequest: RemoteRequest) { + this.remoteRequest = remoteRequest; + } + + getGenesInRange(range: ContigInterval): Q.Promise { + var contig = range.contig; + var start = range.interval.start; + var stop = range.interval.stop; + + return this.remoteRequest.get(contig, start, stop).then(object => { + var d = extractGenes(object); + return d; + }); + } +} + +module.exports = GeneEndpoint; diff --git a/src/main/pileup.js b/src/main/pileup.js index 06f24873..c8145627 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -16,6 +16,7 @@ import ReferenceDataSource from './sources/ReferenceDataSource'; import BigBedDataSource from './sources/BigBedDataSource'; import VcfDataSource from './sources/VcfDataSource'; import VariantDataSource from './sources/VariantDataSource'; +import GeneDataSource from './sources/GeneDataSource'; import GenotypeDataSource from './sources/GenotypeDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; @@ -26,7 +27,7 @@ import EmptySource from './sources/EmptySource'; import CoverageTrack from './viz/CoverageTrack'; import GenomeTrack from './viz/GenomeTrack'; import GeneTrack from './viz/GeneTrack'; -import FeatureTrack from './viz/FeatureTrack'; +import FeatureTrack from './viz/FeatureTrack'; import LocationTrack from './viz/LocationTrack'; import PileupTrack from './viz/PileupTrack'; import ScaleTrack from './viz/ScaleTrack'; @@ -135,6 +136,7 @@ var pileup = { twoBit: TwoBitDataSource.create, reference: ReferenceDataSource.create, bigBed: BigBedDataSource.create, + genes: GeneDataSource.create, empty: EmptySource.create }, viz: { diff --git a/src/main/sources/GeneDataSource.js b/src/main/sources/GeneDataSource.js new file mode 100644 index 00000000..fb1935e1 --- /dev/null +++ b/src/main/sources/GeneDataSource.js @@ -0,0 +1,105 @@ +/* @flow */ +'use strict'; + +import type {Strand} from '../Alignment'; + +import _ from 'underscore'; +import Q from 'q'; +import {Events} from 'backbone'; + +import ContigInterval from '../ContigInterval'; +import Interval from '../Interval'; +import type { BigBedSource, Gene } from './BigBedDataSource'; +import RemoteRequest from '../RemoteRequest'; +import GeneEndpoint from '../data/GeneEndpoint'; + +var BASE_PAIRS_PER_FETCH = 5000; + +function expandRange(range: ContigInterval) { + var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; + var newStart = Math.max(1, roundDown(range.start())), + newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); + + return new ContigInterval(range.contig, newStart, newStop); +} + +function createFromGeneUrl(remoteSource: GeneEndpoint): BigBedSource { + // Collection of genes that have already been loaded. + var genes: {[key:string]: Gene} = {}; + + // Ranges for which we have complete information -- no need to hit network. + var coveredRanges: Array> = []; + + function addGene(newGene) { + if (!genes[newGene.id]) { + genes[newGene.id] = newGene; + } + } + + function getGenesInRange(range: ContigInterval): Gene[] { + if (!range) return []; + var results = []; + _.each(genes, gene => { + if (range.intersects(gene.position)) { + results.push(gene); + } + }); + return results; + } + + function fetch(range: GenomeRange) { + var interval = new ContigInterval(range.contig, range.start, range.stop); + + // Check if this interval is already in the cache. + if (interval.isCoveredBy(coveredRanges)) { + return Q.when(); + } + + interval = expandRange(interval); + + coveredRanges.push(interval); + coveredRanges = ContigInterval.coalesce(coveredRanges); + + return remoteSource.getGenesInRange(interval).then(genes => { + genes.forEach(gene => addGene(gene)); + //we have new data from our internal block range + o.trigger('newdata', interval); + }); + } + + var o = { + rangeChanged: function(newRange: GenomeRange) { + fetch(newRange).done(); + }, + getGenesInRange, + + // These are here to make Flow happy. + on: () => {}, + off: () => {}, + trigger: () => {} + }; + _.extend(o, Events); // Make this an event emitter + + return o; +} + +function create(data: {url?:string, key?:string}): BigBedSource { + var url = data.url; + var key = data.key; + if (!url) { + throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); + } + // verify key was correctly set + if (!key) { + throw new Error(`Missing key from track: ${JSON.stringify(data)}`); + } + + var request = new RemoteRequest(url, key); + var endpoint = new GeneEndpoint(request); + return createFromGeneUrl(endpoint); +} + +module.exports = { + create, + createFromGeneUrl +}; diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index 1ded0b77..5e67c760 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -31,7 +31,7 @@ import utils from '../utils'; // Requests for 2bit ranges are expanded to begin & end at multiples of this // constant. Doing this means that panning typically won't require // additional network requests. -var BASE_PAIRS_PER_FETCH = 10000; +var BASE_PAIRS_PER_FETCH = 15000; var MAX_BASE_PAIRS_TO_FETCH = 100000; diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index 59a3539e..b1cad7fc 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -26,10 +26,6 @@ import type {VcfDataSource} from './VcfDataSource'; import RemoteRequest from '../RemoteRequest'; import VariantEndpoint from '../data/VariantEndpoint'; - -// Requests for 2bit ranges are expanded to begin & end at multiples of this -// constant. Doing this means that panning typically won't require -// additional network requests. var BASE_PAIRS_PER_FETCH = 1000; function expandRange(range: ContigInterval) { diff --git a/src/test/sources/GeneDataSource-test.js b/src/test/sources/GeneDataSource-test.js new file mode 100644 index 00000000..5a565d37 --- /dev/null +++ b/src/test/sources/GeneDataSource-test.js @@ -0,0 +1,58 @@ +/* @flow */ +'use strict'; + +import {expect} from 'chai'; + +import sinon from 'sinon'; + +import ContigInterval from '../../main/ContigInterval'; +import RemoteFile from '../../main/RemoteFile'; +import GeneDataSource from '../../main/sources/GeneDataSource'; + +describe('GeneDataSource', function() { + var server: any = null, response; + + before(function () { + return new RemoteFile('/test-data/genes-chrM-0-30000.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/genes/chrM?start=1&end=100000&key=test', [200, { "Content-Type": "application/json" }, response]); + }); + }); + + after(function () { + server.restore(); + }); + + function getTestSource() { + var source = GeneDataSource.create({ + url: '/genes', + key: 'test' + }); + return source; + } + + it('should extract genes in a range', function(done) { + var source = getTestSource(); + + // No genes fetched initially + var range = new ContigInterval('chrM', 0, 100000); + var emptyGenes = source.getGenesInRange(range); + expect(emptyGenes).to.deep.equal([]); + + // Fetching that one gene should cache its entire block. + source.on('newdata', () => { + var genes = source.getGenesInRange(range); + console.log(genes); + + expect(genes).to.have.length(9); + done(); + }); + source.rangeChanged({ + contig: range.contig, + start: range.start(), + stop: range.stop() + }); + server.respond(); + }); +}); diff --git a/src/test/sources/GenotypeDataSource-test.js b/src/test/sources/GenotypeDataSource-test.js index 74c7cc4c..78e1b572 100644 --- a/src/test/sources/GenotypeDataSource-test.js +++ b/src/test/sources/GenotypeDataSource-test.js @@ -6,7 +6,7 @@ import {expect} from 'chai'; import sinon from 'sinon'; -import VariantDataSource from '../../main/sources/GenotypeDataSource'; +import VariantDataSource from '../../main/sources/VariantDataSource'; import ContigInterval from '../../main/ContigInterval'; import RemoteFile from '../../main/RemoteFile'; diff --git a/test-data/genes-chrM-0-30000.json b/test-data/genes-chrM-0-30000.json new file mode 100644 index 00000000..13bf39e9 --- /dev/null +++ b/test-data/genes-chrM-0-30000.json @@ -0,0 +1,855 @@ +[{ + "position": { + "referenceName": "chrM", + "start": 14362, + "end": 24886, + "orientation": {} + }, + "id": "ENST00000541675", + "strand": false, + "codingRegion": { + "start": 14362, + "end": 24886 + }, + "exons": [{ + "exonId": "ENSE00002254515", + "transcriptId": "ENST00000541675", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 24733, + "end": 24886, + "orientation": {} + } + }, { + "exonId": "ENSE00002303227", + "transcriptId": "ENST00000541675", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 18267, + "end": 18369, + "orientation": {} + } + }, { + "exonId": "ENSE00003638984", + "transcriptId": "ENST00000541675", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17914, + "end": 18061, + "orientation": {} + } + }, { + "exonId": "ENSE00003629019", + "transcriptId": "ENST00000541675", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17605, + "end": 17742, + "orientation": {} + } + }, { + "exonId": "ENSE00002285713", + "transcriptId": "ENST00000541675", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17497, + "end": 17504, + "orientation": {} + } + }, { + "exonId": "ENSE00001656010", + "transcriptId": "ENST00000541675", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17232, + "end": 17364, + "orientation": {} + } + }, { + "exonId": "ENSE00001760358", + "transcriptId": "ENST00000541675", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 16853, + "end": 17055, + "orientation": {} + } + }, { + "exonId": "ENSE00003497546", + "transcriptId": "ENST00000541675", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 14969, + "end": 15038, + "orientation": {} + } + }, { + "exonId": "ENSE00003511598", + "transcriptId": "ENST00000541675", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 14362, + "end": 14829, + "orientation": {} + } + }], + "geneId": "ENSG00000227232", + "name": "ENST00000541675" +}, { + "position": { + "referenceName": "chrM", + "start": 14403, + "end": 29570, + "orientation": {} + }, + "id": "ENST00000488147", + "strand": false, + "codingRegion": { + "start": 14403, + "end": 29570 + }, + "exons": [{ + "exonId": "ENSE00001890219", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 29533, + "end": 29570, + "orientation": {} + } + }, { + "exonId": "ENSE00003507205", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 24737, + "end": 24891, + "orientation": {} + } + }, { + "exonId": "ENSE00003477500", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 18267, + "end": 18366, + "orientation": {} + } + }, { + "exonId": "ENSE00003565697", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17914, + "end": 18061, + "orientation": {} + } + }, { + "exonId": "ENSE00003475637", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17605, + "end": 17742, + "orientation": {} + } + }, { + "exonId": "ENSE00003502542", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17232, + "end": 17368, + "orientation": {} + } + }, { + "exonId": "ENSE00003553898", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 16857, + "end": 17055, + "orientation": {} + } + }, { + "exonId": "ENSE00003621279", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 16606, + "end": 16765, + "orientation": {} + } + }, { + "exonId": "ENSE00002030414", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 15795, + "end": 15947, + "orientation": {} + } + }, { + "exonId": "ENSE00001935574", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 15004, + "end": 15038, + "orientation": {} + } + }, { + "exonId": "ENSE00001843071", + "transcriptId": "ENST00000488147", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 14403, + "end": 14501, + "orientation": {} + } + }], + "geneId": "ENSG00000227232", + "name": "ENST00000488147" +}, { + "position": { + "referenceName": "chrM", + "start": 14362, + "end": 29370, + "orientation": {} + }, + "id": "ENST00000423562", + "strand": false, + "codingRegion": { + "start": 14362, + "end": 29370 + }, + "exons": [{ + "exonId": "ENSE00001718035", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 29320, + "end": 29370, + "orientation": {} + } + }, { + "exonId": "ENSE00003603734", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 24737, + "end": 24891, + "orientation": {} + } + }, { + "exonId": "ENSE00003513603", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17914, + "end": 18061, + "orientation": {} + } + }, { + "exonId": "ENSE00003565315", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17605, + "end": 17742, + "orientation": {} + } + }, { + "exonId": "ENSE00003685767", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 17232, + "end": 17368, + "orientation": {} + } + }, { + "exonId": "ENSE00003553898", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 16857, + "end": 17055, + "orientation": {} + } + }, { + "exonId": "ENSE00003621279", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 16606, + "end": 16765, + "orientation": {} + } + }, { + "exonId": "ENSE00002030414", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 15795, + "end": 15947, + "orientation": {} + } + }, { + "exonId": "ENSE00003591210", + "transcriptId": "ENST00000423562", + "strand": false, + "region": { + "referenceName": "chrM", + "start": 14969, + "end": 15038, + 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"ENSE00002234632", + "transcriptId": "ENST00000515242", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 11871, + "end": 12227, + "orientation": {} + } + }, { + "exonId": "ENSE00003608237", + "transcriptId": "ENST00000515242", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 12612, + "end": 12721, + "orientation": {} + } + }, { + "exonId": "ENSE00002306041", + "transcriptId": "ENST00000515242", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 13224, + "end": 14412, + "orientation": {} + } + }], + "geneId": "ENSG00000223972", + "name": "ENST00000515242" +}, { + "position": { + "referenceName": "chrM", + "start": 11868, + "end": 14409, + "orientation": {} + }, + "id": "ENST00000456328", + "strand": true, + "codingRegion": { + "start": 11868, + "end": 14409 + }, + "exons": [{ + "exonId": "ENSE00002234944", + "transcriptId": "ENST00000456328", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 11868, + "end": 12227, + "orientation": {} + } + }, { + "exonId": "ENSE00003582793", + "transcriptId": "ENST00000456328", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 12612, + "end": 12721, + "orientation": {} + } + }, { + "exonId": "ENSE00002312635", + "transcriptId": "ENST00000456328", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 13220, + "end": 14409, + "orientation": {} + } + }], + "geneId": "ENSG00000223972", + "name": "ENST00000456328" +}, { + "position": { + "referenceName": "chrM", + "start": 12009, + "end": 13670, + "orientation": {} + }, + "id": "ENST00000450305", + "strand": true, + "codingRegion": { + "start": 12009, + "end": 13670 + }, + "exons": [{ + "exonId": "ENSE00001948541", + "transcriptId": "ENST00000450305", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 12009, + "end": 12057, + "orientation": {} + } + }, { + "exonId": "ENSE00001671638", + "transcriptId": "ENST00000450305", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 12178, + "end": 12227, + "orientation": {} + } + }, { + "exonId": "ENSE00001758273", + "transcriptId": "ENST00000450305", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 12612, + "end": 12697, + "orientation": {} + } + }, { + "exonId": "ENSE00001799933", + "transcriptId": "ENST00000450305", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 12974, + "end": 13052, + "orientation": {} + } + }, { + "exonId": "ENSE00001746346", + "transcriptId": "ENST00000450305", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 13220, + "end": 13374, + "orientation": {} + } + }, { + "exonId": "ENSE00001863096", + "transcriptId": "ENST00000450305", + "strand": true, + "region": { + "referenceName": "chrM", + "start": 13452, + "end": 13670, + "orientation": {} + } + }], + "geneId": "ENSG00000223972", + "name": "ENST00000450305" +}] From c4b982ba75c6956870a650d4b26cda8c85ee11db Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sat, 20 Aug 2016 14:46:23 -0700 Subject: [PATCH 106/136] removed prepush hooks --- package.json | 4 ---- 1 file changed, 4 deletions(-) diff --git a/package.json b/package.json index ee1217a8..8df01cad 100644 --- a/package.json +++ b/package.json @@ -46,9 +46,6 @@ "url": "https://github.com/hammerlab/pileup.js/issues" }, "homepage": "https://github.com/hammerlab/pileup.js", - "prepush": [ - "lint" - ], "dependencies": { "backbone": "1.1.2", "d3": "^3.5.5", @@ -86,7 +83,6 @@ "number-to-locale-string": "^1.0.0", "parse-data-uri": "^0.2.0", "phantomjs": "1.9.17", - "prepush-hook": "^0.1.0", "react-addons-test-utils": "^0.14.0", "sinon": "^1.12.2", "smash": "0.0.14", From abe0d7503e8bb466b9dc3126238adf676297e014 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 24 Aug 2016 14:42:11 -0700 Subject: [PATCH 107/136] Passing more tests --- src/main/GA4GHAlignment.js | 2 +- src/main/data/FeatureEndpoint.js | 12 ++++-------- src/main/data/GeneEndpoint.js | 3 ++- src/main/data/GenotypeEndpoint.js | 10 ++-------- src/main/data/VariantEndpoint.js | 10 ++++------ src/main/sources/FeatureDataSource.js | 13 ++++--------- src/main/sources/GA4GHDataSource.js | 1 + src/main/sources/GeneDataSource.js | 13 +++---------- src/main/sources/GenotypeDataSource.js | 11 +++-------- src/main/sources/ReferenceDataSource.js | 5 ++--- src/main/sources/VariantDataSource.js | 18 +++++++----------- src/test/sources/FeatureDataSource-test.js | 5 ++--- src/test/sources/GeneDataSource-test.js | 7 ++----- src/test/sources/GenotypeDataSource-test.js | 15 +++++++-------- src/test/sources/VariantDataSource-test.js | 15 ++++----------- 15 files changed, 48 insertions(+), 92 deletions(-) diff --git a/src/main/GA4GHAlignment.js b/src/main/GA4GHAlignment.js index 6287c643..10ddd18f 100644 --- a/src/main/GA4GHAlignment.js +++ b/src/main/GA4GHAlignment.js @@ -80,7 +80,7 @@ class GA4GHAlignment /* implements Alignment */ { } getMateProperties(): ?MateProperties { - var next = this.nextMatePosition; + var next = this.alignment.nextMatePosition; return next && { ref: next.referenceName, pos: next.position, diff --git a/src/main/data/FeatureEndpoint.js b/src/main/data/FeatureEndpoint.js index d31f0861..631debd8 100644 --- a/src/main/data/FeatureEndpoint.js +++ b/src/main/data/FeatureEndpoint.js @@ -5,10 +5,11 @@ */ 'use strict'; -// import Q from 'q'; +import Q from 'q'; +import ContigInterval from '../ContigInterval'; import type RemoteRequest from '../RemoteRequest'; -type Feature = { +export type Feature = { id: string; featureType: string; contig: string; @@ -16,10 +17,6 @@ type Feature = { stop: number; } -function extractFeatures(features: Object): Feature[] { - return features; -} - class FeatureEndpoint { remoteRequest: RemoteRequest; @@ -33,8 +30,7 @@ class FeatureEndpoint { var stop = range.interval.stop; return this.remoteRequest.get(contig, start, stop).then(object => { - var d = extractFeatures(object); - return d; + return object; }); } } diff --git a/src/main/data/GeneEndpoint.js b/src/main/data/GeneEndpoint.js index aebb6964..a34e7e7a 100644 --- a/src/main/data/GeneEndpoint.js +++ b/src/main/data/GeneEndpoint.js @@ -5,7 +5,8 @@ */ 'use strict'; -// import Q from 'q'; +import Q from 'q'; +import type {Gene} from '../sources/BigBedDataSource'; import type RemoteRequest from '../RemoteRequest'; import Interval from '../Interval'; import ContigInterval from '../../main/ContigInterval'; diff --git a/src/main/data/GenotypeEndpoint.js b/src/main/data/GenotypeEndpoint.js index 5726d89f..dd88c1ba 100644 --- a/src/main/data/GenotypeEndpoint.js +++ b/src/main/data/GenotypeEndpoint.js @@ -5,21 +5,16 @@ */ 'use strict'; +import ContigInterval from '../ContigInterval'; import Q from 'q'; import type RemoteRequest from '../RemoteRequest'; import type {Variant} from './vcf'; - export type Genotype = { sampleIds: string, variant: Variant } - -function extractGenotypes(genotypes: Object): Genotype[] { - return genotypes; -} - class GenotypeEndpoint { remoteRequest: RemoteRequest; @@ -34,8 +29,7 @@ class GenotypeEndpoint { return this.remoteRequest.get(contig, start, stop).then(object => { - var d = extractGenotypes(object); - return d; + return object; }); } } diff --git a/src/main/data/VariantEndpoint.js b/src/main/data/VariantEndpoint.js index 59425dda..fdfa13d4 100644 --- a/src/main/data/VariantEndpoint.js +++ b/src/main/data/VariantEndpoint.js @@ -5,12 +5,10 @@ */ 'use strict'; +import ContigInterval from '../ContigInterval'; import Q from 'q'; import type RemoteRequest from '../RemoteRequest'; - -function extractVariants(variants: Object): Variant[] { - return variants; -} +import type {Variant} from './vcf'; class VariantEndpoint { remoteRequest: RemoteRequest; @@ -25,8 +23,8 @@ class VariantEndpoint { var stop = range.interval.stop; return this.remoteRequest.get(contig, start, stop).then(object => { - var d = extractVariants(object); // TODO: should parts to Variant[] - return d; + console.log("variant endpoint", object); + return object; }); } } diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index e63b0465..b84ea697 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -22,7 +22,7 @@ import {Events} from 'backbone'; import ContigInterval from '../ContigInterval'; import RemoteRequest from '../RemoteRequest'; import FeatureEndpoint from '../data/FeatureEndpoint'; -import type {Feature} from '../data/FeatureEndPoint'; +import type {Feature} from '../data/FeatureEndpoint'; // Flow type for export. export type FeatureDataSource = { @@ -106,16 +106,11 @@ function createFromFeatureUrl(remoteSource: FeatureEndpoint): FeatureDataSource return o; } -function create(data: {url?:string, key?:string}): FeatureDataSource { - var {url, key} = data; - if (!url) { +function create(data: {url?:string}): FeatureDataSource { + if (!data.url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } - // verify key was correctly set - if (!key) { - throw new Error(`Missing key from track: ${JSON.stringify(data)}`); - } - var request = new RemoteRequest(url, key); + var request = new RemoteRequest(data.url); var endpoint = new FeatureEndpoint(request); return createFromFeatureUrl(endpoint); } diff --git a/src/main/sources/GA4GHDataSource.js b/src/main/sources/GA4GHDataSource.js index e978fdf6..4fe58a4d 100644 --- a/src/main/sources/GA4GHDataSource.js +++ b/src/main/sources/GA4GHDataSource.js @@ -9,6 +9,7 @@ import type {Alignment, AlignmentDataSource} from '../Alignment'; import _ from 'underscore'; import {Events} from 'backbone'; +import Q from 'q'; import ContigInterval from '../ContigInterval'; import GA4GHAlignment from '../GA4GHAlignment'; diff --git a/src/main/sources/GeneDataSource.js b/src/main/sources/GeneDataSource.js index fb1935e1..1a027bdd 100644 --- a/src/main/sources/GeneDataSource.js +++ b/src/main/sources/GeneDataSource.js @@ -83,18 +83,11 @@ function createFromGeneUrl(remoteSource: GeneEndpoint): BigBedSource { return o; } -function create(data: {url?:string, key?:string}): BigBedSource { - var url = data.url; - var key = data.key; - if (!url) { +function create(data: {url?:string}): BigBedSource { + if (!data.url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } - // verify key was correctly set - if (!key) { - throw new Error(`Missing key from track: ${JSON.stringify(data)}`); - } - - var request = new RemoteRequest(url, key); + var request = new RemoteRequest(data.url); var endpoint = new GeneEndpoint(request); return createFromGeneUrl(endpoint); } diff --git a/src/main/sources/GenotypeDataSource.js b/src/main/sources/GenotypeDataSource.js index 7c0c140c..c32274b3 100644 --- a/src/main/sources/GenotypeDataSource.js +++ b/src/main/sources/GenotypeDataSource.js @@ -105,16 +105,11 @@ function createFromGenotypeUrl(remoteSource: GenotypeEndpoint): GenotypeDataSour return o; } -function create(data: {url?:string, key?:string}): GenotypeDataSource { - var {url, key} = data; - if (!url) { +function create(data: {url?:string}): GenotypeDataSource { + if (!data.url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } - // verify key was correctly set - if (!key) { - throw new Error(`Missing key from track: ${JSON.stringify(data)}`); - } - var request = new RemoteRequest(url, key); + var request = new RemoteRequest(data.url); var endpoint = new GenotypeEndpoint(request); return createFromGenotypeUrl(endpoint); } diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index 5e67c760..05551ff6 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -31,7 +31,7 @@ import utils from '../utils'; // Requests for 2bit ranges are expanded to begin & end at multiples of this // constant. Doing this means that panning typically won't require // additional network requests. -var BASE_PAIRS_PER_FETCH = 15000; +var BASE_PAIRS_PER_FETCH = 10000; var MAX_BASE_PAIRS_TO_FETCH = 100000; @@ -149,8 +149,7 @@ function create(data: {url:string, contigList: SequenceRecord[]}): TwoBitSource if (!contigList) { throw new Error(`Missing ContigList from track: ${JSON.stringify(data)}`); } - var key = "reference"; // key is not required for reference but required for Remote Request - return createFromReferenceUrl(new Sequence(new RemoteRequest(urlPrefix, key), contigList)); + return createFromReferenceUrl(new Sequence(new RemoteRequest(urlPrefix), contigList)); } // Getter/setter for base pairs per fetch. diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index b1cad7fc..3338fe41 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -67,13 +67,15 @@ function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { // "Cover" the range immediately to prevent duplicate fetches. coveredRanges.push(interval); coveredRanges = ContigInterval.coalesce(coveredRanges); - return remoteSource.getFeaturesInRange(interval).then(variants => { - variants.forEach(variant => addVariant(variant)); + return remoteSource.getFeaturesInRange(interval).then(object => { + console.log(object, variants); + object.forEach(variant => addVariant(variant)); o.trigger('newdata', interval); }); } function getFeaturesInRange(range: ContigInterval): Variant[] { + console.log("getFeaturesinRange", range); if (!range) return []; // XXX why would this happen? return _.filter(variants, v => range.chrContainsLocus(v.contig, v.position)); } @@ -94,17 +96,11 @@ function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { return o; } -function create(data: {url:string, contigList: SequenceRecord[]}): VcfDataSource { - var url = data.url; - var contigList = data.contigList; - if (!url) { +function create(data: {url?:string}): VcfDataSource { + if (!data.url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } - // verify contiglist was correctly set - if (!contigList) { - throw new Error(`Missing ContigList from track: ${JSON.stringify(data)}`); - } - var request = new RemoteRequest(url, contigList); + var request = new RemoteRequest(data.url); var endpoint = new VariantEndpoint(request); return createFromVariantUrl(endpoint); } diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js index 6c5224b2..4fb56cf1 100644 --- a/src/test/sources/FeatureDataSource-test.js +++ b/src/test/sources/FeatureDataSource-test.js @@ -16,7 +16,7 @@ describe('FeatureDataSource', function() { return new RemoteFile('/test-data/features-chrM-1000-1200.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); - server.respondWith('GET', '/features/chrM?start=1000&end=2000&key=test', [200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/features/chrM?start=1000&end=2000', [200, { "Content-Type": "application/json" }, response]); }); }); @@ -26,8 +26,7 @@ describe('FeatureDataSource', function() { function getTestSource() { var source = FeatureDataSource.create({ - url: '/features', - key: 'test' + url: '/features' }); return source; } diff --git a/src/test/sources/GeneDataSource-test.js b/src/test/sources/GeneDataSource-test.js index 5a565d37..5a11e478 100644 --- a/src/test/sources/GeneDataSource-test.js +++ b/src/test/sources/GeneDataSource-test.js @@ -16,7 +16,7 @@ describe('GeneDataSource', function() { return new RemoteFile('/test-data/genes-chrM-0-30000.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); - server.respondWith('GET', '/genes/chrM?start=1&end=100000&key=test', [200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/genes/chrM?start=1&end=100000', [200, { "Content-Type": "application/json" }, response]); }); }); @@ -26,8 +26,7 @@ describe('GeneDataSource', function() { function getTestSource() { var source = GeneDataSource.create({ - url: '/genes', - key: 'test' + url: '/genes' }); return source; } @@ -43,8 +42,6 @@ describe('GeneDataSource', function() { // Fetching that one gene should cache its entire block. source.on('newdata', () => { var genes = source.getGenesInRange(range); - console.log(genes); - expect(genes).to.have.length(9); done(); }); diff --git a/src/test/sources/GenotypeDataSource-test.js b/src/test/sources/GenotypeDataSource-test.js index 78e1b572..3133a989 100644 --- a/src/test/sources/GenotypeDataSource-test.js +++ b/src/test/sources/GenotypeDataSource-test.js @@ -6,7 +6,7 @@ import {expect} from 'chai'; import sinon from 'sinon'; -import VariantDataSource from '../../main/sources/VariantDataSource'; +import GenotypeDataSource from '../../main/sources/GenotypeDataSource'; import ContigInterval from '../../main/ContigInterval'; import RemoteFile from '../../main/RemoteFile'; @@ -17,7 +17,7 @@ describe('GenotypeDataSource', function() { return new RemoteFile('/test-data/genotypes-chrM-0-100.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); - server.respondWith('GET', '/genotypes/chrM?start=1&end=1000&key=test',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/genotypes/chrM?start=1&end=1000',[200, { "Content-Type": "application/json" }, response]); }); }); @@ -26,9 +26,8 @@ describe('GenotypeDataSource', function() { }); function getTestSource() { - var source = VariantDataSource.create({ - url: '/genotypes', - key: 'test' + var source = GenotypeDataSource.create({ + url: '/genotypes' }); return source; } @@ -36,12 +35,12 @@ describe('GenotypeDataSource', function() { var source = getTestSource(); var range = new ContigInterval('chrM', 0, 25); // No variants are cached yet. - var variants = source.getFeaturesInRange(range); - expect(variants).to.deep.equal([]); + var genotypes = source.getFeaturesInRange(range); + expect(genotypes).to.deep.equal([]); source.on('newdata', () => { var genotypes = source.getFeaturesInRange(range); - expect(genotypes).to.have.length(3); + expect(genotypes).to.have.length(2); expect(genotypes[1].sampleIds).to.contain('sample1'); expect(genotypes[1].variant.contig).to.equal('chrM'); expect(genotypes[1].variant.position).to.equal(20); diff --git a/src/test/sources/VariantDataSource-test.js b/src/test/sources/VariantDataSource-test.js index b074909f..1cf08079 100644 --- a/src/test/sources/VariantDataSource-test.js +++ b/src/test/sources/VariantDataSource-test.js @@ -17,7 +17,6 @@ describe('VariantDataSource', function() { return new RemoteFile('/test-data/variants-chrM-0-100.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); - // server.respondWith('GET', '/variants',[200, { "Content-Type": "application/json" }, response]); server.respondWith('GET', '/variants/chrM?start=1&end=1000',[200, { "Content-Type": "application/json" }, response]); }); }); @@ -28,27 +27,21 @@ describe('VariantDataSource', function() { function getTestSource() { var source = VariantDataSource.create({ - url: '/variants', - contigList: [{ - name:"chrM", - length: 1000 - },{ - name:"22", - length: 1000 - }] + url: '/variants' }); return source; } it('should extract features in a range', function(done) { var source = getTestSource(); - var range = new ContigInterval('chrM', 0, 25); + var range = new ContigInterval('chrM', 0, 50); // No variants are cached yet. var variants = source.getFeaturesInRange(range); expect(variants).to.deep.equal([]); source.on('newdata', () => { var variants = source.getFeaturesInRange(range); - expect(variants).to.have.length(2); + console.log(variants); + expect(variants).to.have.length(3); expect(variants[1].contig).to.equal('chrM'); expect(variants[1].position).to.equal(20); expect(variants[1].ref).to.equal('G'); From 561287bc62a931dfde80ebfbecc9287a20ca8596 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 24 Aug 2016 18:00:34 -0700 Subject: [PATCH 108/136] merge in main pileup updates and modified RemoteRequest --- src/main/RemoteRequest.js | 63 ++++--- src/main/ResolutionCache.js | 168 +++++++++++++++++++ src/main/data/FeatureEndpoint.js | 6 +- src/main/data/GeneEndpoint.js | 6 +- src/main/data/GenotypeEndpoint.js | 7 +- src/main/data/Sequence.js | 7 +- src/main/data/VariantEndpoint.js | 7 +- src/main/pileup.js | 2 +- src/main/sources/CoverageDataSource.js | 103 ++++++++++++ src/main/sources/GA4GHDataSource.js | 4 +- src/main/sources/ReferenceDataSource.js | 2 +- src/main/sources/VariantDataSource.js | 4 +- src/test/RemoteRequest-test.js | 29 +--- src/test/ResolutionCache-test.js | 88 ++++++++++ src/test/sources/CoverageDataSource-test.js | 99 +++++++++++ src/test/sources/GA4GHDataSource-test.js | 8 +- src/test/sources/ReferenceDataSource-test.js | 14 +- src/test/sources/VariantDataSource-test.js | 1 - test-data/chrM-coverage.json | 49 ++++++ test-data/variants-chrM-0-100.json | 2 +- 20 files changed, 574 insertions(+), 95 deletions(-) create mode 100644 src/main/ResolutionCache.js create mode 100644 src/main/sources/CoverageDataSource.js create mode 100644 src/test/ResolutionCache-test.js create mode 100644 src/test/sources/CoverageDataSource-test.js create mode 100644 test-data/chrM-coverage.json diff --git a/src/main/RemoteRequest.js b/src/main/RemoteRequest.js index 7fc9b269..d5a1fcf2 100644 --- a/src/main/RemoteRequest.js +++ b/src/main/RemoteRequest.js @@ -9,60 +9,69 @@ import Q from 'q'; import ContigInterval from './ContigInterval'; +var BASE_PAIRS_PER_FETCH = 1000; class RemoteRequest { url: string; - cache: Object; + basePairsPerFetch: number; numNetworkRequests: number; // track this for debugging/testing - constructor(url: string) { - this.cache = require('memory-cache'); + constructor(url: string, basePairsPerFetch?: number) { this.url = url; + if (!basePairsPerFetch) + this.basePairsPerFetch = BASE_PAIRS_PER_FETCH; + else + this.basePairsPerFetch = basePairsPerFetch; this.numNetworkRequests = 0; } - get(contig: string, start: number, stop: number): Q.Promise { - var length = stop - start; + expandRange(range: ContigInterval): ContigInterval { + var roundDown = x => x - x % this.basePairsPerFetch; + var newStart = Math.max(1, roundDown(range.start())), + newStop = roundDown(range.stop() + this.basePairsPerFetch - 1); + + return new ContigInterval(range.contig, newStart, newStop); + } + + getFeaturesInRange(range: ContigInterval, modifier: string = ""): Q.Promise { + var expandedRange = this.expandRange(range); + return this.get(expandedRange, modifier); + } + + get(range: ContigInterval, modifier: string = ""): Q.Promise { + + var length = range.stop() - range.start(); if (length <= 0) { return Q.reject(`Requested <0 interval (${length}) from ${this.url}`); + } else if (length > 5000000) { + throw `Monster request: Won't fetch ${length} sized ranges from ${this.url}`; } - - // First check the cache. - var contigInterval = new ContigInterval(contig, start, stop); - var buf = this.cache.get(contigInterval); - if (buf) { - return Q.when(buf); - } - - // Need to fetch from the network. - return this.getFromNetwork(contig, start, stop); + // get endpoint + var endpoint = this.getEndpointFromContig(range.contig, range.start(), range.stop(), modifier); + // Fetch from the network + return this.getFromNetwork(endpoint); } /** * Request must be of form "url/contig?start=start&end=stop" */ - getFromNetwork(contig: string, start: number, stop: number): Q.Promise { - var length = stop - start; - if (length > 5000000) { - throw `Monster request: Won't fetch ${length} sized ranges from ${this.url}`; - } + getFromNetwork(endpoint: string): Q.Promise { var xhr = new XMLHttpRequest(); - var endpoint = this.getEndpointFromContig(contig, start, stop); xhr.open('GET', endpoint); xhr.responseType = 'json'; xhr.setRequestHeader('Content-Type', 'application/json'); return this.promiseXHR(xhr).then(json => { // extract response from promise - var buffer = json[0]; - var contigInterval = new ContigInterval(contig, start, stop); - this.cache.put(contigInterval, buffer); - return buffer; + return json[0]; }); } - getEndpointFromContig(contig: string, start: number, stop: number): string { - return `${this.url}/${contig}?start=${start}&end=${stop}`; + getEndpointFromContig(contig: string, start: number, stop: number, modifier: string = ""): string { + if (modifier.length < 1) + return `${this.url}/${contig}?start=${start}&end=${stop}`; + else + return `${this.url}/${contig}?start=${start}&end=${stop}&${modifier}`; } // Wrapper to convert XHRs to Promises. diff --git a/src/main/ResolutionCache.js b/src/main/ResolutionCache.js new file mode 100644 index 00000000..8e347136 --- /dev/null +++ b/src/main/ResolutionCache.js @@ -0,0 +1,168 @@ +/** + * Cache for any Data Sources that rely on resolution. For example, + * this is used by coverage to keep track of the difference resolutions + * that have been fetched already. + * + * @flow + */ +'use strict'; + +import _ from 'underscore'; +import Interval from './Interval'; +import ContigInterval from './ContigInterval'; + +class ResolutionCache { + coveredRanges: ResolutionCacheKey[]; + cache: {[key: string]: T}; + filterFunction: Function; // should take form (range: ContigInterval, T) => boolean; + keyFunction: Function; // should take form (d: T) => string; + + constructor(filterFunction: Function, keyFunction: Function) { + this.coveredRanges = []; + this.cache = {}; + this.filterFunction = filterFunction; + this.keyFunction = keyFunction; + } + + // gets data from cache at the Resolution defined by the interval + get(range: ContigInterval): T[] { + if (this.coversRange(range)) { + if (!range) return []; + return _.filter(this.cache, d => this.filterFunction(range, d)); + } else { + return []; + } + } + + // puts new ranges into list of ranges covered by cache + coverRange(range: ContigInterval) { + var resolution = ResolutionCache.getResolution(range.interval); + var resolvedRange = new ResolutionCacheKey(range, resolution); + this.coveredRanges.push(resolvedRange); + // coalesce new contigIntervals + this.coveredRanges = ResolutionCacheKey.coalesce(this.coveredRanges); + } + + // puts data in cache + put(value: T) { + var key = this.keyFunction(value); + if (!this.cache[key]) { + this.cache[key] = value; + } + } + + // checks weather cache contains data for the + // specified interval and its corresponding resolution + coversRange(range: ContigInterval): boolean { + var resolution = ResolutionCache.getResolution(range.interval); + if (range.isCoveredBy(this.coveredRanges.map(r => r.contigInterval))) { + // if covered by the data, verify that the correct base pair density is + // available + var correctResolution = true; + for (var i = 0; i < this.coveredRanges.length; i++) { + var r: ContigInterval = this.coveredRanges[i].contigInterval; + var thisRes = this.coveredRanges[i].resolution; + if (r.intersects(range)) { + if (thisRes > resolution) { // resolution not fine enough for query + correctResolution = false; + break; + } + } + } + return correctResolution; + } else { + return false; + } + } + + // clears out all content in cache + clear() { + this.coveredRanges = []; + this.cache = {}; + } + + /** + * Gets the Base Pairs per bin given a specified interval + * This is used to bin coverage when viewing large regions + * + * Values were chosen based on a 1000 pixel screen (a conservative estimate): + * - For regions < 10,000 base pairs, no binning is performed (return 1) + * - For regions >= 10,000 and < 100,000, bin 10 bp into 1 (return 10) + * - For regions >= 100,000 and < 1,000,000, bin 100 bp into 1 (return 100) + * - For regions >= 1,000,000, bin 1000 bp into 1 (return 1000) + */ + static getResolution(range: Interval): number { + if (range.length() < 10000) + return 1; + else if (range.length() >= 10000 && range.length() < 100000 ) + return 10; + else if (range.length() >= 100000 && range.length() < 1000000 ) + return 100; + else + return 1000; + } +} + +/** + * Class holds a ContigInterval and resolution that designates whether + * a contig interval represents data at a certain resolution. The + * parameters for choosing a resolution based on interval length are set + * in getResolution. + * + */ +class ResolutionCacheKey { + contigInterval: ContigInterval; + resolution: number; + + constructor(contigInterval: ContigInterval, resolution: number) { + this.contigInterval = contigInterval; + this.resolution = resolution; + } + + clone(): ResolutionCacheKey { + return new ResolutionCacheKey(this.contigInterval.clone(), this.resolution); + } + + // Sort an array of intervals & coalesce adjacent/overlapping ranges. + // NB: this may re-order the intervals parameter + static coalesce(intervals: ResolutionCacheKey[]): ResolutionCacheKey[] { + intervals.sort(ResolutionCacheKey.compare); + + var rs = []; + intervals.forEach(r => { + if (rs.length === 0) { + rs.push(r); + return; + } + + var lastR: ResolutionCacheKey = rs[rs.length - 1]; + if (r.contigInterval.intersects(lastR.contigInterval) || + r.contigInterval.isAdjacentTo(lastR.contigInterval) && + r.resolution == lastR.resolution) { + lastR = rs[rs.length - 1] = lastR.clone(); + lastR.contigInterval.interval.stop = + Math.max(r.contigInterval.interval.stop, lastR.contigInterval.interval.stop); + } else { + rs.push(r); + } + }); + + return rs; + } + + // Comparator for use with Array.prototype.sort + static compare(a: ResolutionCacheKey, b: ResolutionCacheKey): number { + if (a.contigInterval.contig > b.contigInterval.contig) { + return -1; + } else if (a.contigInterval.contig < b.contigInterval.contig) { + return +1; + } else { + return a.contigInterval.start() - b.contigInterval.start(); + } + } + +} + +module.exports = { + ResolutionCache +}; diff --git a/src/main/data/FeatureEndpoint.js b/src/main/data/FeatureEndpoint.js index 631debd8..d0de28f3 100644 --- a/src/main/data/FeatureEndpoint.js +++ b/src/main/data/FeatureEndpoint.js @@ -25,11 +25,7 @@ class FeatureEndpoint { } getFeaturesInRange(range: ContigInterval): Q.Promise { - var contig = range.contig; - var start = range.interval.start; - var stop = range.interval.stop; - - return this.remoteRequest.get(contig, start, stop).then(object => { + return this.remoteRequest.get(range).then(object => { return object; }); } diff --git a/src/main/data/GeneEndpoint.js b/src/main/data/GeneEndpoint.js index a34e7e7a..a63f954a 100644 --- a/src/main/data/GeneEndpoint.js +++ b/src/main/data/GeneEndpoint.js @@ -49,11 +49,7 @@ class GeneEndpoint { } getGenesInRange(range: ContigInterval): Q.Promise { - var contig = range.contig; - var start = range.interval.start; - var stop = range.interval.stop; - - return this.remoteRequest.get(contig, start, stop).then(object => { + return this.remoteRequest.get(range).then(object => { var d = extractGenes(object); return d; }); diff --git a/src/main/data/GenotypeEndpoint.js b/src/main/data/GenotypeEndpoint.js index dd88c1ba..01e0dad0 100644 --- a/src/main/data/GenotypeEndpoint.js +++ b/src/main/data/GenotypeEndpoint.js @@ -23,12 +23,7 @@ class GenotypeEndpoint { } getFeaturesInRange(range: ContigInterval): Q.Promise { - var contig = range.contig; - var start = range.interval.start; - var stop = range.interval.stop; - - - return this.remoteRequest.get(contig, start, stop).then(object => { + return this.remoteRequest.get(range).then(object => { return object; }); } diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index 4d5562ad..8532831b 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -6,6 +6,7 @@ 'use strict'; import Q from 'q'; +import ContigInterval from '../ContigInterval'; import type RemoteRequest from '../RemoteRequest'; export type SequenceRecord = { @@ -32,11 +33,13 @@ class Sequence { * The range is inclusive and zero-based. * Returns empty string if no data is available on this range. */ - getFeaturesInRange(contig: string, start: number, stop: number): Q.Promise { + getFeaturesInRange(range: ContigInterval): Q.Promise { + var start = range.start(); + var stop = range.stop(); if (start > stop) { throw `Requested a range with start > stop (${start}, ${stop})`; } - return this.remoteRequest.get(contig, start, stop).then(sequence => { + return this.remoteRequest.get(range).then(sequence => { var d = sequence.substring(start, (stop-start + 1)); return d; }); diff --git a/src/main/data/VariantEndpoint.js b/src/main/data/VariantEndpoint.js index fdfa13d4..cf6447c0 100644 --- a/src/main/data/VariantEndpoint.js +++ b/src/main/data/VariantEndpoint.js @@ -18,12 +18,7 @@ class VariantEndpoint { } getFeaturesInRange(range: ContigInterval): Q.Promise { - var contig = range.contig; - var start = range.interval.start; - var stop = range.interval.stop; - - return this.remoteRequest.get(contig, start, stop).then(object => { - console.log("variant endpoint", object); + return this.remoteRequest.get(range).then(object => { return object; }); } diff --git a/src/main/pileup.js b/src/main/pileup.js index c8145627..afb726ce 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -150,7 +150,7 @@ var pileup = { genotypes: makeVizObject(GenotypeTrack), pileup: makeVizObject(PileupTrack) }, - version: '0.6.6' + version: '0.6.7' }; module.exports = pileup; diff --git a/src/main/sources/CoverageDataSource.js b/src/main/sources/CoverageDataSource.js new file mode 100644 index 00000000..4f428f0e --- /dev/null +++ b/src/main/sources/CoverageDataSource.js @@ -0,0 +1,103 @@ +/** + * Remote Endpoint for coverage. + * + * CoverageDataSource is purely for data parsing and fetching. + * Coverage for CoverageDataSource can be calculated from any source, + * including, but not limited to, Alignment Records, + * variants or features. + * + * @flow + */ +'use strict'; + +import Q from 'q'; +import _ from 'underscore'; +import {Events} from 'backbone'; +import {ResolutionCache} from '../ResolutionCache'; +import ContigInterval from '../ContigInterval'; +import RemoteRequest from '../RemoteRequest'; + +export type CoverageDataSource = { + rangeChanged: (newRange: GenomeRange) => void; + getCoverageInRange: (range: ContigInterval) => PositionCount[]; + on: (event: string, handler: Function) => void; + off: (event: string) => void; + trigger: (event: string, ...args:any) => void; +}; + +var BASE_PAIRS_PER_FETCH = 1000; + +export type PositionCount = { + contig: string; + position: number; + count: number; +} + +function keyFunction(p: PositionCount): string { + return `${p.contig}:${p.position}`; +} + +function filterFunction(range: ContigInterval, p: PositionCount): boolean { + return range.chrContainsLocus(p.contig, p.position); +} + +function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource { + var cache: ResolutionCache = + new ResolutionCache(filterFunction, keyFunction); + + function fetch(range: GenomeRange) { + var interval = new ContigInterval(range.contig, range.start, range.stop); + + // Check if this interval is already in the cache. + if (cache.coversRange(interval)) { + return Q.when(); + + } + + // modify endpoint to calculate coverage using binning + var basePairsPerBin = ResolutionCache.getResolution(interval.interval); + var endpointModifier = `binning=${basePairsPerBin}`; + + // Cover the range immediately to prevent duplicate fetches. + cache.coverRange(interval); + return remoteSource.getFeaturesInRange(interval, endpointModifier).then(positions => { + positions.forEach(p => cache.put(p)); + o.trigger('newdata', interval); + }); + } + + function getCoverageInRange(range: ContigInterval): PositionCount[] { + if (!range) return []; + return cache.get(range); + } + + var o = { + rangeChanged: function(newRange: GenomeRange) { + fetch(newRange).done(); + }, + getCoverageInRange, + + // These are here to make Flow happy. + on: () => {}, + off: () => {}, + trigger: () => {} + }; + _.extend(o, Events); + + return o; +} + +function create(data: {url?:string}): CoverageDataSource { + if (!data.url) { + throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); + } + + var endpoint = new RemoteRequest(data.url, BASE_PAIRS_PER_FETCH); + return createFromCoverageUrl(endpoint); +} + + +module.exports = { + create, + createFromCoverageUrl +}; diff --git a/src/main/sources/GA4GHDataSource.js b/src/main/sources/GA4GHDataSource.js index 4fe58a4d..ad0caa43 100644 --- a/src/main/sources/GA4GHDataSource.js +++ b/src/main/sources/GA4GHDataSource.js @@ -42,7 +42,7 @@ type GA4GHSpec = { }; function create(spec: GA4GHSpec): AlignmentDataSource { - var url = spec.endpoint ; + var url = spec.endpoint; var reads: {[key:string]: Alignment} = {}; @@ -95,7 +95,7 @@ function create(spec: GA4GHSpec): AlignmentDataSource { } var xhr = new XMLHttpRequest(); - var endpoint = url + "/" + range.contig + "?start=" + range.start() + "&end=" + range.stop()+"&key="+spec.readGroupId; + var endpoint = `${url}/${spec.readGroupId}/${range.contig}?start=${range.start()}&end=${range.stop()}`; xhr.open('GET', endpoint); xhr.responseType = 'json'; diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index 05551ff6..1982b998 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -59,7 +59,7 @@ var createFromReferenceUrl = function(remoteSource: Sequence): TwoBitSource { } // TODO remote Source - remoteSource.getFeaturesInRange(range.contig, range.start(), range.stop()) + remoteSource.getFeaturesInRange(range) .then(letters => { if (!letters) return; if (letters.length < range.length()) { diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index 3338fe41..d7d13649 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -68,14 +68,12 @@ function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { coveredRanges.push(interval); coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getFeaturesInRange(interval).then(object => { - console.log(object, variants); object.forEach(variant => addVariant(variant)); o.trigger('newdata', interval); }); } function getFeaturesInRange(range: ContigInterval): Variant[] { - console.log("getFeaturesinRange", range); if (!range) return []; // XXX why would this happen? return _.filter(variants, v => range.chrContainsLocus(v.contig, v.position)); } @@ -100,7 +98,7 @@ function create(data: {url?:string}): VcfDataSource { if (!data.url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } - var request = new RemoteRequest(data.url); + var request = new RemoteRequest(data.url, BASE_PAIRS_PER_FETCH); var endpoint = new VariantEndpoint(request); return createFromVariantUrl(endpoint); } diff --git a/src/test/RemoteRequest-test.js b/src/test/RemoteRequest-test.js index b24dec91..9b5b1a99 100644 --- a/src/test/RemoteRequest-test.js +++ b/src/test/RemoteRequest-test.js @@ -7,6 +7,7 @@ import sinon from 'sinon'; import RemoteRequest from '../main/RemoteRequest'; import RemoteFile from '../main/RemoteFile'; +import ContigInterval from '../main/ContigInterval'; describe('RemoteRequest', function() { var server: any = null, response; @@ -14,6 +15,8 @@ describe('RemoteRequest', function() { var contig = 'chr17'; var start = 10; var stop = 20; + var interval = new ContigInterval(contig, start, stop); + var basePairsPerFetch = 1000; before(function () { return new RemoteFile('/test-data/chr17.1-250.json').getAllString().then(data => { @@ -27,12 +30,12 @@ describe('RemoteRequest', function() { }); it('should fetch json from a server', function(done) { - var remoteRequest = new RemoteRequest(url); + var remoteRequest = new RemoteRequest(url, basePairsPerFetch); var endpoint = remoteRequest.getEndpointFromContig(contig, start, stop); server.respondWith('GET', endpoint, [200, { "Content-Type": "application/json" }, response]); - var promisedData = remoteRequest.get(contig, start, stop); + var promisedData = remoteRequest.get(interval); promisedData.then(obj => { var ret = obj.alignments; expect(remoteRequest.numNetworkRequests).to.equal(1); @@ -42,26 +45,4 @@ describe('RemoteRequest', function() { server.respond(); }); - - it('should cache data after server response', function(done) { - var remoteRequest = new RemoteRequest(url); - // verify cache is cleared for testing - remoteRequest.cache.clear(); - var endpoint = remoteRequest.getEndpointFromContig(contig, start, stop); - server.respondWith('GET', endpoint, - [200, { "Content-Type": "application/json" }, response]); - - var promisedData = remoteRequest.get(contig, start, stop); - promisedData.then(obj => { - var promisedData2 = remoteRequest.get(contig, start, stop); - promisedData2.then(obj2 => { - var ret = obj2.alignments; - expect(remoteRequest.numNetworkRequests).to.equal(1); - expect(ret.length).to.equal(14); - done(); - }); - }); - - server.respond(); - }); }); diff --git a/src/test/ResolutionCache-test.js b/src/test/ResolutionCache-test.js new file mode 100644 index 00000000..07a94d2a --- /dev/null +++ b/src/test/ResolutionCache-test.js @@ -0,0 +1,88 @@ +/** @flow */ +'use strict'; + +import {expect} from 'chai'; + +import ContigInterval from '../main/ContigInterval'; +import {ResolutionCache} from '../main/ResolutionCache'; + +describe('ResolutionCache', function() { + + // Type used for testing cache + type Position = { + contig: string; + position: number; + } + + var smRange = new ContigInterval("chrM", 0, 100); + var smRange2 = new ContigInterval("chrM", 100, 200); + var smRange3 = new ContigInterval("chrM", 300, 400); + + var bigRange = new ContigInterval("chrM", 0, 1000000); + var data: Position[] = [{contig:'chrM',position:2}, + {contig:'chrM',position:3}, + {contig:'chrM',position:6}, + {contig:'chrM',position:107}]; + + function filterFunction(range: ContigInterval, p: Position): boolean { + return range.chrContainsLocus(p.contig, p.position); + } + + function keyFunction(p: Position): string { + return `${p.contig}:${p.position}`; + } + + function createCache(): ResolutionCache { + var cache = new ResolutionCache(filterFunction, keyFunction); + return cache; + } + + + it('should create cache', function() { + var cache: ResolutionCache = createCache(); + expect(cache == {}); + }); + + it('should put and get data in range', function() { + var cache: ResolutionCache = createCache(); + cache.coverRange(smRange); + data.forEach(p => cache.put(p)); + var d = cache.get(smRange); + expect(d.length == 3); + }); + + it('should cover ranges after put', function() { + var cache: ResolutionCache = createCache(); + cache.coverRange(smRange); + data.forEach(p => cache.put(p)); + var covered = cache.coversRange(smRange); + expect(covered === true); + }); + + it('should clear the cache', function() { + var cache: ResolutionCache = createCache(); + cache.coverRange(smRange); + data.forEach(p => cache.put(p)); + cache.clear(); + expect(cache.cache == {}); + expect(cache.coveredRanges == []); + }); + + it('should return false when finer resolution was not yet loaded', function() { + var cache: ResolutionCache = createCache(); + cache.coverRange(bigRange); + var covered = cache.coversRange(smRange); + expect(covered === false); + }); + + it('should coalesce the covered ranges', function() { + var cache: ResolutionCache = createCache(); + cache.coverRange(smRange); + cache.coverRange(smRange3); + expect(cache.coveredRanges.length == 2); + + cache.coverRange(smRange2); + expect(cache.coveredRanges.length == 2); + }); + +}); diff --git a/src/test/sources/CoverageDataSource-test.js b/src/test/sources/CoverageDataSource-test.js new file mode 100644 index 00000000..2c4ec87b --- /dev/null +++ b/src/test/sources/CoverageDataSource-test.js @@ -0,0 +1,99 @@ +/** @flow */ +'use strict'; + +import {expect} from 'chai'; + +import sinon from 'sinon'; + +import ContigInterval from '../../main/ContigInterval'; +import CoverageDataSource from '../../main/sources/CoverageDataSource'; +import RemoteFile from '../../main/RemoteFile'; + +describe('CoverageDataSource', function() { + var server: any = null, response; + + before(function () { + return new RemoteFile('/test-data/chrM-coverage.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/coverage/chrM?start=1&end=1000&binning=1',[200, { "Content-Type": "application/json" }, response]); + }); + }); + + after(function () { + server.restore(); + }); + + it('should fetch coverage points from a server', function(done) { + + var source = CoverageDataSource.create({ + url: '/coverage' + }); + + var requestInterval = new ContigInterval('chrM', 10, 30); + expect(source.getCoverageInRange(requestInterval)) + .to.deep.equal([]); + + source.on('newdata', () => { + var coverage = source.getCoverageInRange(requestInterval); + expect(coverage).to.have.length(12); + done(); + }); + + source.rangeChanged({contig: 'chrM', start: 10, stop: 30}); + server.respond(); + }); + + it('should cache coverage after first call', function(done) { + + var source = CoverageDataSource.create({ + url: '/coverage' + }); + var requestCount = 0; + var requestInterval = new ContigInterval('chrM', 10, 20); + expect(source.getCoverageInRange(requestInterval)) + .to.deep.equal([]); + + var progress = []; + source.on('networkprogress', e => { progress.push(e); }); + source.on('networkdone', e => { progress.push('done'); }); + source.on('newdata', () => { + requestCount += 1; + expect(requestCount == 1); + done(); + }); + + source.rangeChanged({contig: 'chrM', start: 1, stop: 30}); + source.rangeChanged({contig: 'chrM', start: 2, stop: 8}); + + server.respond(); + + }); + + it('should bin coverage over large regions', function(done) { + + var source = CoverageDataSource.create({ + url: '/coverage' + }); + var requestCount = 0; + var requestInterval = new ContigInterval('chrM', 10, 20); + expect(source.getCoverageInRange(requestInterval)) + .to.deep.equal([]); + + var progress = []; + source.on('networkprogress', e => { progress.push(e); }); + source.on('networkdone', e => { progress.push('done'); }); + source.on('newdata', () => { + requestCount += 1; + expect(requestCount == 1); + done(); + }); + + source.rangeChanged({contig: 'chrM', start: 1, stop: 30}); + source.rangeChanged({contig: 'chrM', start: 2, stop: 8}); + + server.respond(); + + }); + +}); diff --git a/src/test/sources/GA4GHDataSource-test.js b/src/test/sources/GA4GHDataSource-test.js index e6fd6467..c507cfad 100644 --- a/src/test/sources/GA4GHDataSource-test.js +++ b/src/test/sources/GA4GHDataSource-test.js @@ -8,7 +8,7 @@ import sinon from 'sinon'; import ContigInterval from '../../main/ContigInterval'; import GA4GHDataSource from '../../main/sources/GA4GHDataSource'; import RemoteFile from '../../main/RemoteFile'; - + describe('GA4GHDataSource', function() { var server: any = null, response; @@ -24,12 +24,12 @@ describe('GA4GHDataSource', function() { }); it('should fetch alignments from a server', function(done) { - server.respondWith('POST', '/v0.5.1/reads/search', + server.respondWith('POST', '/v0.5.1/reads/search/chr17?start=1&end=1000', [200, { "Content-Type": "application/json" }, response]); var source = GA4GHDataSource.create({ - endpoint: '/v0.5.1', - readGroupId: 'some-group-set:some-read-group', + endpoint: '/v0.5.1/reads', + readGroupId: 'search', killChr: false }); diff --git a/src/test/sources/ReferenceDataSource-test.js b/src/test/sources/ReferenceDataSource-test.js index c8b7f25c..ab1c86d4 100644 --- a/src/test/sources/ReferenceDataSource-test.js +++ b/src/test/sources/ReferenceDataSource-test.js @@ -63,13 +63,13 @@ it('should fetch base pairs', function(done) { var range = {contig: 'chrM', start: 0, stop: 3}; // Before data has been fetched, all base pairs are null. - expect(source.getRange(range)).to.deep.equal({ - 'chrM:0': null, - 'chrM:1': null, - 'chrM:2': null, - 'chrM:3': null - }); - expect(source.getRangeAsString(range)).to.equal('....'); + expect(source.getRange(range)).to.deep.equal({ + 'chrM:0': null, + 'chrM:1': null, + 'chrM:2': null, + 'chrM:3': null + }); + expect(source.getRangeAsString(range)).to.equal('....'); source.on('newdata', () => { expect(source.getRange(range)).to.deep.equal({ diff --git a/src/test/sources/VariantDataSource-test.js b/src/test/sources/VariantDataSource-test.js index 1cf08079..bedbc400 100644 --- a/src/test/sources/VariantDataSource-test.js +++ b/src/test/sources/VariantDataSource-test.js @@ -40,7 +40,6 @@ describe('VariantDataSource', function() { source.on('newdata', () => { var variants = source.getFeaturesInRange(range); - console.log(variants); expect(variants).to.have.length(3); expect(variants[1].contig).to.equal('chrM'); expect(variants[1].position).to.equal(20); diff --git a/test-data/chrM-coverage.json b/test-data/chrM-coverage.json new file mode 100644 index 00000000..caaeab28 --- /dev/null +++ b/test-data/chrM-coverage.json @@ -0,0 +1,49 @@ +[{ + "contig": "chrM", + "position": 10, + "count": 50 +}, { + "contig": "chrM", + "position": 11, + "count": 52 +}, { + "contig": "chrM", + "position": 12, + "count": 54 +}, { + "contig": "chrM", + "position": 13, + "count": 56 +}, { + "contig": "chrM", + "position": 14, + "count": 58 +}, { + "contig": "chrM", + "position": 15, + "count": 58 +}, { + "contig": "chrM", + "position": 16, + "count": 58 +}, { + "contig": "chrM", + "position": 17, + "count": 58 +}, { + "contig": "chrM", + "position": 18, + "count": 68 +}, { + "contig": "chrM", + "position": 19, + "count": 72 +}, { + "contig": "chrM", + "position": 20, + "count": 75 +}, { + "contig": "chrM", + "position": 21, + "count": 62 +}] diff --git a/test-data/variants-chrM-0-100.json b/test-data/variants-chrM-0-100.json index c48c5b03..44598dae 100644 --- a/test-data/variants-chrM-0-100.json +++ b/test-data/variants-chrM-0-100.json @@ -10,7 +10,7 @@ "alt": "T" }, { "contig": "chrM", - "position": 20, + "position": 23, "ref": "A", "alt": "C" }] From 1e2c14781aaf842d3932a7ef2ac920fdf426adf1 Mon Sep 17 00:00:00 2001 From: dorislee0309 Date: Fri, 1 Jul 2016 09:28:18 -0700 Subject: [PATCH 109/136] customized ALT REF colors for variants, greyed genotype --- src/main/style.js | 4 +--- src/main/viz/VariantTrack.js | 8 ++++---- 2 files changed, 5 insertions(+), 7 deletions(-) diff --git a/src/main/style.js b/src/main/style.js index e1e3d40a..a1fcd216 100644 --- a/src/main/style.js +++ b/src/main/style.js @@ -62,12 +62,10 @@ module.exports = { LOC_FONT_COLOR: 'black', // Variant Track - VARIANT_STROKE: 'blue', - VARIANT_FILL: 'blue', VARIANT_HEIGHT: 14, // Genotype Track GENOTYPE_SPACING: 1, - GENOTYPE_FILL: 'red', + GENOTYPE_FILL: '#9494b8', GENOTYPE_HEIGHT: 10, }; diff --git a/src/main/viz/VariantTrack.js b/src/main/viz/VariantTrack.js index 45ebe2c6..d19b8c8c 100644 --- a/src/main/viz/VariantTrack.js +++ b/src/main/viz/VariantTrack.js @@ -77,14 +77,14 @@ class VariantTrack extends React.Component { ctx.reset(); ctx.save(); - ctx.fillStyle = style.VARIANT_FILL; - ctx.strokeStyle = style.VARIANT_STROKE; variants.forEach(variant => { ctx.pushObject(variant); + ctx.fillStyle = style.BASE_COLORS[variant.alt]; + ctx.strokeStyle = style.BASE_COLORS[variant.ref]; var x = Math.round(scale(variant.position)); var width = Math.round(scale(variant.position + 1)) - 1 - x; - ctx.fillRect(x - 0.5, y - 0.5, width, style.VARIANT_HEIGHT); - ctx.strokeRect(x - 0.5, y - 0.5, width, style.VARIANT_HEIGHT); + ctx.fillRect(x - 0.2, y - 0.2, width, style.VARIANT_HEIGHT); + ctx.strokeRect(x - 0.2, y - 0.2, width, style.VARIANT_HEIGHT); ctx.popObject(); }); From 15a9c6c993205c6f31b95450fc00e10f32fe8305 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 4 Oct 2016 09:04:20 -0700 Subject: [PATCH 110/136] fixed versions, shorted build time --- scripts/test.sh | 3 - src/main/pileup.js | 4 +- src/test/sources/ReferenceDataSource-test.js | 210 +++++++++---------- 3 files changed, 104 insertions(+), 113 deletions(-) diff --git a/scripts/test.sh b/scripts/test.sh index 2b734566..9914fba4 100755 --- a/scripts/test.sh +++ b/scripts/test.sh @@ -3,9 +3,6 @@ # Note that you must run `npm run build` or `npm run watch` before running this. set -o errexit -# compile files for test -./scripts/quick-build.sh - # Run http-server and save its PID http-server -p 8081 > /dev/null & SERVER_PID=$! diff --git a/src/main/pileup.js b/src/main/pileup.js index afb726ce..b7328eeb 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -21,7 +21,7 @@ import GenotypeDataSource from './sources/GenotypeDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; import EmptySource from './sources/EmptySource'; -// import FeatureDataSource from './sources/FeatureDataSource'; +import FeatureDataSource from './sources/FeatureDataSource'; // Visualizations import CoverageTrack from './viz/CoverageTrack'; @@ -150,7 +150,7 @@ var pileup = { genotypes: makeVizObject(GenotypeTrack), pileup: makeVizObject(PileupTrack) }, - version: '0.6.7' + version: '0.6.8' }; module.exports = pileup; diff --git a/src/test/sources/ReferenceDataSource-test.js b/src/test/sources/ReferenceDataSource-test.js index ab1c86d4..eba5bd39 100644 --- a/src/test/sources/ReferenceDataSource-test.js +++ b/src/test/sources/ReferenceDataSource-test.js @@ -24,132 +24,126 @@ describe('ReferenceDataSource', function() { after(function () { server.restore(); }); -}); -after(function () { - server.restore(); -}); + function getTestSource() { + var source = ReferenceDataSource.create({ + url: '/reference', + contigList: [{ + name:"chrM", + length: 1000 + },{ + name:"22", + length: 1000 + }] + }); + return source; + } -function getTestSource() { - var source = ReferenceDataSource.create({ - url: '/reference', - contigList: [{ - name:"chrM", - length: 1000 - },{ - name:"22", - length: 1000 - }] + it('should fetch contigs', function() { + var source = getTestSource(); + var contigs = source.contigList(); + expect(contigs).to.deep.equal(['chrM','22']); }); - return source; -} - -it('should fetch contigs', function() { - var source = getTestSource(); - var contigs = source.contigList(); - expect(contigs).to.deep.equal(['chrM','22']); -}); - -it('should normalize range', function() { - var source = getTestSource(); - var range = {contig: 'chrM', start: 0, stop: 3}; - source.normalizeRange(range).then(normalized => { - expect(normalized.to.deep.equal(range)); - }).done(); -}); -it('should fetch base pairs', function(done) { - var source = getTestSource(); - var range = {contig: 'chrM', start: 0, stop: 3}; - - // Before data has been fetched, all base pairs are null. - expect(source.getRange(range)).to.deep.equal({ - 'chrM:0': null, - 'chrM:1': null, - 'chrM:2': null, - 'chrM:3': null + it('should normalize range', function() { + var source = getTestSource(); + var range = {contig: 'chrM', start: 0, stop: 3}; + source.normalizeRange(range).then(normalized => { + expect(normalized.to.deep.equal(range)); + }).done(); }); - expect(source.getRangeAsString(range)).to.equal('....'); - source.on('newdata', () => { + it('should fetch base pairs', function(done) { + var source = getTestSource(); + var range = {contig: 'chrM', start: 0, stop: 3}; + + // Before data has been fetched, all base pairs are null. expect(source.getRange(range)).to.deep.equal({ - 'chrM:0': 'N', - 'chrM:1': 'G', - 'chrM:2': 'T', - 'chrM:3': 'T' + 'chrM:0': null, + 'chrM:1': null, + 'chrM:2': null, + 'chrM:3': null }); - expect(source.getRangeAsString(range)).to.equal('NGTT'); + expect(source.getRangeAsString(range)).to.equal('....'); - done(); - }); - source.rangeChanged(range); - server.respond(); -}); + source.on('newdata', () => { + expect(source.getRange(range)).to.deep.equal({ + 'chrM:0': 'N', + 'chrM:1': 'G', + 'chrM:2': 'T', + 'chrM:3': 'T' + }); + expect(source.getRangeAsString(range)).to.equal('NGTT'); -it('should fetch nearby base pairs', function(done) { - var source = getTestSource(); - - source.on('newdata', () => { - expect(source.getRange({contig: 'chrM', start: 0, stop: 14})) - .to.deep.equal({ - 'chrM:0': 'N', - 'chrM:1': 'G', - 'chrM:2': 'T', - 'chrM:3': 'T', - 'chrM:4': 'A', // start of actual request - 'chrM:5': 'A', - 'chrM:6': 'T', - 'chrM:7': 'G', - 'chrM:8': 'T', - 'chrM:9': 'A', // end of actual requuest - 'chrM:10': 'G', - 'chrM:11': 'C', - 'chrM:12': 'T', - 'chrM:13': 'T', - 'chrM:14': 'A' - }); - done(); + done(); + }); + source.rangeChanged(range); + server.respond(); }); - source.rangeChanged({contig: 'chrM', start: 4, stop: 9}); - server.respond(); -}); - -it('should add chr', function(done) { - var source = getTestSource(); - var range = {contig: '22', start: 0, stop: 3}; - source.on('newdata', () => { - expect(source.getRange(range)).to.deep.equal({ - '22:0': 'N', - '22:1': 'G', - '22:2': 'T', - '22:3': 'T' + it('should fetch nearby base pairs', function(done) { + var source = getTestSource(); + + source.on('newdata', () => { + expect(source.getRange({contig: 'chrM', start: 0, stop: 14})) + .to.deep.equal({ + 'chrM:0': 'N', + 'chrM:1': 'G', + 'chrM:2': 'T', + 'chrM:3': 'T', + 'chrM:4': 'A', // start of actual request + 'chrM:5': 'A', + 'chrM:6': 'T', + 'chrM:7': 'G', + 'chrM:8': 'T', + 'chrM:9': 'A', // end of actual requuest + 'chrM:10': 'G', + 'chrM:11': 'C', + 'chrM:12': 'T', + 'chrM:13': 'T', + 'chrM:14': 'A' + }); + done(); }); - expect(source.getRangeAsString(range)).to.equal('NGTT'); - done(); + source.rangeChanged({contig: 'chrM', start: 4, stop: 9}); + server.respond(); }); - source.rangeChanged(range); - server.respond(); -}); - -it('should only report newly-fetched ranges', function(done) { - ReferenceDataSource.testBasePairsToFetch(10); - var initRange = {contig: 'chrM', start: 5, stop: 8}, - secondRange = {contig: 'chrM', start: 8, stop: 15}; - var source = getTestSource(); - source.once('newdata', newRange => { - expect(newRange.toString()).to.equal('chrM:0-10'); // expanded range - source.once('newdata', newRange => { - // This expanded range excludes previously-fetched data. - expect(newRange.toString()).to.equal('chrM:11-20'); + it('should add chr', function(done) { + var source = getTestSource(); + var range = {contig: '22', start: 0, stop: 3}; + + source.on('newdata', () => { + expect(source.getRange(range)).to.deep.equal({ + '22:0': 'N', + '22:1': 'G', + '22:2': 'T', + '22:3': 'T' + }); + expect(source.getRangeAsString(range)).to.equal('NGTT'); done(); }); - source.rangeChanged(secondRange); + source.rangeChanged(range); server.respond(); }); - source.rangeChanged(initRange); - server.respond(); -}); + it('should only report newly-fetched ranges', function(done) { + ReferenceDataSource.testBasePairsToFetch(10); + var initRange = {contig: 'chrM', start: 5, stop: 8}, + secondRange = {contig: 'chrM', start: 8, stop: 15}; + var source = getTestSource(); + source.once('newdata', newRange => { + expect(newRange.toString()).to.equal('chrM:0-10'); // expanded range + + source.once('newdata', newRange => { + // This expanded range excludes previously-fetched data. + expect(newRange.toString()).to.equal('chrM:11-20'); + done(); + }); + source.rangeChanged(secondRange); + server.respond(); + }); + source.rangeChanged(initRange); + server.respond(); + }); }); From a0f5c4d7e1886674fea141cf48b4d5625b2d4a4a Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 5 Oct 2016 09:42:56 -0700 Subject: [PATCH 111/136] small formatting nits and removing double 'strict' statement --- examples/data.js | 127 +++++++++++++++------------------ scripts/quick-build.sh | 19 ----- src/main/data/TwoBit.js | 2 +- src/main/data/VirtualOffset.js | 2 - src/main/style.js | 2 - 5 files changed, 57 insertions(+), 95 deletions(-) delete mode 100755 scripts/quick-build.sh diff --git a/examples/data.js b/examples/data.js index 86b0f074..77d16e35 100644 --- a/examples/data.js +++ b/examples/data.js @@ -1,83 +1,68 @@ // Some data for the demo. -//// We are going to use the same data source for multiple tracks -//var bamSource = pileup.formats.bam({ -// url: '/test-data/synth3.normal.17.7500000-7515000.bam', -// indexUrl: '/test-data/synth3.normal.17.7500000-7515000.bam.bai' -//}); +// We are going to use the same data source for multiple tracks +var bamSource = pileup.formats.bam({ + url: '/test-data/synth3.normal.17.7500000-7515000.bam', + indexUrl: '/test-data/synth3.normal.17.7500000-7515000.bam.bai' +}); var sources = [ { viz: pileup.viz.genome(), isReference: true, - data: pileup.formats.reference({ - url: '/reference', - contigList: [{ - name:"chrM", - length: 1000 - },{ - name:"22", - length: 1000 - }] + data: pileup.formats.twoBit({ + url: 'http://www.biodalliance.org/datasets/hg19.2bit' }), name: 'Reference' + }, + { + viz: pileup.viz.scale(), + name: 'Scale' + }, + { + viz: pileup.viz.location(), + name: 'Location' + }, + { + viz: pileup.viz.variants(), + data: pileup.formats.vcf({ + url: '/test-data/snv.chr17.vcf' + }), + name: 'Variants' + }, + { + viz: pileup.viz.genes(), + data: pileup.formats.bigBed({ + url: 'http://www.biodalliance.org/datasets/ensGene.bb' + }), + name: 'Genes' + }, + { + viz: pileup.viz.coverage(), + data: bamSource, + cssClass: 'normal', + name: 'Coverage' + }, + { + viz: pileup.viz.pileup(), + data: bamSource, + cssClass: 'normal', + name: 'Alignments' + }, + { + viz: pileup.viz.coverage(), + data: bamSource, + cssClass: 'tumor', + name: 'Coverage' + }, + { + viz: pileup.viz.pileup({ + viewAsPairs: true + }), + data: bamSource, + cssClass: 'tumor', + name: 'Alignments' } -// { -// viz: pileup.viz.genome(), -// isReference: true, -// data: pileup.formats.reference({ -// prefix:"../json/" -// }), -// name: 'Reference' -// } -// { -// viz: pileup.viz.scale(), -// name: 'Scale' -// }, -// { -// viz: pileup.viz.location(), -// name: 'Location' -// }, -// { -// viz: pileup.viz.variants(), -// data: pileup.formats.vcf({ -// url: '/test-data/snv.chr17.vcf' -// }), -// name: 'Variants' -// }, -// { -// viz: pileup.viz.genes(), -// data: pileup.formats.bigBed({ -// url: 'http://www.biodalliance.org/datasets/ensGene.bb' -// }), -// name: 'Genes' -// }, -// { -// viz: pileup.viz.coverage(), -// data: bamSource, -// cssClass: 'normal', -// name: 'Coverage' -// }, -// { -// viz: pileup.viz.pileup(), -// data: bamSource, -// cssClass: 'normal', -// name: 'Alignments' -// }, -// { -// viz: pileup.viz.coverage(), -// data: bamSource, -// cssClass: 'tumor', -// name: 'Coverage' -// }, -// { -// viz: pileup.viz.pileup({ -// viewAsPairs: true -// }), -// data: bamSource, -// cssClass: 'tumor', -// name: 'Alignments' -// } ]; -var range = {contig: 'chrM', start: 0, stop: 10}; +var range = {contig: 'chr17', start: 7512284, stop: 7512644}; diff --git a/scripts/quick-build.sh b/scripts/quick-build.sh deleted file mode 100755 index 1c617c78..00000000 --- a/scripts/quick-build.sh +++ /dev/null @@ -1,19 +0,0 @@ -#!/bin/bash -# Build require-ale and minified assets for distribution. -set -o errexit -# ./scripts/make-mini-d3.sh # TODO: remove - -# Transpile individual files. This is useful if another module, -# e.g. cycledash, wants to require('pileup'). -# The dist/test files are required for code coverage -mkdir -p dist/test/{data,source,viz} -babel src --retain-lines --ignore src/lib --out-dir dist -cp -r src/lib dist/ - -# Create dist/tests -browserify \ - -v \ - -t [ babelify --ignore src/lib ] \ - --debug \ - -o dist/tests.js \ - $(find src/test -name '*.js') diff --git a/src/main/data/TwoBit.js b/src/main/data/TwoBit.js index 1858da08..ca0231f4 100644 --- a/src/main/data/TwoBit.js +++ b/src/main/data/TwoBit.js @@ -270,4 +270,4 @@ class TwoBit { } } -module.exports = TwoBit; \ No newline at end of file +module.exports = TwoBit; diff --git a/src/main/data/VirtualOffset.js b/src/main/data/VirtualOffset.js index b3136b40..5d3dcc78 100644 --- a/src/main/data/VirtualOffset.js +++ b/src/main/data/VirtualOffset.js @@ -8,8 +8,6 @@ */ 'use strict'; -"use strict"; - class VirtualOffset { coffset: number; uoffset: number; diff --git a/src/main/style.js b/src/main/style.js index a1fcd216..b3b77a01 100644 --- a/src/main/style.js +++ b/src/main/style.js @@ -6,8 +6,6 @@ */ 'use strict'; -"use strict"; - module.exports = { // Colors for individual base pairs BASE_COLORS: { From 28451b3b4714ea7bb2b7432dc98ba52fbb603332 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 5 Oct 2016 09:43:15 -0700 Subject: [PATCH 112/136] fixed genotype samples and added unit tests --- src/main/data/GenotypeEndpoint.js | 2 +- src/main/viz/GenotypeTrack.js | 3 +- src/test/viz/GenotypeTrack-test.js | 84 ++++++++++++++++++++++++++++++ 3 files changed, 87 insertions(+), 2 deletions(-) create mode 100644 src/test/viz/GenotypeTrack-test.js diff --git a/src/main/data/GenotypeEndpoint.js b/src/main/data/GenotypeEndpoint.js index 01e0dad0..d5c04431 100644 --- a/src/main/data/GenotypeEndpoint.js +++ b/src/main/data/GenotypeEndpoint.js @@ -11,7 +11,7 @@ import type RemoteRequest from '../RemoteRequest'; import type {Variant} from './vcf'; export type Genotype = { - sampleIds: string, + sampleIds: string[], variant: Variant } diff --git a/src/main/viz/GenotypeTrack.js b/src/main/viz/GenotypeTrack.js index 56297a78..f43c6d9a 100644 --- a/src/main/viz/GenotypeTrack.js +++ b/src/main/viz/GenotypeTrack.js @@ -94,7 +94,8 @@ class GenotypeTrack extends React.Component { // This is a hack to adjust parent div for resize var el = d3utils.findParent(canvas, 'track-content'); - if (el) el.style.height = newHeight; + console.log("el", el); + // if (el) el.style.height = newHeight; ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); ctx.reset(); diff --git a/src/test/viz/GenotypeTrack-test.js b/src/test/viz/GenotypeTrack-test.js new file mode 100644 index 00000000..71cd1395 --- /dev/null +++ b/src/test/viz/GenotypeTrack-test.js @@ -0,0 +1,84 @@ +/** + * This tests that the Controls and reference track render correctly, even when + * an externally-set range uses a different chromosome naming system (e.g. '17' + * vs 'chr17'). See https://github.com/hammerlab/pileup.js/issues/146 + * @flow + */ + +'use strict'; + +import {expect} from 'chai'; + +import sinon from 'sinon'; + +import pileup from '../../main/pileup'; +import dataCanvas from 'data-canvas'; +import {waitFor} from '../async'; +import RemoteFile from '../../main/RemoteFile'; + +describe('GenotypeTrack', function() { + var server: any = null, response; + + before(function () { + return new RemoteFile('/test-data/genotypes-17.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/genotypes/17?start=1&end=1000',[200, { "Content-Type": "application/json" }, response]); + }); + }); + + var testDiv = document.getElementById('testdiv'); + + beforeEach(() => { + testDiv.style.width = '800px'; + dataCanvas.RecordingContext.recordAll(); + }); + + afterEach(() => { + dataCanvas.RecordingContext.reset(); + // avoid pollution between tests. + testDiv.innerHTML = ''; + }); + var {drawnObjects, callsOf} = dataCanvas.RecordingContext; + + function ready() { + return testDiv.querySelector('canvas') && + drawnObjects(testDiv, '.genotypes').length > 0; + } + + it('should render genotypes', function() { + var p = pileup.create(testDiv, { + // range: {contig: 'chrM', start: 0, stop: 30}, + range: {contig: '17', start: 9386380, stop: 9537420}, + tracks: [ + { + viz: pileup.viz.genome(), + data: pileup.formats.twoBit({ + url: '/test-data/test.2bit' + }), + isReference: true + }, + { + data: pileup.formats.genotypes({ + url: '/test-data/genotypes-17.json' + }), + viz: pileup.viz.genotypes(), + } + ] + }); + + return waitFor(ready, 2000) + .then(() => { + var genotypes = drawnObjects(testDiv, '.genotypes'); + var sampleIds = ["sample1", "sample2", "sample3"]; + expect(genotypes).to.have.length(3); + expect(genotypes.map(g => g.variant.position)).to.deep.equal( + [10, 20, 30]); + expect(genotypes.map(g => g.sampleIds)).to.deep.equal( + [sampleIds, sampleIds, sampleIds]); + + p.destroy(); + }); + }); + +}); From 737ca19a43596e169ab13ebbacd99b56caa3a899 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 5 Oct 2016 09:43:59 -0700 Subject: [PATCH 113/136] Removed alignment test file and renamed Alignment test suite --- src/test/ADAMAlignment-test.js | 4 +- src/test/sources/GA4GHDataSource-test.js | 3 +- test-data/adam-alignments.json | 33390 --------------------- 3 files changed, 4 insertions(+), 33393 deletions(-) delete mode 100644 test-data/adam-alignments.json diff --git a/src/test/ADAMAlignment-test.js b/src/test/ADAMAlignment-test.js index 07191353..9edda342 100644 --- a/src/test/ADAMAlignment-test.js +++ b/src/test/ADAMAlignment-test.js @@ -7,11 +7,11 @@ import GA4GHAlignment from '../main/GA4GHAlignment'; import RemoteFile from '../main/RemoteFile'; import Bam from '../main/data/bam'; -describe('GA4GHAlignment', function() { +describe('ADAMAlignment', function() { var sampleAlignments = []; before(function() { - return new RemoteFile('/test-data/adam-alignments.json').getAllString().then(data => { + return new RemoteFile('/test-data/chr17.1-250.json').getAllString().then(data => { sampleAlignments = JSON.parse(data).alignments; }); }); diff --git a/src/test/sources/GA4GHDataSource-test.js b/src/test/sources/GA4GHDataSource-test.js index c507cfad..5d85a63b 100644 --- a/src/test/sources/GA4GHDataSource-test.js +++ b/src/test/sources/GA4GHDataSource-test.js @@ -24,7 +24,8 @@ describe('GA4GHDataSource', function() { }); it('should fetch alignments from a server', function(done) { - server.respondWith('POST', '/v0.5.1/reads/search/chr17?start=1&end=1000', + // ALYSSA: TODO: should move back to POST as in original API + server.respondWith('GET', '/v0.5.1/reads/search/chr17?start=1&end=1000', [200, { "Content-Type": "application/json" }, response]); var source = GA4GHDataSource.create({ diff --git a/test-data/adam-alignments.json b/test-data/adam-alignments.json deleted file mode 100644 index e8866aa4..00000000 --- a/test-data/adam-alignments.json +++ /dev/null @@ -1,33390 +0,0 @@ -{ - "alignments": [{ - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:47:2891:8862", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 0, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 59, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 42, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATCATTGTATCCCATAAACACAAAGTTTTGGTCCTGGCCTTATAATTACTTAG", - "alignedQuality": [17, 28, 10, 23, 27, 28, 17, 31, 22, 10, 16, 19, 9, 15, 16, 22, 15, 14, 15, 20, 15, 9, 15, 15, 9, 32, 32, 25, 27, 9, 21, 25, 32, 28, 28, 31, 31, 23, 22, 22, 9, 17, 22, 12, 25, 24, 14, 10, 26, 26, 10, 32, 26, 30, 32, 31, 25, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:40:17115:17222", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 154, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 1, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 31, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 70, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTCATGTAGCTTGATAACAGCGCAAAGAACTCCAAATGCTTAGATGGATAATTGTATCCCATAAAAACAAAGGATTGGGCCTGGCCTTATAANTATTTTGA", - "alignedQuality": [31, 31, 7, 30, 7, 11, 31, 7, 31, 7, 7, 11, 6, 28, 11, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:27:8808:3060", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 2, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATNAATTAGAG", - "alignedQuality": [38, 38, 38, 38, 35, 37, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 38, 37, 38, 38, 38, 38, 38, 38, 30, 37, 35, 38, 37, 37, 37, 37, 38, 38, 38, 35, 36, 37, 37, 36, 38, 38, 38, 35, 38, 36, 37, 36, 38, 36, 37, 36, 36, 37, 33, 33, 34, 35, 36, 36, 34, 35, 35, 35, 35, 35, 36, 25, 35, 36, 30, 35, 32, 25, 26, 0, 26, 6, 29, 26, 29, 28, 22, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.3", - "fragmentName": "613F0AAXX100423:3:93:11085:15551", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 138, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 2, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "CLIP_SOFT", - "operationLength": 47, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 54, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACCAAAACTCTAATCATACTCTATTACGCAATAAACATTAACAAGATAATGTAGCTTAATAACAAAGCAAAGCACTGCATATGCTTAGATGGGTAATTGT", - "alignedQuality": [23, 18, 23, 29, 18, 30, 27, 30, 24, 27, 26, 21, 21, 11, 18, 30, 29, 23, 11, 24, 29, 18, 23, 27, 27, 30, 23, 27, 30, 27, 24, 29, 32, 24, 29, 29, 31, 31, 32, 31, 33, 33, 28, 33, 33, 27, 7, 23, 23, 23, 32, 33, 33, 27, 31, 32, 25, 33, 33, 28, 31, 24, 29, 33, 31, 16, 32, 31, 31, 19, 16, 16, 27, 29, 17, 27, 30, 29, 10, 25, 9, 29, 29, 30, 29, 31, 21, 33, 18, 31, 33, 31, 10, 18, 31, 33, 32, 32, 19, 32, 25], - 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"fragmentName": "613F0AAXX100423:7:103:9796:21327", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 26, - "reverseStrand": false - }, - "mappingQuality": 25, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGCACTGAAAATGCTTAGATGGATAATTGTATCCNATAAACACAAAGGTTTGGTCCTGGCCTTATANTTAATTAGAGGTAAAATTACAAGANNGGNNNNNN", - "alignedQuality": [24, 26, 12, 26, 25, 26, 26, 24, 26, 26, 32, 29, 30, 31, 32, 30, 34, 32, 34, 34, 28, 28, 28, 31, 28, 20, 28, 33, 25, 30, 26, 26, 29, 12, 0, 26, 32, 26, 26, 26, 32, 32, 32, 32, 32, 34, 30, 34, 34, 25, 32, 34, 32, 30, 32, 35, 35, 35, 25, 35, 35, 35, 25, 35, 30, 33, 0, 28, 30, 29, 23, 27, 24, 25, 26, 31, 29, 24, 13, 29, 32, 30, 29, 32, 28, 35, 35, 20, 25, 30, 2, 0, 0, 2, 2, 0, 0, 0, 0, 0, 0], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:43:1543:11173", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 29, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACTGAAAATGCTTAGATGGATACTTGTATCCCATAAACACAAAGGTTTGGGCCTGGCCTTATACTTAATTAGAGGTAAAATCACACATGCAANACCTCTAT", - "alignedQuality": [32, 32, 15, 32, 9, 23, 28, 30, 20, 15, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - 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"properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 187, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 32, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCNCCCATAGA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 33, 38, 37, 38, 38, 38, 38, 36, 36, 38, 38, 38, 37, 38, 38, 37, 38, 37, 36, 38, 38, 38, 33, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 34, 38, 37, 38, 37, 38, 36, 38, 38, 35, 38, 38, 38, 37, 38, 38, 37, 38, 32, 30, 0, 7, 30, 25, 25, 27, 25, 28, 31], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:107:18142:17511", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 40, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGANCGGTGTAA", - "alignedQuality": [38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 34, 37, 38, 38, 37, 36, 38, 37, 33, 37, 37, 38, 38, 38, 37, 38, 36, 37, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 34, 34, 35, 36, 37, 37, 37, 37, 38, 36, 36, 36, 37, 36, 36, 38, 36, 35, 35, 36, 35, 35, 36, 35, 33, 35, 36, 26, 32, 0, 32, 27, 19, 15, 27, 18, 21, 34], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:100:2715:9259", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 164, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 41, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 22, - "referenceSequence": null - }, { - "operation": "DELETE", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 79, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAGATGGATAATTGTATCCCATAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAA", - "alignedQuality": [36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 36, 38, 35, 38, 38, 38, 38, 35, 35, 38, 38, 38, 35, 35, 37, 38, 33, 35, 37, 38, 38, 37, 38, 37, 38, 37, 36, 30, 38, 37, 35, 37, 37, 38, 36, 35, 38, 38, 28, 36, 37, 37, 37, 37, 36, 36, 34, 36, 34, 35, 35, 32, 33, 32, 36, 36, 36, 35, 35, 36, 34, 35, 33, 34, 32, 34, 32, 36, 34, 20, 29, 33, 27, 33, 33, 33, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:21:16353:12115", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 181, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 41, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 100, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 1, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCCTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 36, 37, 36, 38, 37, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 36, 38, 38, 36, 31, 36, 36, 38, 36, 34, 38, 37, 36, 36, 37, 38, 36, 9, 37, 37, 37, 33, 34, 35, 35, 34, 35, 37, 38, 33, 37, 36, 37, 36, 34, 37, 36, 37, 37, 38, 36, 38, 35, 37, 36, 38, 36, 30, 34, 37, 35, 36, 37, 35, 36, 36, 35, 37, 36, 37, 36, 37, 36, 35, 36, 34, 31, 32, 30, 25, 31, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:101:7284:15284", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 41, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 86, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 15, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGGAAAATTACACATGCAAACCTCCAAGATCGGAAGAGCG", - "alignedQuality": [31, 21, 18, 14, 31, 15, 15, 18, 31, 16, 24, 14, 32, 23, 11, 28, 21, 33, 26, 33, 34, 25, 34, 30, 34, 34, 34, 34, 34, 28, 34, 34, 25, 12, 28, 10, 17, 28, 16, 22, 22, 7, 17, 30, 22, 14, 17, 14, 28, 13, 32, 24, 24, 27, 33, 27, 23, 22, 34, 32, 30, 29, 15, 5, 33, 11, 26, 17, 15, 16, 33, 30, 33, 19, 32, 21, 22, 22, 29, 22, 30, 20, 22, 15, 11, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:16:11065:2362", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 177, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 43, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGNGTGTAAAA", - "alignedQuality": [37, 38, 38, 38, 38, 35, 37, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 37, 38, 38, 37, 35, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 37, 38, 38, 35, 38, 38, 36, 37, 38, 37, 37, 38, 37, 37, 37, 36, 36, 38, 38, 38, 38, 38, 37, 38, 37, 36, 38, 36, 34, 36, 37, 38, 36, 38, 35, 38, 37, 37, 36, 36, 36, 36, 35, 36, 36, 35, 36, 36, 35, 36, 35, 35, 33, 36, 35, 35, 35, 30, 34, 0, 21, 24, 22, 21, 23, 25, 15, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.8", - "fragmentName": "6141AAAXX100423:8:119:13184:13731", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGTGGCTAACGAAAAAGCTTTGAAATGCTTTCTGAAGGTCCTGAAACATGCCTTTAAAATTAAAAATAAGTTTAAATGAGTTTTACACACGTTTGTGGTGT", - "alignedQuality": [16, 19, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.8", - "fragmentName": "6141AAAXX100423:8:119:13184:13731", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 43, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 88, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 13, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GATGGATAATTGTATCCCATAAACACAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGAAGACAGGA", - "alignedQuality": [18, 11, 28, 26, 11, 18, 26, 26, 11, 18, 28, 11, 30, 27, 23, 33, 23, 30, 11, 29, 30, 30, 23, 23, 18, 23, 17, 26, 11, 32, 17, 9, 23, 30, 11, 19, 22, 10, 8, 15, 15, 9, 8, 8, 30, 21, 15, 22, 8, 8, 30, 32, 18, 9, 28, 9, 32, 29, 14, 21, 11, 31, 21, 18, 21, 22, 23, 28, 28, 11, 23, 23, 9, 33, 27, 32, 33, 28, 18, 31, 33, 25, 31, 25, 31, 31, 18, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:7:7712:11139", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 43, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAGT", - "alignedQuality": [38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 37, 37, 38, 38, 38, 38, 36, 38, 38, 38, 38, 35, 38, 37, 36, 38, 38, 37, 37, 38, 38, 38, 38, 36, 38, 37, 34, 38, 36, 36, 37, 38, 38, 38, 38, 37, 37, 38, 37, 36, 37, 37, 35, 36, 35, 36, 36, 36, 36, 36, 36, 38, 33, 35, 35, 35, 36, 34, 33, 36, 34, 35, 35, 30, 34, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:45:14089:3113", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 187, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 46, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 84, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 17, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGATAATTGTATCCCATAAACACAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCC", - "alignedQuality": [28, 25, 20, 20, 28, 26, 26, 30, 26, 17, 26, 20, 27, 26, 26, 32, 30, 30, 26, 30, 34, 34, 34, 34, 34, 30, 34, 34, 20, 34, 28, 28, 20, 18, 33, 28, 18, 29, 25, 25, 28, 28, 28, 20, 25, 34, 34, 34, 34, 34, 34, 32, 26, 34, 30, 28, 20, 28, 13, 33, 32, 29, 32, 26, 19, 34, 34, 34, 30, 34, 34, 25, 20, 28, 34, 34, 30, 19, 18, 32, 26, 17, 29, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.2", - "fragmentName": "6141AAAXX100423:2:106:17757:15738", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 46, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAATCTCCATAGACCGGTGTGGGTTGGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 37, 36, 37, 38, 37, 38, 38, 38, 35, 38, 38, 37, 38, 37, 38, 38, 38, 37, 37, 38, 38, 38, 38, 37, 38, 38, 33, 37, 37, 38, 38, 36, 37, 35, 38, 37, 36, 37, 36, 37, 37, 37, 36, 37, 37, 35, 36, 36, 35, 35, 36, 36, 36, 34, 34, 33, 36, 36, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 189, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 46, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 89, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 12, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGATAATTGTATCCCATAAACACAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCC", - "alignedQuality": [32, 32, 22, 19, 17, 23, 20, 31, 23, 17, 33, 26, 26, 20, 26, 24, 25, 26, 24, 31, 21, 26, 33, 33, 18, 28, 18, 20, 5, 21, 17, 13, 26, 28, 31, 28, 16, 34, 28, 22, 34, 25, 28, 25, 29, 22, 31, 24, 22, 33, 28, 25, 34, 34, 31, 16, 29, 26, 12, 29, 10, 14, 30, 22, 29, 25, 29, 30, 29, 29, 28, 29, 20, 20, 20, 32, 29, 31, 25, 31, 33, 21, 20, 30, 30, 32, 32, 30, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:4:11279:10553", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAAATTCCCAAATAAAGACATTAACACAGCTCTACAAAGTCCAAACTCTGCATTTCTACCTCTAATGACTAATAAGTCCACAACCAACCACTCCTGTTTC", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:4:11279:10553", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 50, - "reverseStrand": false - }, - "mappingQuality": 25, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATTGGATCCCATAAACACAAAGGATTGGTCCTGGCGTTATAATTAATTAGAGGAAAGATTAGACATGCAAACCTCTACAGACCGGTGTAAAATCCCTTAA", - "alignedQuality": [31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:50:14496:18474", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 52, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGTATCCCATAAACACAAAGGTTTGGTCCTAGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 37, 30, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 32, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 35, 38, 38, 37, 37, 38, 38, 36, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 34, 38, 37, 38, 37, 38, 38, 37, 34, 38, 36, 37, 37, 35, 38, 36, 38, 37, 38, 36, 35, 37, 36, 33, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:61:6403:21082", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTGGGGGTGTGGCTATAGACACAAACGAACACACATGTTATGTACTCTCTGATCCCCACCTATTCATCAAAGAAAGTGGAATACGCATATCACCACTCCCC", - "alignedQuality": [25, 32, 24, 29, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:61:6403:21082", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 52, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 65, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 36, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGTATCCCATAAACACAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCTAACCTCCATAGACCGGTGTAAAACCCCTTAAAC", - "alignedQuality": [25, 19, 29, 25, 27, 33, 28, 28, 33, 28, 29, 29, 11, 19, 25, 26, 26, 18, 18, 18, 17, 15, 8, 31, 28, 21, 9, 16, 32, 26, 31, 33, 21, 23, 33, 33, 32, 18, 31, 18, 20, 30, 26, 23, 22, 20, 33, 22, 10, 8, 26, 27, 30, 16, 20, 24, 9, 30, 30, 21, 20, 17, 20, 17, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:69:1823:1645", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 52, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATACCTTAAAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 36, 37, 38, 34, 37, 38, 38, 38, 36, 35, 38, 37, 38, 38, 36, 37, 38, 36, 37, 37, 37, 36, 38, 35, 37, 37, 38, 37, 35, 38, 35, 37, 33, 32, 35, 37, 34, 36, 37, 30, 37, 37, 37, 36, 30, 34, 35, 36, 36, 30, 34, 31, 28, 32, 34, 34, 34, 32, 28, 34, 31, 34, 34, 32, 28, 30, 32, 29, 32, 25, 34, 27, 17, 7, 25, 22, 28, 27, 32, 27, 32, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:99:18637:3397", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 100, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 52, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATNCCCTTAAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 38, 38, 38, 36, 38, 38, 38, 36, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 36, 37, 38, 38, 38, 36, 35, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 35, 38, 36, 37, 34, 37, 38, 33, 37, 37, 37, 38, 37, 38, 37, 36, 35, 38, 35, 38, 37, 30, 37, 36, 33, 37, 32, 36, 33, 37, 25, 25, 0, 19, 27, 30, 30, 27, 28, 26, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:78:6316:4697", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGAGTCCAGAAGGACAGCGCCCACAATCCCTCGCGCCTAGCCCTTTCTTCGCCTTCCTCTCTCCTCCCTCAATTTTAAGAACATAATTATAGCTGCAAAAC", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:78:6316:4697", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 52, - "reverseStrand": false - }, - "mappingQuality": 25, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGCATCCCATAAACACAAAGGTTTGGACCTGGCCTTATAATTCATTAGAGGTAAAATTACACATGCAAACGTCCATCGACTGGTGTAAAATCCCTCAAAC", - "alignedQuality": [28, 20, 26, 13, 20, 26, 20, 26, 28, 22, 20, 24, 28, 26, 24, 32, 29, 21, 21, 34, 32, 26, 34, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:26:1496:7922", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 53, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCNACTTAAAC", - "alignedQuality": [37, 37, 37, 37, 36, 37, 32, 32, 35, 35, 37, 32, 37, 37, 37, 37, 37, 33, 37, 35, 35, 36, 37, 37, 35, 37, 37, 37, 37, 32, 37, 37, 30, 37, 37, 35, 30, 37, 36, 37, 37, 37, 36, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 35, 28, 33, 37, 37, 37, 36, 37, 37, 35, 35, 37, 37, 33, 36, 37, 37, 36, 36, 36, 33, 36, 37, 37, 36, 37, 35, 25, 36, 36, 33, 28, 33, 33, 28, 33, 33, 18, 25, 0, 10, 22, 28, 26, 28, 25, 23, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:74:10712:3372", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 53, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCACTTAAAC", - "alignedQuality": [37, 35, 38, 36, 38, 37, 37, 36, 37, 37, 38, 37, 35, 38, 37, 38, 38, 35, 35, 37, 37, 35, 37, 37, 35, 36, 33, 36, 36, 34, 37, 38, 37, 38, 35, 32, 36, 36, 36, 36, 38, 36, 36, 38, 33, 37, 35, 35, 37, 35, 36, 32, 36, 36, 36, 28, 31, 31, 34, 32, 37, 36, 37, 32, 36, 36, 35, 35, 37, 37, 31, 35, 35, 32, 30, 36, 32, 33, 36, 33, 33, 35, 30, 31, 33, 32, 35, 28, 31, 35, 22, 20, 27, 6, 27, 27, 26, 25, 22, 23, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:84:2459:12292", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 54, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCNCTTAAACA", - "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 35, 38, 37, 38, 37, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 34, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 37, 37, 37, 37, 32, 37, 36, 36, 37, 35, 36, 36, 37, 35, 36, 34, 34, 36, 35, 33, 35, 34, 35, 35, 35, 35, 35, 24, 30, 0, 8, 18, 20, 23, 23, 20, 24, 30], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:37:8169:13015", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 55, - "reverseStrand": false - }, - "mappingQuality": 25, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATCCCATAAACACAAAGGTCTGGTCCTGGCCCTATAACTAATTAGAGGTAAAATTACACATGCACACCTCTATAGACCCGTGTCAAATCTTCTACACCTC", - "alignedQuality": [32, 11, 33, 32, 33, 24, 14, 30, 20, 13, 12, 8, 6, 29, 25, 12, 21, 14, 7, 30, 10, 31, 7, 32, 15, 32, 16, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 55, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 75, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 26, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGCAAAATTACACATGCAAACCTCCATAGCCCGGAGAAAAACCCCNATACACAT", - "alignedQuality": [22, 21, 25, 9, 28, 17, 22, 17, 27, 31, 26, 17, 26, 27, 26, 22, 17, 17, 17, 18, 32, 26, 15, 9, 9, 22, 22, 17, 8, 21, 14, 29, 33, 21, 30, 21, 13, 16, 17, 24, 27, 23, 11, 33, 18, 25, 14, 26, 9, 8, 9, 21, 21, 23, 29, 31, 31, 28, 28, 25, 32, 32, 33, 32, 33, 33, 33, 29, 11, 32, 20, 7, 15, 25, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:48:2158:5284", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGTGTGGCTAAAAAAAGGGGCTTTAACCATTTTTATTTGCTTGTTACCCCCTCCCTTTATTTTTAAAAAAAATTTATAGGATTTTTCACCCGGCTCTGGGG", - "alignedQuality": [31, 31, 28, 31, 30, 31, 32, 31, 30, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:45:14369:17254", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCGTGGGGGTGTGGCTAACTAAAGAATCGTTATGTCATTTTAAATTAATTTTACACTTTCCTCTAATTTTAAAGAAAAATTTTATGGGTTGTTTACAGCAC", - "alignedQuality": [26, 26, 26, 27, 23, 23, 27, 27, 23, 32, 31, 32, 33, 11, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:45:14369:17254", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 61, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGAGTAAAATCCCTTAAACATTTACTTA", - "alignedQuality": [30, 28, 24, 26, 25, 29, 28, 28, 30, 29, 17, 22, 22, 19, 22, 31, 31, 26, 34, 33, 25, 34, 34, 25, 32, 28, 28, 28, 31, 28, 31, 31, 31, 21, 30, 20, 26, 26, 26, 26, 25, 28, 20, 33, 30, 32, 33, 35, 33, 30, 30, 29, 26, 31, 31, 29, 29, 32, 32, 33, 32, 30, 28, 34, 34, 32, 32, 25, 32, 33, 34, 28, 12, 34, 34, 8, 22, 10, 20, 30, 28, 17, 23, 26, 11, 15, 31, 25, 28, 18, 15, 15, 23, 20, 32, 34, 25, 20, 32, 25, 28], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:97:6550:8373", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 179, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 61, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACGCATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACCTCTACTTC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 35, 38, 38, 38, 37, 37, 35, 36, 38, 38, 37, 38, 36, 36, 38, 38, 37, 38, 36, 36, 36, 37, 36, 33, 36, 37, 36, 37, 35, 33, 36, 36, 34, 36, 34, 36, 35, 33, 36, 36, 35, 36, 31, 35, 35, 32, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:8:19398:15767", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 97, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 61, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACNATTTAAGA", - "alignedQuality": [37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 35, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 35, 38, 38, 38, 38, 37, 38, 38, 37, 35, 38, 38, 38, 38, 38, 36, 38, 38, 35, 38, 33, 38, 38, 36, 37, 36, 38, 36, 37, 36, 37, 36, 37, 37, 38, 36, 38, 35, 36, 36, 36, 32, 37, 34, 36, 35, 36, 35, 35, 34, 35, 34, 35, 34, 36, 35, 21, 18, 0, 15, 24, 22, 22, 25, 23, 23, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.7", - "fragmentName": "6141AAAXX100423:7:116:1040:2014", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 180, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 61, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 64, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 37, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAAACACAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAAACTCCATAGATTGNAGNNNNNNNNNNNNNNNNNNNNNNNN", - "alignedQuality": [28, 16, 14, 28, 17, 21, 29, 26, 27, 28, 24, 26, 26, 17, 20, 24, 24, 20, 24, 32, 26, 24, 24, 30, 17, 24, 24, 20, 24, 26, 28, 28, 33, 28, 13, 25, 30, 18, 28, 29, 34, 34, 26, 25, 34, 32, 32, 30, 34, 29, 25, 10, 12, 33, 30, 30, 32, 34, 34, 32, 34, 21, 28, 34, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:83:17153:4354", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 62, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACANTTTACTTA", - "alignedQuality": [38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 38, 37, 35, 37, 37, 37, 37, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 35, 38, 37, 37, 35, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 36, 38, 36, 38, 38, 38, 36, 37, 38, 36, 38, 38, 38, 36, 33, 37, 33, 37, 30, 33, 38, 35, 36, 32, 36, 35, 35, 31, 36, 35, 35, 35, 36, 31, 33, 28, 20, 0, 9, 19, 18, 18, 23, 19, 21, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:38:19313:14863", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 177, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 63, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 75, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 26, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGCGTAAAATCCTTTAACAATTCACTTAAA", - "alignedQuality": [33, 36, 30, 35, 36, 36, 35, 30, 36, 33, 35, 36, 20, 36, 35, 30, 34, 36, 36, 33, 35, 32, 30, 33, 36, 37, 37, 37, 37, 37, 37, 35, 30, 35, 32, 36, 30, 36, 30, 33, 20, 29, 34, 25, 34, 30, 32, 34, 34, 34, 33, 36, 36, 36, 36, 35, 37, 35, 36, 32, 30, 33, 30, 31, 28, 33, 33, 33, 12, 20, 26, 30, 20, 8, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:113:6641:2087", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 105, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 64, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTNACTTAAAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 36, 35, 38, 38, 38, 36, 36, 37, 36, 37, 37, 37, 36, 37, 35, 33, 36, 37, 36, 35, 34, 37, 34, 36, 35, 28, 36, 35, 36, 35, 35, 35, 34, 35, 34, 35, 35, 35, 31, 31, 0, 31, 31, 29, 30, 29, 25, 29, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:103:10989:15255", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCCGTGGGGGTGTGGCTAAAAAAAGGGGCTTTAGACATTTTTATTTTCTTGGTACACTCTCCTTCAATTTTTAATAAAATTTTTTAGGGTTTTTTTACGGG", - "alignedQuality": [32, 31, 29, 32, 30, 32, 25, 31, 31, 31, 26, 32, 29, 31, 32, 32, 29, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:103:10989:15255", - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:94:5017:20924", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 66, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAACATT", - "alignedQuality": [37, 37, 37, 37, 37, 34, 36, 36, 36, 36, 37, 37, 37, 37, 37, 36, 38, 38, 37, 38, 38, 38, 38, 38, 35, 36, 37, 37, 38, 38, 38, 38, 38, 36, 36, 35, 37, 37, 35, 37, 38, 35, 38, 38, 37, 38, 38, 38, 38, 35, 37, 38, 38, 33, 37, 37, 35, 38, 37, 38, 36, 36, 35, 38, 36, 37, 35, 32, 35, 36, 28, 32, 33, 34, 32, 33, 37, 36, 30, 32, 36, 33, 35, 33, 12, 25, 32, 29, 23, 26, 33, 31, 32, 33, 32, 32, 20, 12, 33, 32, 33], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:90:5251:10922", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 168, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 67, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGCGTAAAATCCCTTAAACATTTACTTAAAATTT", - "alignedQuality": [38, 38, 38, 38, 37, 38, 36, 37, 38, 38, 38, 38, 36, 38, 38, 38, 36, 37, 38, 38, 38, 38, 38, 37, 35, 38, 38, 38, 38, 37, 38, 38, 38, 32, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 30, 37, 38, 38, 35, 35, 37, 38, 36, 37, 36, 38, 38, 37, 38, 35, 38, 37, 38, 36, 37, 37, 37, 12, 31, 30, 25, 31, 31, 36, 36, 36, 32, 32, 36, 35, 33, 28, 33, 36, 35, 35, 32, 31, 35, 35, 36, 35, 36, 30, 35, 30, 36, 35, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:13:1683:1249", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 178, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 67, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAACTTT", - "alignedQuality": [38, 38, 38, 38, 38, 37, 37, 34, 37, 37, 35, 36, 33, 36, 34, 36, 38, 37, 38, 38, 38, 38, 36, 38, 37, 37, 38, 36, 35, 38, 37, 37, 37, 37, 32, 37, 37, 34, 37, 37, 38, 38, 38, 33, 37, 36, 38, 36, 32, 38, 38, 33, 37, 36, 38, 36, 35, 35, 38, 36, 36, 36, 36, 36, 36, 34, 36, 35, 35, 33, 35, 32, 35, 34, 35, 34, 35, 30, 34, 34, 34, 34, 34, 34, 33, 34, 34, 34, 34, 30, 34, 30, 34, 32, 34, 30, 32, 8, 32, 25, 15], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.8", - "fragmentName": "6141AAAXX100423:8:30:1383:5864", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 168, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 67, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 80, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 21, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTACAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTCGCCCCCCCCC", - "alignedQuality": [29, 28, 29, 12, 20, 32, 32, 32, 32, 32, 25, 35, 33, 33, 35, 32, 30, 25, 32, 34, 35, 35, 25, 35, 25, 12, 32, 29, 30, 32, 26, 29, 20, 24, 24, 25, 22, 21, 9, 9, 21, 21, 17, 22, 22, 25, 22, 6, 23, 22, 35, 30, 32, 35, 32, 35, 35, 20, 33, 33, 28, 30, 12, 12, 20, 34, 31, 26, 26, 28, 21, 24, 29, 31, 31, 34, 30, 12, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:10:3803:7158", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 101, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 68, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 97, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 4, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAAGGCTTGGTCCTGGCCTTATAATTAATTAGAGGAAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCTCTAAACATTTACTNAAAATATA", - "alignedQuality": [22, 19, 9, 7, 19, 21, 11, 26, 24, 14, 24, 29, 20, 12, 15, 11, 11, 11, 18, 22, 24, 26, 26, 25, 16, 24, 24, 20, 23, 20, 11, 22, 18, 29, 17, 16, 10, 20, 20, 22, 25, 28, 28, 28, 13, 27, 26, 20, 12, 20, 18, 18, 28, 22, 17, 18, 31, 22, 21, 22, 18, 17, 22, 17, 14, 26, 26, 20, 31, 32, 16, 12, 33, 33, 21, 18, 9, 16, 8, 7, 32, 30, 10, 32, 21, 17, 29, 28, 33, 16, 15, 18, 0, 21, 18, 26, 32, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.6", - "fragmentName": "613F0AAXX100423:6:99:6691:8008", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 68, - "reverseStrand": false - }, - "mappingQuality": 17, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAAGGCTTGGTCCTGGCCTTATACTTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTA", - "alignedQuality": [32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:15:18178:9141", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 118, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 68, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 86, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 15, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGAACGGTGTAAAATCCCTTAAACATTTAGTTACTATTTC", - "alignedQuality": [35, 35, 35, 35, 32, 35, 30, 25, 35, 32, 28, 27, 29, 28, 27, 34, 28, 35, 33, 35, 35, 32, 28, 35, 33, 35, 34, 33, 25, 35, 28, 34, 29, 26, 29, 24, 12, 11, 32, 20, 16, 33, 33, 33, 21, 31, 31, 34, 32, 30, 25, 34, 32, 20, 12, 23, 23, 33, 15, 13, 19, 13, 18, 27, 4, 25, 33, 28, 18, 29, 25, 20, 29, 29, 25, 17, 29, 22, 19, 19, 23, 18, 22, 21, 19, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:84:13828:6520", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 163, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 70, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 91, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 10, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTCACAACTACAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 37, 35, 36, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 37, 38, 38, 37, 38, 38, 36, 38, 38, 36, 38, 37, 38, 38, 38, 38, 36, 38, 30, 38, 38, 38, 38, 36, 38, 32, 37, 36, 38, 36, 38, 35, 38, 35, 34, 25, 36, 34, 28, 20, 28, 28, 33, 30, 31, 25, 20, 30, 30, 27, 9, 25, 34, 12, 28, 11, 10, 23, 16, 24, 33, 30, 20, 36, 25, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:15:10605:11846", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 71, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAANAATTTAAG", - "alignedQuality": [36, 36, 36, 34, 36, 37, 37, 37, 35, 38, 37, 36, 37, 37, 37, 38, 38, 38, 36, 38, 37, 37, 38, 38, 38, 36, 38, 37, 38, 37, 36, 36, 37, 34, 38, 36, 37, 28, 38, 37, 37, 36, 36, 37, 37, 36, 38, 38, 38, 38, 36, 36, 35, 30, 36, 35, 35, 36, 36, 36, 36, 35, 34, 36, 35, 34, 36, 34, 36, 34, 33, 36, 34, 33, 34, 34, 34, 34, 32, 34, 34, 36, 35, 35, 25, 35, 34, 35, 34, 34, 28, 29, 0, 7, 26, 24, 26, 24, 27, 25, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:94:18554:7515", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 186, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 71, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGGTTTGGTCCTGGCCCTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGG", - "alignedQuality": [38, 37, 38, 36, 38, 38, 38, 38, 35, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 37, 38, 37, 38, 38, 36, 38, 37, 35, 38, 35, 38, 38, 37, 37, 38, 36, 38, 36, 35, 38, 37, 37, 36, 38, 37, 36, 36, 38, 35, 36, 35, 36, 37, 35, 35, 36, 36, 36, 35, 37, 35, 33, 36, 33, 36, 25, 36, 34, 34, 34, 36, 35, 35, 35, 35, 35, 28, 34, 35, 35, 34, 35, 33, 35, 36, 34, 36, 33, 35, 28, 35, 29, 32, 34, 28, 34, 22], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:56:8831:15599", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 72, - "reverseStrand": false - }, - "mappingQuality": 25, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAAAGATCGGA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 38, 38, 38, 37, 35, 38, 37, 38, 37, 38, 37, 38, 38, 37, 37, 37, 37, 38, 37, 38, 37, 38, 37, 36, 37, 36, 36, 37, 37, 37, 31, 35, 36, 36, 36, 34, 33, 35, 33, 35, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.3", - "fragmentName": "613F0AAXX100423:3:82:8502:16782", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 130, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 74, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCACACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGA", - "alignedQuality": [35, 33, 35, 20, 25, 33, 34, 33, 35, 25, 35, 25, 33, 35, 35, 30, 35, 25, 35, 35, 29, 32, 30, 34, 25, 35, 28, 33, 35, 35, 34, 30, 33, 35, 35, 34, 35, 25, 34, 35, 32, 34, 32, 28, 35, 34, 12, 28, 31, 25, 29, 29, 20, 30, 28, 20, 30, 32, 26, 30, 30, 20, 27, 32, 25, 29, 10, 11, 26, 30, 33, 33, 30, 20, 33, 17, 24, 12, 17, 15, 30, 20, 33, 30, 30, 25, 22, 26, 10, 26, 28, 28, 29, 29, 25, 30, 28, 12, 30, 20, 22], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:86:18532:14392", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 75, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTNAAGGAGAG", - "alignedQuality": [38, 38, 38, 37, 37, 38, 38, 38, 36, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 35, 38, 38, 38, 37, 38, 38, 30, 38, 38, 38, 38, 38, 38, 38, 35, 38, 37, 38, 37, 38, 38, 38, 38, 38, 36, 38, 38, 37, 37, 38, 38, 37, 37, 37, 35, 37, 36, 37, 38, 38, 32, 38, 37, 38, 37, 35, 37, 38, 33, 37, 38, 35, 38, 36, 37, 38, 38, 37, 38, 38, 37, 37, 37, 30, 32, 0, 26, 32, 17, 26, 23, 16, 22, 31], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:24:8390:5967", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 78, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAANGGAGAGGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 38, 38, 35, 37, 37, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 37, 37, 38, 38, 37, 38, 32, 38, 36, 38, 36, 37, 38, 38, 38, 38, 38, 38, 38, 36, 36, 36, 37, 37, 38, 36, 36, 37, 37, 38, 36, 38, 35, 36, 35, 37, 36, 36, 30, 28, 0, 16, 25, 26, 25, 18, 30, 25, 24], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:37:11670:10031", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 117, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 79, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 9, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCCTGGCCTTATAATTAATTGGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGNAAGAGGGT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 36, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 36, 38, 36, 38, 38, 38, 37, 38, 36, 38, 36, 37, 38, 37, 37, 36, 37, 37, 37, 36, 36, 37, 37, 35, 37, 36, 33, 28, 35, 38, 37, 37, 36, 26, 33, 0, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:68:10831:5608", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 82, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 80, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 21, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGGCCTTATAATTCATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGCAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGACACACAAC", - "alignedQuality": [33, 18, 28, 20, 28, 30, 31, 28, 31, 34, 34, 32, 34, 12, 28, 17, 24, 32, 25, 31, 34, 33, 32, 34, 34, 32, 34, 32, 34, 34, 30, 34, 32, 32, 34, 26, 30, 33, 19, 32, 26, 31, 34, 28, 32, 34, 34, 33, 25, 33, 34, 22, 24, 34, 32, 29, 8, 34, 22, 16, 23, 30, 30, 24, 25, 17, 20, 34, 34, 28, 23, 23, 8, 25, 30, 33, 23, 17, 27, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:2:12805:15961", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 82, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 9, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGGCCTTATAATTAATTAGAGGTAAAATTACACATGTAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGNAGGGTATC", - "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 37, 35, 38, 38, 38, 38, 35, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 37, 38, 37, 38, 38, 36, 38, 38, 38, 37, 38, 38, 38, 38, 38, 35, 38, 35, 38, 38, 37, 37, 38, 38, 38, 38, 38, 38, 38, 36, 28, 31, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:78:13618:8833", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 84, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGCGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGCGTATCAA", - "alignedQuality": [38, 35, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 20, 36, 36, 36, 36, 36, 38, 38, 36, 38, 38, 38, 36, 38, 38, 38, 38, 38, 35, 37, 38, 37, 38, 38, 38, 38, 37, 35, 12, 37, 35, 38, 36, 36, 37, 38, 38, 36, 38, 36, 36, 35, 28, 36, 37, 36, 37, 35, 37, 36, 37, 37, 37, 36, 34, 35, 35, 36, 35, 36, 36, 37, 35, 34, 33, 36, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:84:4613:3792", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 85, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGTATATCAAG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 38, 37, 36, 38, 38, 38, 38, 38, 36, 38, 36, 38, 37, 37, 36, 37, 38, 37, 38, 37, 33, 37, 37, 37, 36, 38, 37, 35, 35, 36, 36, 36, 28, 30, 30, 20, 11, 25, 20, 21, 24, 15, 20, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:107:6156:15270", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 116, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 85, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 9, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCTTATAATTAATTAGAGGTAAAATTACACATACAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGNATATCAAG", - "alignedQuality": [38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 35, 38, 38, 38, 35, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 20, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 32, 36, 36, 36, 36, 38, 38, 35, 38, 38, 38, 38, 38, 38, 25, 36, 28, 36, 28, 36, 36, 36, 28, 36, 36, 37, 37, 33, 30, 25, 36, 35, 36, 36, 36, 38, 35, 33, 36, 38, 33, 30, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:99:1424:17385", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 86, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTTTTAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCACGCA", - "alignedQuality": [38, 38, 38, 37, 38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 36, 38, 38, 38, 35, 35, 36, 38, 36, 38, 34, 37, 34, 37, 37, 37, 37, 38, 33, 38, 37, 37, 38, 28, 37, 37, 38, 37, 38, 38, 38, 37, 35, 38, 38, 38, 33, 35, 36, 33, 37, 25, 36, 38, 36, 36, 36, 37, 28, 25, 31, 25, 23, 15, 30, 30, 30], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:82:6224:14395", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 95, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCACGCACACACACAA", - "alignedQuality": [37, 37, 38, 38, 36, 37, 37, 37, 37, 34, 35, 36, 33, 36, 36, 38, 38, 36, 38, 38, 35, 35, 37, 38, 38, 38, 36, 38, 36, 37, 36, 38, 35, 38, 38, 37, 38, 33, 32, 38, 37, 32, 37, 35, 36, 35, 37, 37, 37, 37, 35, 36, 34, 36, 35, 28, 37, 34, 37, 36, 37, 35, 31, 36, 28, 32, 32, 34, 34, 34, 36, 35, 36, 20, 35, 32, 30, 25, 34, 34, 20, 31, 11, 7, 30, 27, 28, 28, 6, 21, 33, 15, 31, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:82:10630:4431", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 168, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 96, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACNTTTAAAAT", - "alignedQuality": [38, 38, 38, 38, 38, 36, 37, 38, 38, 38, 37, 36, 25, 37, 37, 38, 37, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 36, 38, 38, 38, 38, 38, 38, 37, 38, 37, 35, 38, 37, 37, 33, 36, 37, 38, 38, 38, 38, 36, 38, 37, 37, 38, 37, 38, 37, 38, 37, 38, 35, 36, 35, 37, 38, 36, 38, 36, 36, 37, 36, 36, 38, 36, 37, 36, 37, 33, 33, 37, 33, 28, 33, 34, 31, 27, 27, 0, 8, 18, 19, 22, 22, 18, 25, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:15:4665:11101", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 96, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTAGAGGAAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATATAAGGAGAGGGTATCAAGCACATTAAAATA", - "alignedQuality": [28, 20, 18, 30, 13, 7, 8, 12, 7, 21, 33, 14, 33, 33, 33, 33, 15, 20, 14, 18, 32, 16, 32, 32, 17, 12, 14, 12, 29, 26, 33, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:51:4149:16879", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 96, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTAGGGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 28, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 38, 38, 38, 38, 35, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 35, 38, 38, 38, 37, 38, 38, 37, 38, 38, 38, 38, 36, 38, 38, 36, 35, 37, 38, 37, 38, 35, 37, 35, 37, 37, 37, 38, 37, 37, 38, 33, 36, 35, 36, 30, 36, 36, 37, 35, 38, 38, 36, 35, 35, 37, 36, 37, 32, 37], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:87:8203:7507", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 96, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACNTTTAAAAT", - "alignedQuality": [38, 38, 38, 28, 35, 38, 38, 35, 37, 38, 35, 36, 30, 37, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 36, 36, 32, 36, 36, 36, 36, 37, 38, 38, 38, 34, 35, 37, 37, 37, 33, 38, 36, 38, 38, 37, 38, 38, 38, 37, 38, 36, 35, 32, 36, 37, 36, 35, 36, 37, 36, 35, 36, 38, 36, 37, 37, 36, 33, 35, 36, 36, 36, 35, 35, 36, 28, 29, 0, 11, 25, 22, 23, 22, 16, 23, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:83:12309:12275", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 178, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 97, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACACTAAAATAG", - "alignedQuality": [37, 38, 37, 38, 38, 38, 38, 37, 38, 38, 36, 20, 36, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 36, 38, 37, 38, 38, 35, 38, 36, 36, 38, 36, 38, 38, 38, 38, 38, 37, 37, 38, 33, 38, 37, 37, 37, 33, 37, 37, 36, 37, 36, 35, 37, 38, 36, 36, 32, 36, 36, 32, 35, 36, 36, 35, 35, 35, 36, 35, 35, 35, 32, 33, 33, 25, 34, 34, 34, 34, 35, 35, 33, 33, 27, 33, 20, 28, 29, 29, 29, 31, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:99:2873:11239", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 180, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 98, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATNAAAATAGC", - "alignedQuality": [38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 30, 36, 36, 33, 36, 38, 37, 38, 38, 38, 38, 37, 35, 38, 38, 35, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 37, 35, 38, 36, 38, 37, 37, 38, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 37, 36, 37, 36, 37, 34, 38, 33, 33, 37, 37, 30, 37, 35, 37, 36, 37, 30, 35, 35, 37, 36, 36, 36, 36, 37, 35, 29, 31, 0, 29, 7, 17, 24, 21, 21, 17, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:89:9024:14985", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 99, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTNAAATAGCT", - "alignedQuality": [36, 38, 38, 38, 38, 38, 38, 37, 38, 25, 35, 36, 36, 36, 36, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 36, 38, 32, 38, 38, 38, 37, 35, 36, 37, 37, 38, 38, 30, 37, 36, 38, 36, 37, 38, 37, 38, 38, 35, 38, 38, 38, 36, 38, 37, 38, 38, 38, 38, 33, 36, 37, 38, 36, 38, 37, 38, 32, 37, 36, 37, 37, 37, 30, 35, 31, 28, 36, 36, 33, 36, 36, 38, 28, 36, 37, 24, 28, 0, 25, 15, 20, 20, 21, 26, 24, 37], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:7:14929:17117", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 99, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGAGGGAAAGTTACACATGCAAACCTCCATACACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCTAGCACATTGAAATAGCT", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:35:11834:16627", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 178, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 102, - "reverseStrand": false - }, - "mappingQuality": 17, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGCAAAATTACACATGCAAACCTCCATAGACCGGAGAAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGAGCATCACGCACATTACCATCGCTTAA", - "alignedQuality": [32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:103:2795:18322", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 103, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAANAGCTTAAG", - "alignedQuality": [38, 38, 38, 38, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 32, 35, 10, 35, 35, 36, 36, 36, 34, 36, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 38, 38, 36, 37, 38, 37, 36, 37, 37, 38, 37, 38, 33, 36, 36, 36, 36, 36, 36, 36, 36, 36, 35, 33, 36, 37, 36, 31, 33, 0, 18, 25, 23, 23, 26, 23, 27, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:18:16997:14849", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 167, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 103, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAANAGCTTAAG", - "alignedQuality": [36, 36, 36, 36, 36, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 36, 38, 36, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 37, 38, 38, 38, 36, 37, 38, 38, 36, 33, 38, 38, 38, 37, 38, 34, 38, 38, 38, 36, 37, 37, 37, 38, 38, 36, 36, 37, 38, 35, 32, 33, 0, 18, 27, 24, 23, 29, 24, 27, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:12:5463:17668", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 178, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 105, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATANACTTAAGA", - "alignedQuality": [38, 38, 38, 36, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 37, 37, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 35, 37, 36, 37, 37, 38, 37, 38, 37, 33, 35, 36, 36, 38, 37, 38, 36, 38, 33, 38, 37, 36, 36, 36, 37, 36, 30, 33, 38, 36, 36, 37, 30, 36, 37, 28, 31, 0, 15, 26, 28, 26, 27, 28, 27, 35], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.6", - "fragmentName": "613F0AAXX100423:6:81:2952:2378", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 178, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 106, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACG", - "alignedQuality": [37, 38, 30, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 36, 38, 38, 38, 38, 37, 38, 37, 38, 36, 38, 38, 38, 37, 38, 35, 37, 38, 38, 36, 36, 38, 35, 36, 38, 37, 36, 25, 34, 22, 32, 32, 34, 33, 34, 34, 36, 36, 35, 35, 36, 34, 36, 25, 36, 35, 36, 37, 35, 30, 33, 35, 35, 36, 36, 36, 35, 35], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.2", - "fragmentName": "6141AAAXX100423:2:83:5909:16925", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 168, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 110, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 91, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 10, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGGGGGTATCAAGCACATTAAAATAGCTTAAGACCCCCA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 35, 38, 35, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 37, 28, 31, 16, 34, 29, 34, 34, 32, 32, 34, 38, 37, 37, 35, 38, 37, 37, 38, 35, 34, 36, 37, 36, 36, 36, 35, 34, 38, 26, 35, 35, 35, 36, 35, 36, 36, 37, 37, 38, 35, 36, 35, 36, 36, 38, 35, 36, 33, 28, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:51:4491:5009", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 101, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 112, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CACATGCAAACCTCCATAGACCGATGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTACGAACACTAGC", - "alignedQuality": [37, 36, 37, 37, 35, 37, 35, 35, 32, 37, 35, 30, 36, 36, 33, 36, 36, 35, 35, 30, 36, 35, 34, 33, 34, 35, 37, 35, 37, 35, 37, 37, 33, 35, 35, 36, 28, 28, 36, 33, 37, 33, 30, 37, 37, 20, 29, 30, 30, 29, 19, 17, 24, 24, 29, 32, 26, 12, 20, 30, 27, 29, 29, 25, 29, 31, 14, 31, 31, 28, 32, 32, 30, 33, 31, 30, 33, 25, 31, 31, 25, 33, 31, 30, 30, 30, 25, 30, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.7", - "fragmentName": "613F0AAXX100423:7:89:1974:2032", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 179, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 113, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 95, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 6, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGGATCAAGCACATTAAAATAGCTTAAGACACCTTGCC", - "alignedQuality": [34, 34, 33, 34, 34, 28, 34, 34, 34, 30, 34, 34, 34, 34, 26, 26, 34, 34, 30, 21, 28, 28, 25, 20, 28, 34, 34, 34, 33, 34, 34, 34, 34, 25, 34, 34, 34, 25, 30, 33, 34, 34, 20, 25, 34, 23, 33, 32, 29, 30, 34, 33, 34, 34, 33, 33, 28, 33, 33, 20, 28, 21, 28, 17, 28, 10, 30, 33, 30, 18, 29, 24, 8, 16, 29, 30, 30, 30, 33, 12, 33, 32, 30, 33, 30, 19, 30, 33, 33, 33, 30, 28, 32, 28, 32, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:1:5113:6786", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 129, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 114, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 95, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 6, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACNCCTTGCCT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 36, 26, 36, 36, 36, 36, 38, 38, 37, 35, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 37, 38, 30, 37, 33, 33, 36, 36, 36, 34, 36, 38, 34, 37, 37, 38, 37, 38, 35, 38, 37, 37, 38, 36, 32, 33, 36, 37, 36, 25, 32, 32, 0, 25, 30, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:86:12263:12921", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 139, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 116, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACATTGCCTAG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 30, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 28, 38, 38, 38, 38, 38, 38, 38, 38, 34, 37, 38, 38, 36, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 36, 38, 37, 38, 37, 37, 37, 36, 35, 37, 36, 38, 37, 34, 35, 8, 32, 32, 33, 30, 33, 31, 33, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:10:3273:9196", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 116, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTATGACACCTTGCCTAG", - "alignedQuality": [28, 28, 29, 28, 28, 26, 33, 21, 29, 31, 35, 28, 35, 33, 30, 29, 26, 31, 31, 29, 28, 32, 30, 32, 25, 17, 9, 28, 25, 23, 35, 30, 33, 35, 33, 35, 32, 35, 35, 35, 30, 35, 33, 35, 34, 35, 30, 33, 35, 35, 33, 35, 25, 35, 35, 35, 25, 35, 34, 35, 35, 33, 22, 35, 35, 30, 28, 34, 34, 34, 35, 20, 33, 34, 32, 35, 30, 33, 35, 32, 25, 33, 30, 33, 30, 29, 11, 29, 31, 28, 32, 32, 20, 25, 29, 31, 25, 28, 9, 31, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:99:15593:8631", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 117, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 35, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 36, 38, 38, 38, 38, 36, 38, 37, 36, 38, 36, 38, 36, 37, 34, 37, 36, 37, 36, 36, 37, 38, 36, 37, 36, 37, 33, 32, 36, 35, 36, 36, 36, 33, 37, 25, 36, 33, 36, 35, 36, 37, 36, 35, 34, 35, 35, 35, 33, 35, 35, 36, 28, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:19:15882:10660", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 118, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTNGCCTAGCC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 37, 37, 36, 38, 37, 38, 35, 37, 38, 38, 37, 37, 37, 38, 38, 38, 38, 38, 38, 36, 38, 37, 36, 37, 37, 38, 38, 38, 36, 36, 38, 38, 38, 38, 37, 37, 38, 37, 36, 38, 37, 36, 38, 37, 33, 33, 36, 36, 37, 36, 35, 37, 37, 37, 37, 35, 37, 36, 37, 35, 37, 36, 36, 36, 36, 35, 36, 36, 36, 36, 36, 36, 36, 35, 29, 31, 0, 29, 28, 29, 25, 29, 29, 28, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:16:19656:17183", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 118, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTNGCCTAGCC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 30, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 34, 37, 38, 38, 35, 38, 38, 37, 37, 37, 37, 38, 37, 38, 37, 36, 38, 37, 38, 33, 35, 36, 37, 36, 38, 36, 36, 36, 33, 36, 31, 31, 0, 31, 20, 28, 27, 24, 27, 27, 37], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:120:2445:12049", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 186, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 119, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTNCCCTAGCC", - "alignedQuality": [38, 37, 38, 37, 38, 38, 38, 38, 37, 38, 35, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 35, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 37, 33, 38, 36, 37, 37, 37, 32, 37, 37, 37, 37, 35, 37, 37, 37, 36, 37, 37, 37, 37, 35, 36, 36, 35, 35, 36, 36, 35, 35, 36, 36, 35, 35, 33, 37, 36, 35, 23, 18, 0, 16, 24, 28, 22, 23, 23, 25, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:94:1337:1612", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 121, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGTACATTAAAATAGCTTAAGACACCTTGCCTAGCTACA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 36, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 37, 37, 38, 38, 36, 38, 36, 38, 37, 38, 35, 35, 37, 36, 35, 36, 34, 37, 33, 36, 32, 34, 35, 32, 33, 33, 33, 11, 34, 34, 36, 34, 34, 35, 33, 35, 35, 35, 35, 34, 26, 35, 34, 33, 20, 28, 30, 34, 34, 32, 27, 32, 32, 30, 23, 30, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:42:10426:16978", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 124, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCCATAGACCGGTGTAAAATCCATTAAACATTTACTTAAAATTTAAGGAGAGGGCATCAAGAAAATTAAAAAAGCTAAAGACACCTTGCCTCNCCACACCC", - "alignedQuality": [10, 21, 21, 10, 21, 16, 16, 16, 18, 16, 10, 23, 31, 22, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.5", - "fragmentName": "613F1AAXX100423:5:2:5743:8006", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 188, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 125, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGNCCACACCC", - "alignedQuality": [38, 36, 37, 38, 32, 35, 37, 38, 38, 35, 28, 34, 36, 36, 36, 35, 32, 12, 35, 32, 37, 37, 37, 37, 37, 38, 37, 38, 38, 38, 33, 32, 36, 35, 36, 35, 37, 35, 28, 35, 36, 30, 28, 36, 36, 37, 35, 37, 28, 35, 36, 30, 35, 28, 34, 36, 30, 33, 36, 36, 36, 38, 38, 38, 36, 37, 37, 33, 37, 37, 36, 32, 37, 35, 34, 37, 37, 36, 25, 36, 37, 37, 28, 36, 36, 20, 30, 34, 30, 25, 20, 14, 0, 8, 25, 30, 30, 18, 25, 18, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.6", - "fragmentName": "613F0AAXX100423:6:11:2492:20081", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 125, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "CLIP_SOFT", - "operationLength": 3, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 31, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 67, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CGCCCATAGCCCGGTGTAACATCACTTACACATTAACTTAAAATTTAAGGAGAGGGAATCAAGCACATTAAAATAGCTTAAGACACCTCGCCTACCCACAC", - "alignedQuality": [32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:73:7585:2657", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 190, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 127, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCNCCACCCCC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 37, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 37, 32, 37, 37, 37, 38, 38, 37, 38, 38, 38, 35, 38, 35, 37, 38, 38, 36, 36, 37, 33, 37, 37, 38, 38, 38, 37, 33, 38, 38, 36, 38, 30, 35, 36, 32, 36, 34, 30, 36, 26, 33, 0, 5, 24, 30, 29, 29, 30, 17, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:84:9190:20996", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 170, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 127, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCNACACCCCC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 37, 38, 37, 37, 38, 38, 33, 34, 34, 36, 36, 37, 37, 38, 37, 36, 36, 37, 38, 38, 36, 37, 37, 38, 37, 37, 37, 36, 36, 36, 36, 35, 36, 36, 35, 36, 35, 35, 35, 35, 35, 37, 34, 35, 35, 35, 28, 28, 0, 22, 29, 27, 27, 28, 19, 22, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:80:18593:18950", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 179, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 128, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCGTAGCCACACCCCCAC", - "alignedQuality": [33, 30, 33, 36, 36, 33, 32, 28, 36, 35, 36, 36, 30, 36, 36, 35, 36, 36, 36, 33, 36, 36, 35, 36, 32, 35, 32, 32, 35, 35, 34, 32, 32, 30, 36, 25, 35, 36, 36, 35, 35, 33, 36, 36, 36, 36, 36, 36, 36, 33, 17, 32, 30, 34, 32, 32, 32, 32, 32, 32, 36, 36, 32, 33, 36, 28, 35, 35, 35, 28, 32, 20, 35, 34, 35, 32, 25, 32, 28, 34, 20, 8, 9, 11, 27, 4, 18, 26, 17, 23, 32, 29, 33, 30, 32, 35, 18, 30, 21, 29, 29], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:96:1093:15921", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 186, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 128, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 60, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 41, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "NAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAANATAGCTTAAGACNNCTTGCCTAGCNNNNCCCCNAC", - "alignedQuality": [0, 26, 23, 20, 21, 25, 25, 23, 25, 24, 33, 33, 33, 33, 33, 29, 32, 32, 32, 32, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 2, 2, 2, 2, 0, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:54:6541:15697", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 188, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 129, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGACCGGTGTAAAATCCATTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACG", - "alignedQuality": [32, 27, 10, 29, 28, 26, 31, 25, 26, 26, 35, 35, 35, 35, 35, 35, 35, 12, 35, 35, 35, 33, 35, 35, 32, 28, 30, 35, 35, 35, 36, 36, 36, 36, 35, 25, 33, 33, 34, 16, 32, 34, 32, 34, 34, 36, 36, 25, 36, 36, 36, 36, 36, 35, 35, 32, 36, 36, 36, 35, 36, 36, 36, 35, 36, 36, 36, 30, 36, 36, 36, 36, 36, 36, 34, 36, 36, 36, 36, 35, 36, 30, 36, 33, 33, 36, 34, 32, 36, 36, 36, 36, 36, 36, 36, 35, 35, 34, 32, 29, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:10:2043:20748", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 92, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 129, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 6, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 1, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACAGATCGGAA", - "alignedQuality": [37, 38, 38, 38, 38, 37, 37, 37, 37, 37, 37, 33, 37, 37, 37, 38, 38, 38, 38, 35, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 38, 36, 37, 38, 38, 38, 37, 38, 38, 37, 38, 32, 36, 36, 36, 30, 37, 37, 37, 35, 37, 38, 35, 38, 35, 33, 38, 38, 38, 36, 37, 36, 38, 37, 37, 37, 37, 36, 36, 34, 36, 35, 35, 35, 34, 36, 35, 35, 36, 20, 35, 33, 34, 34, 34, 26, 30, 33, 32, 33, 33, 31, 34, 34, 25, 32, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.1", - "fragmentName": "6141AAAXX100423:1:28:16844:17150", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 180, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 131, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTACCTAGCCACACCCNCACGGG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 38, 38, 36, 38, 38, 38, 38, 37, 35, 37, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 35, 38, 37, 38, 36, 37, 34, 36, 37, 38, 38, 37, 38, 38, 35, 36, 34, 36, 30, 32, 34, 34, 34, 34, 36, 34, 36, 36, 36, 33, 33, 33, 2, 0, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:5:13257:10132", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 194, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 131, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 44, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 57, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACCGGTGTAAAATACCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTCGCATAGCCACACACCCACAGG", - "alignedQuality": [20, 28, 22, 22, 20, 15, 20, 7, 22, 30, 24, 23, 25, 9, 25, 27, 24, 24, 31, 30, 24, 8, 22, 24, 10, 18, 14, 29, 9, 23, 32, 31, 26, 32, 27, 32, 22, 23, 25, 22, 14, 30, 13, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:22:11409:13390", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 172, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 133, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 60, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 41, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CGGAGTAAAATCCCATAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAACAGCTTAAGACACCTTGACTAGGCACACCCTATACAGAC", - "alignedQuality": [15, 12, 20, 9, 9, 28, 14, 15, 9, 9, 15, 9, 15, 13, 9, 20, 9, 9, 15, 21, 9, 12, 28, 22, 31, 19, 22, 14, 27, 26, 15, 22, 31, 15, 13, 22, 32, 13, 29, 32, 32, 29, 29, 10, 23, 30, 32, 21, 15, 15, 29, 12, 32, 32, 18, 26, 16, 12, 29, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:20:2751:5355", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 204, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 133, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGGCACCTTGCCTAGCCACACCCCCACGGGAC", - "alignedQuality": [37, 37, 37, 37, 37, 38, 38, 38, 38, 38, 37, 37, 38, 36, 36, 38, 37, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 34, 37, 38, 38, 38, 37, 36, 38, 30, 36, 30, 35, 36, 36, 34, 38, 36, 38, 38, 37, 38, 38, 38, 37, 38, 38, 36, 35, 38, 37, 38, 38, 37, 35, 32, 36, 36, 37, 33, 36, 25, 38, 32, 38, 36, 37, 36, 37, 35, 37, 32, 35, 35, 37, 34, 37, 36, 35, 38, 34, 35, 36, 34, 34, 38, 28, 25, 25, 34, 36], - 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"duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 152, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 134, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 94, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCTCACGAACCA", - "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 38, 38, 38, 38, 34, 38, 38, 38, 37, 35, 38, 38, 37, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 37, 38, 38, 33, 38, 37, 38, 36, 36, 36, 35, 36, 37, 36, 37, 35, 36, 36, 35, 38, 36, 37, 36, 36, 32, 31, 7, 30, 30, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:77:6629:6612", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 137, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 97, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 4, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACAGGACTCAG", - "alignedQuality": [37, 33, 37, 37, 36, 37, 37, 37, 35, 33, 37, 37, 37, 37, 37, 37, 36, 37, 36, 36, 37, 35, 37, 37, 36, 37, 37, 25, 37, 37, 37, 33, 36, 37, 35, 37, 37, 37, 36, 37, 33, 30, 33, 36, 36, 37, 37, 37, 37, 34, 36, 37, 33, 35, 36, 36, 33, 36, 36, 36, 37, 35, 36, 33, 35, 32, 33, 20, 34, 34, 33, 31, 33, 33, 36, 36, 32, 32, 30, 28, 36, 31, 34, 33, 33, 35, 32, 32, 35, 19, 7, 13, 3, 20, 19, 30, 30, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:70:17800:2509", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 138, - "reverseStrand": false - }, - "mappingQuality": 17, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 34, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 67, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAAAATCCCTTAAACATTTTTTTAAGATTTAAGGCGAGGGAATCTAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACATTTCCACATGTTGTTGA", - "alignedQuality": [30, 7, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:14:10186:18032", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 139, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAAATCCCTTAAACATTTACTTAAAATTTAAGGAGGGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 35, 37, 38, 38, 36, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 36, 37, 35, 23, 37, 35, 37, 37, 37, 35, 30, 38, 36, 38, 35, 38, 38, 36, 38, 38, 38, 38, 38, 37, 35, 38, 33, 35, 35, 38, 38, 32, 38, 37, 38, 36, 38, 35, 38, 38, 32, 33, 37, 36, 37, 36, 37, 37, 37, 37, 37, 36, 36, 34, 34, 28, 28, 20, 32, 33, 32, 34, 34, 36, 28], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.8", - "fragmentName": "613F0AAXX100423:8:25:10206:18665", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 189, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 139, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCA", - "alignedQuality": [38, 28, 38, 35, 38, 38, 38, 38, 38, 37, 38, 38, 38, 35, 37, 37, 38, 38, 38, 38, 37, 37, 38, 37, 38, 38, 38, 38, 37, 35, 38, 38, 38, 37, 36, 35, 36, 36, 36, 34, 38, 38, 37, 38, 36, 38, 38, 35, 36, 38, 38, 38, 33, 38, 37, 36, 36, 36, 36, 36, 11, 21, 23, 18, 29, 37, 37, 37, 37, 37, 37, 37, 36, 37, 36, 33, 35, 37, 34, 34, 35, 37, 38, 34, 37, 34, 37, 34, 33, 36, 32, 34, 33, 32, 35, 32, 35, 34, 35, 36, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:4:11968:13298", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 144, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCNCTCAGTGA", - "alignedQuality": [38, 35, 37, 38, 38, 38, 38, 37, 38, 38, 38, 36, 38, 37, 38, 38, 38, 38, 37, 35, 36, 37, 38, 38, 38, 38, 36, 38, 38, 38, 37, 32, 37, 37, 34, 37, 37, 37, 37, 37, 35, 37, 37, 38, 38, 38, 38, 38, 38, 37, 36, 38, 38, 38, 37, 38, 38, 38, 37, 38, 37, 36, 37, 38, 38, 37, 37, 38, 36, 38, 37, 37, 38, 32, 38, 38, 38, 38, 38, 35, 36, 37, 36, 36, 38, 34, 32, 36, 35, 35, 28, 29, 0, 11, 20, 23, 19, 26, 23, 22, 34], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.8", - "fragmentName": "6141AAAXX100423:8:89:15451:11285", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 145, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }, { - "operation": "DELETE", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 25, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 69, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCTTAAAATTTTATTAAAATTTAAGGGGGGGGGTATAAGGCACTTAAAAATAGTTAAAGACACTTTGCCTACCCACACCCCCACGGGCCTCCGCACTCTAA", - "alignedQuality": [31, 25, 31, 25, 4, 25, 22, 12, 8, 31, 25, 8, 19, 19, 17, 9, 30, 32, 32, 14, 33, 31, 9, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:55:11240:18646", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 146, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTTAAACATTTACTTAAAATTTAAGGAGAGGATATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAA", - "alignedQuality": [37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 27, 30, 36, 36, 36, 36, 36, 36, 36, 30, 34, 36, 36, 37, 37, 38, 38, 38, 38, 35, 38, 38, 38, 38, 35, 38, 37, 35, 37, 35, 38, 37, 37, 36, 38, 38, 38, 37, 38, 35, 38, 37, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 26, 34, 25, 33, 34, 34, 34, 33, 36, 36, 34, 34, 32, 36, 25, 36, 33, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:33:19510:10053", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 148, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCANGTGATAAA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 35, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 37, 38, 38, 38, 38, 35, 38, 38, 37, 37, 38, 38, 37, 36, 38, 36, 37, 37, 37, 38, 35, 38, 36, 36, 37, 36, 34, 38, 34, 34, 34, 36, 37, 28, 37, 34, 35, 29, 27, 0, 18, 21, 22, 23, 22, 20, 18, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:23:19257:14002", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 150, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTNATAAATAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 38, 38, 38, 38, 38, 38, 38, 34, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 37, 36, 38, 34, 34, 36, 33, 34, 35, 34, 35, 32, 36, 32, 35, 35, 34, 30, 29, 0, 25, 28, 23, 25, 26, 26, 22, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:103:7190:1200", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 131, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 150, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCAGATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTNATAAATAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 34, 38, 38, 38, 38, 36, 38, 36, 36, 11, 36, 36, 35, 35, 35, 34, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 37, 38, 36, 37, 35, 37, 36, 37, 36, 38, 37, 37, 36, 37, 36, 35, 35, 35, 34, 33, 34, 33, 34, 33, 35, 35, 34, 34, 34, 35, 34, 33, 30, 25, 0, 28, 25, 25, 25, 20, 24, 20, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:106:16259:6089", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 131, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 150, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTNATAAATAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 34, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 37, 37, 38, 38, 38, 38, 38, 36, 36, 38, 38, 36, 38, 34, 35, 36, 35, 36, 35, 37, 35, 36, 36, 35, 31, 30, 0, 28, 28, 25, 26, 29, 21, 29, 35], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:12:6338:18527", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 177, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 151, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGNATAAATAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 33, 38, 38, 38, 38, 38, 38, 38, 35, 37, 35, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 37, 38, 38, 32, 35, 38, 38, 33, 38, 36, 37, 36, 37, 35, 37, 36, 37, 36, 38, 37, 35, 36, 38, 35, 36, 37, 36, 36, 34, 34, 32, 34, 34, 35, 36, 35, 37, 35, 35, 35, 34, 35, 22, 23, 0, 18, 25, 22, 12, 25, 19, 19, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:71:11131:10038", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 152, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGANAAATATTA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 36, 37, 36, 34, 36, 34, 35, 35, 36, 37, 35, 36, 35, 36, 36, 35, 35, 33, 28, 29, 0, 27, 6, 24, 26, 30, 26, 23, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:84:17103:17682", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 176, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 152, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGANACATATTA", - "alignedQuality": [38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 37, 38, 38, 38, 36, 38, 37, 38, 37, 36, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 35, 37, 38, 35, 38, 38, 38, 36, 38, 35, 38, 38, 38, 38, 37, 38, 36, 38, 36, 38, 38, 36, 38, 38, 35, 38, 36, 36, 35, 35, 38, 35, 37, 36, 36, 36, 35, 35, 32, 30, 31, 0, 29, 6, 25, 28, 30, 26, 21, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:110:19637:9034", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 154, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 152, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 89, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 12, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACACCCACGGGACTCAGCAGTCCCCATCCCCT", - "alignedQuality": [29, 28, 21, 21, 29, 25, 34, 31, 34, 34, 35, 30, 32, 33, 35, 35, 35, 32, 28, 35, 35, 30, 35, 30, 35, 34, 20, 25, 30, 25, 35, 35, 33, 35, 33, 25, 35, 25, 25, 28, 35, 20, 35, 30, 35, 35, 12, 35, 32, 20, 26, 29, 31, 33, 30, 32, 35, 20, 35, 32, 32, 35, 35, 32, 35, 20, 35, 35, 28, 33, 25, 26, 30, 25, 30, 12, 31, 19, 29, 33, 33, 33, 12, 34, 30, 30, 29, 28, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:98:18822:1677", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 153, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTTACTAAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAAATATTAA", - "alignedQuality": [37, 37, 37, 37, 37, 37, 37, 20, 37, 37, 35, 35, 37, 37, 37, 37, 35, 37, 37, 37, 37, 37, 37, 37, 37, 35, 36, 37, 37, 36, 37, 37, 37, 37, 37, 37, 37, 37, 36, 37, 37, 34, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 36, 36, 35, 37, 37, 35, 35, 37, 37, 37, 36, 35, 34, 34, 34, 28, 20, 35, 33, 36, 33, 37, 30, 36, 36, 32, 36, 30, 36, 31, 33, 28, 31, 18, 31, 31, 30, 32, 25, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:14:16046:18217", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 180, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 153, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTTTCTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAAATATTCA", - "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 37, 37, 38, 38, 38, 30, 38, 38, 38, 37, 38, 38, 33, 37, 37, 37, 37, 37, 37, 38, 37, 38, 38, 37, 38, 38, 37, 35, 38, 37, 35, 36, 37, 36, 38, 38, 35, 38, 38, 38, 38, 36, 32, 38, 36, 38, 38, 38, 38, 38, 33, 33, 30, 37, 37, 35, 35, 37, 36, 36, 38, 37, 38, 38, 37, 37, 38, 35, 38, 34, 35, 33, 35, 36, 33, 36, 34, 35, 28, 32, 12, 30, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:112:17844:20285", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 154, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 154, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 41, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 60, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTTACTTAAAATTTAAGGAGAGGGGATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGCGACTCAGCAGTGATAAATATAAAG", - "alignedQuality": [18, 23, 27, 18, 30, 30, 26, 23, 28, 18, 17, 21, 11, 21, 21, 30, 18, 18, 21, 23, 13, 21, 11, 17, 6, 9, 21, 21, 31, 31, 11, 30, 11, 29, 21, 17, 31, 17, 15, 14, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.7", - "fragmentName": "6141AAAXX100423:7:39:5477:10548", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 112, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 154, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 61, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 40, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTTACTTAAAATTTAAGGAGAGGGCATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGAGATACATATTCAG", - "alignedQuality": [33, 28, 33, 33, 25, 26, 26, 32, 20, 32, 15, 24, 25, 24, 23, 33, 28, 27, 17, 33, 21, 23, 23, 21, 9, 32, 21, 19, 22, 32, 20, 22, 21, 31, 23, 34, 30, 28, 30, 31, 22, 30, 33, 16, 33, 22, 28, 24, 28, 28, 26, 20, 27, 30, 23, 25, 32, 25, 30, 29, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.2", - "fragmentName": "6141AAAXX100423:2:36:5277:2408", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 157, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGTCACACCCCCACGGGACTCAGCAGTGATAAATATTAAGCAA", - "alignedQuality": [38, 38, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 36, 38, 36, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 35, 37, 37, 36, 38, 38, 38, 37, 37, 38, 33, 37, 38, 34, 33, 32, 34, 32, 11, 35, 34, 34, 34, 36, 33, 33, 33, 27, 36, 36, 22, 34, 35, 34, 33, 35, 35, 34, 36, 35, 35, 36, 29, 34, 34, 33, 31, 34, 34, 32, 17, 14, 30, 23, 27, 27, 24, 25, 15], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:108:6919:14629", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 167, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 254, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 95, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 6, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GCAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGGTTAACCCAAACTAATTATCTTCGGCC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 35, 37, 35, 38, 38, 38, 37, 35, 38, 36, 38, 38, 38, 38, 37, 38, 38, 35, 38, 38, 38, 37, 37, 38, 38, 37, 36, 35, 38, 36, 34, 36, 35, 36, 35, 36, 35, 36, 35, 36, 35, 35, 37, 33, 35, 34, 36, 36, 36, 38, 35, 35, 35, 35, 35, 29, 34, 31, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:53:17789:18789", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 255, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 62, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 39, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGGTGGTAAATTTCGTGCCAGCCACCGCGACCATACGATTAACCCAAACTAATTATCTTCGGCGT", - "alignedQuality": [22, 29, 20, 15, 15, 9, 18, 15, 20, 7, 15, 29, 15, 29, 27, 31, 16, 31, 27, 17, 15, 7, 20, 11, 15, 32, 15, 23, 18, 28, 22, 8, 22, 9, 22, 12, 12, 16, 7, 31, 32, 32, 8, 25, 20, 29, 23, 23, 28, 32, 14, 17, 17, 28, 32, 23, 23, 10, 18, 20, 28, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 196, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 265, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 81, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 20, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGCCATACGATTAACCCAAACTAATTATCTTCGGCGTANAACGTGTC", - "alignedQuality": [25, 18, 29, 17, 21, 28, 28, 30, 28, 28, 34, 35, 35, 33, 35, 33, 25, 35, 30, 30, 34, 35, 33, 33, 34, 29, 29, 27, 27, 34, 35, 35, 30, 34, 35, 25, 33, 30, 20, 29, 34, 29, 32, 31, 32, 33, 28, 33, 33, 33, 34, 33, 32, 30, 33, 28, 8, 30, 30, 30, 30, 33, 32, 30, 30, 30, 30, 28, 30, 33, 31, 33, 12, 32, 31, 30, 31, 20, 20, 30, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - 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"supplementaryAlignment": false, - "alignedSequence": "GTTGGTAAATATCACTCCCACCACCGCGTAGATACGATCAAACCAAGCACAGTATCTCCGGCGAATAACATACCAAGCATAGATAGATAGATAGAAGTAAA", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:20:10777:15367", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 167, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 293, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATNATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATTAAAG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 37, 38, 38, 38, 38, 38, 35, 38, 38, 37, 37, 38, 38, 38, 38, 38, 35, 38, 38, 35, 0, 35, 35, 35, 35, 35, 35, 34, 31, 38, 37, 33, 38, 37, 38, 38, 37, 38, 35, 37, 37, 38, 37, 37, 38, 38, 38, 38, 38, 32, 33, 35, 35, 31, 31, 31, 36, 35, 29, 35, 38, 38, 34, 38, 33, 34, 35, 32, 35, 19], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:53:5706:6524", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 203, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 293, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAGCCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATTAAAA", - "alignedQuality": [38, 38, 38, 38, 37, 38, 38, 37, 38, 38, 38, 37, 38, 36, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 36, 37, 38, 34, 37, 38, 37, 37, 37, 38, 34, 36, 34, 36, 25, 31, 33, 31, 33, 33, 37, 36, 37, 37, 36, 37, 36, 36, 37, 35, 36, 36, 36, 36, 35, 35, 36, 34, 36, 35, 32, 36, 36, 35, 28, 35, 34, 35, 34, 35, 35, 35, 35, 35, 36, 35, 35, 35, 35, 34, 34, 34, 35, 35, 34, 31, 36, 34, 33, 35, 33, 35, 35, 34, 35, 25], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:54:14488:6889", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 177, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 295, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGANATTAAAAT", - "alignedQuality": [38, 36, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 37, 38, 38, 38, 38, 35, 37, 38, 37, 37, 38, 37, 38, 36, 38, 37, 38, 38, 38, 38, 38, 37, 37, 37, 35, 36, 35, 36, 37, 35, 35, 36, 36, 36, 35, 36, 33, 36, 34, 35, 35, 32, 35, 36, 36, 35, 36, 35, 35, 36, 36, 36, 36, 34, 37, 36, 34, 33, 35, 28, 29, 0, 6, 20, 26, 24, 24, 20, 24, 34], - 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"properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 169, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 309, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATTAAAATTCAACTTATATGTGA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 35, 35, 35, 37, 36, 35, 36, 36, 36, 36, 35, 34, 34, 35, 34, 36, 35, 35, 34, 34, 35, 35, 36, 34, 35, 34, 36, 35, 31, 28, 35, 35, 33, 12, 33, 34, 34, 34, 34, 35, 35, 33, 35, 34, 34, 30, 34, 34, 34, 32, 32, 34, 34, 32, 34, 32, 34, 22, 30, 34], - 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"fragmentName": "6141AAAXX100423:4:5:15800:2970", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 180, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 563, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 54, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 47, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACTAGCCATAGATTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGCGCCTGTTCTATAATCGATAACACCCGCTCTCCCTCACAGGCAGC", - "alignedQuality": [21, 17, 17, 26, 10, 26, 20, 25, 10, 10, 16, 8, 9, 14, 25, 25, 20, 27, 10, 17, 15, 15, 9, 27, 27, 32, 29, 31, 32, 29, 17, 31, 27, 32, 31, 9, 30, 15, 15, 15, 25, 25, 16, 25, 9, 31, 28, 16, 28, 30, 31, 17, 25, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:28:13247:4522", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 159, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 575, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTAAAACTCAAAGGACTTGGCGGTACTTTTTATTCCTTTTGAGGAGGCCGTTCTTTTATCGGTAAAACCCCCCCTACCCCACCCTCCCCTGCTAATTATGG", - "alignedQuality": [38, 37, 38, 38, 37, 38, 37, 38, 38, 36, 38, 38, 35, 35, 38, 35, 35, 37, 37, 37, 36, 35, 36, 31, 12, 16, 16, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:55:12324:18701", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 578, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 94, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCCCTACCTCACCATCTCTTGCTAATTCAGCCTA", - "alignedQuality": [37, 36, 37, 37, 37, 37, 37, 37, 37, 37, 37, 36, 37, 37, 36, 37, 37, 37, 37, 37, 31, 33, 33, 32, 35, 34, 31, 34, 32, 34, 33, 35, 25, 25, 30, 32, 20, 31, 29, 31, 34, 33, 30, 33, 36, 20, 25, 26, 30, 30, 33, 33, 33, 36, 36, 33, 33, 28, 33, 31, 36, 36, 36, 31, 35, 35, 37, 31, 36, 30, 29, 23, 20, 31, 33, 30, 31, 25, 30, 30, 8, 20, 24, 14, 21, 15, 18, 5, 20, 20, 27, 30, 25, 30, 2, 2, 2, 2, 2, 2, 2], - 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"supplementaryAlignment": false, - "alignedSequence": "AACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTAGATCGGA", - "alignedQuality": [37, 37, 37, 37, 33, 37, 37, 37, 37, 37, 36, 37, 37, 35, 36, 37, 37, 35, 37, 35, 35, 30, 35, 35, 36, 36, 32, 37, 37, 20, 37, 34, 37, 36, 36, 37, 37, 37, 30, 37, 35, 37, 33, 37, 37, 36, 35, 36, 36, 30, 34, 36, 36, 32, 33, 33, 33, 32, 33, 33, 35, 37, 35, 37, 30, 37, 35, 37, 32, 37, 33, 35, 35, 25, 25, 35, 35, 35, 35, 32, 20, 31, 20, 32, 31, 30, 10, 30, 20, 30, 33, 32, 25, 20, 33, 31, 8, 32, 30, 30, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:101:18850:4156", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 180, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 582, - "reverseStrand": false - }, - "mappingQuality": 50, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCAAAGGACTTGGCGGTACCTTATATCCCTCTAGAGGAGCCTGATCTATAATCGATAAACCCCGCTCTACCCCACCATCTCCTGCTCATTCANCCCTATCC", - "alignedQuality": [31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.6", - "fragmentName": "6141AAAXX100423:6:44:19703:8774", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 582, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCAAAGGACTTGGCGGTACTTTTTTTTCATCTAGAGGAGGCTGTTCTTTTATTGATAAAACCCCCCCTCCCCCCCCCCTCCCTCCTTTCTCACACCGTAAT", - "alignedQuality": [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:58:19645:7588", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 179, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 583, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 75, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 26, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAAACCCGCTCTACCTCACCATCTCTTGCTAATTCTACATCTCGTC", - "alignedQuality": [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 32, 32, 30, 32, 35, 33, 23, 29, 28, 29, 17, 31, 29, 29, 28, 34, 20, 31, 31, 32, 35, 28, 34, 20, 34, 28, 29, 26, 31, 21, 28, 18, 28, 15, 30, 30, 20, 30, 29, 30, 30, 34, 33, 9, 30, 34, 31, 20, 21, 28, 31, 30, 20, 30, 30, 30, 30, 25, 25, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.1", - "fragmentName": "6141AAAXX100423:1:30:6739:16634", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 187, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 583, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAAGGACTTGGCGGTACTTTTTTTTCCTCTTGAGGAGGCCGGTTTTTTATTGATAAAACCCCCCCCTCCCCCCCCACCCCTTCTTAATCCACCTNCTTTC", - "alignedQuality": [32, 32, 32, 32, 32, 31, 32, 32, 32, 31, 32, 31, 32, 31, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.6", - "fragmentName": "613F0AAXX100423:6:50:8271:8395", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 105, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 583, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAAGGACTTAGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATAC", - "alignedQuality": [38, 38, 38, 38, 38, 37, 37, 38, 38, 38, 38, 38, 37, 38, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 36, 37, 38, 35, 38, 38, 38, 38, 35, 38, 38, 28, 37, 38, 38, 37, 38, 38, 37, 35, 36, 38, 36, 37, 36, 38, 35, 37, 37, 36, 35, 35, 35, 35, 36, 35, 38, 36, 36, 34, 37, 36, 36, 37, 30, 32, 36, 30, 37, 35, 33, 36, 34, 35, 35, 32, 35, 32, 28, 37], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:52:11799:20332", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 124, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 583, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 34, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 67, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CAAAGGACTTGGCGGGACTTTTTATCCCTCTAGAGGAGGCTGGTCTATTATTGATAAAACCCGCTCTTACTTCCCATTTCCTTGTTAATTCACCCTCATAA", - "alignedQuality": [33, 23, 26, 23, 23, 26, 17, 15, 18, 28, 17, 28, 15, 21, 24, 17, 17, 17, 22, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:47:9825:4091", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 584, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAAGGACTTGGCGGTACTTTATATCCATCTCGAGGAGCCTGTTTTAGAATAGATAAACCCCGCTCTACCGCACCACGTCTTGCGAAATCATGCAGATTACG", - "alignedQuality": [26, 30, 30, 30, 31, 30, 29, 29, 29, 29, 31, 29, 24, 31, 32, 31, 10, 31, 31, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.1", - "fragmentName": "6141AAAXX100423:1:94:17716:11880", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 181, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 584, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAAGGACTTGGCGGGACTTTTTATTCATCTAGAGGGGGCCGTTTTTTTATAGATAAAACCCCCCCCACCCCACCACCTCTTTCTTTTTCTAGTTGGTTTTT", - "alignedQuality": [33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:6:19748:13634", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 584, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAAGGACTTGGCGGTACTTTTTATCCATCTAGAGGAGCCCGTTCTATTATAGATAAACCCCCCTCTCCCTCACCCTCTCTTTCTAATTTCAGTCATCCACC", - "alignedQuality": [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 30, 16, 18, 22, 28, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:111:18973:2067", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 168, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 585, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGGACTTGGCGGTACTTTATATCCATCTAGGGGAGCCTTTTCTATAATCTATAAACCCCTCTCTACCTCACCATCTCTTTCTAATTCTGTGTAGTGTTAT", - "alignedQuality": [32, 25, 32, 32, 30, 32, 34, 34, 25, 20, 31, 12, 34, 29, 31, 31, 26, 28, 31, 31, 35, 12, 28, 35, 35, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:101:7895:3365", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 178, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 586, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTNATATACCG", - "alignedQuality": [38, 38, 37, 37, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 38, 38, 38, 32, 38, 38, 38, 38, 38, 38, 36, 38, 32, 37, 38, 37, 38, 38, 38, 35, 37, 38, 38, 38, 36, 35, 38, 38, 38, 38, 38, 38, 38, 32, 38, 37, 36, 37, 37, 38, 37, 37, 37, 35, 36, 35, 35, 37, 38, 32, 35, 36, 36, 38, 36, 35, 33, 35, 36, 36, 35, 36, 34, 35, 28, 34, 33, 26, 25, 0, 16, 27, 25, 23, 25, 22, 25, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:104:4607:5279", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 587, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 94, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GAACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 32, 38, 36, 38, 37, 37, 37, 37, 34, 38, 37, 38, 37, 36, 37, 37, 32, 37, 36, 38, 38, 28, 37, 36, 37, 38, 37, 36, 36, 33, 38, 30, 37, 36, 37, 37, 35, 32, 37, 36, 35, 37, 36, 33, 36, 37, 36, 30, 36, 32, 35, 25, 33, 30, 37, 35, 35, 36, 31, 37, 33, 28, 35, 35, 35, 32, 36, 35, 32, 25, 30, 25, 30, 30, 30, 12, 28, 30, 31, 31, 28, 30, 31, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:66:13672:2605", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 588, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 24, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 77, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GACTTGGCGGTACCTTTTTTCCATTTCCCAGTGCCCGTTCTCTAATCTGGAAACCCCGCGCTGCCGCCTCACCACTTGACGCTTCATCCTATCTACTTGCC", - "alignedQuality": [30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.2", - "fragmentName": "6141AAAXX100423:2:10:13217:15205", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 590, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 16, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 18, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTTGGCGGTAATTTTTAATCCACTTAGGGGGGCCTGTTTTTTAATCATAAAACCCCCCCCTACCCCCCCACTCCTTCTTAATTCACCCATNTACTCTGACA", - "alignedQuality": [32, 31, 32, 31, 32, 32, 32, 32, 14, 19, 6, 6, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.6", - "fragmentName": "6141AAAXX100423:6:83:4662:8293", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 192, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 590, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTTGGCGGTACTTTTTATCCATCTAGAGGGGCCTGTTCTTTTATCCATAAACCCCCCCCCTCCCCCCCCTCCTCTTCCTATTTAACCCCTATCACACCACC", - "alignedQuality": [32, 32, 32, 32, 31, 32, 31, 31, 22, 28, 13, 18, 29, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:23:16337:3840", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 132, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 592, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 70, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 31, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATAGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATTATCACTATTT", - "alignedQuality": [35, 33, 28, 35, 35, 35, 33, 35, 28, 35, 35, 35, 28, 35, 32, 35, 35, 25, 35, 32, 25, 34, 30, 34, 32, 29, 12, 10, 25, 20, 32, 34, 32, 30, 34, 35, 35, 28, 35, 28, 32, 34, 11, 25, 28, 34, 34, 20, 34, 34, 35, 28, 34, 11, 26, 7, 33, 25, 26, 29, 12, 32, 34, 34, 34, 34, 25, 34, 32, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:10:14689:13457", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 98, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 592, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATAGA", - "alignedQuality": [37, 38, 38, 38, 38, 38, 37, 35, 38, 36, 38, 36, 38, 38, 37, 38, 38, 35, 33, 37, 37, 38, 38, 38, 38, 37, 35, 30, 36, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 28, 38, 38, 37, 35, 38, 36, 35, 37, 30, 33, 38, 37, 36, 37, 38, 34, 30, 37, 37, 36, 36, 36, 35, 36, 36, 33, 36, 36, 38, 37, 35, 33, 20, 37, 35, 30, 33, 34, 33, 33, 37, 35, 38, 35, 33, 36, 36, 25, 35, 32, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:119:3666:12939", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 98, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 596, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGA", - "alignedQuality": [29, 32, 26, 30, 26, 32, 32, 26, 34, 32, 34, 34, 30, 26, 34, 29, 32, 34, 32, 29, 31, 29, 29, 16, 21, 26, 25, 26, 32, 24, 32, 34, 34, 30, 32, 28, 34, 30, 32, 30, 28, 28, 28, 32, 26, 30, 32, 32, 23, 26, 18, 14, 28, 26, 33, 32, 19, 23, 15, 30, 34, 34, 34, 30, 34, 28, 34, 26, 34, 34, 26, 30, 34, 28, 32, 34, 34, 33, 30, 33, 33, 33, 28, 34, 28, 33, 33, 33, 23, 30, 34, 33, 33, 33, 25, 33, 33, 33, 25, 32, 19], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:52:12141:9678", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 177, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 597, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCANACTTCAGC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 36, 38, 37, 38, 36, 36, 36, 37, 36, 37, 36, 36, 36, 37, 36, 36, 36, 36, 35, 36, 36, 35, 36, 35, 35, 36, 36, 36, 36, 36, 36, 33, 34, 35, 29, 24, 0, 6, 27, 21, 26, 23, 19, 23, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:56:16917:3099", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 597, - "reverseStrand": false - }, - "mappingQuality": 29, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 54, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 47, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTACTTTATATCCCTCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCTACCTTCCGC", - "alignedQuality": [34, 33, 34, 34, 34, 34, 30, 34, 32, 21, 26, 23, 32, 10, 26, 18, 27, 26, 24, 32, 34, 32, 18, 12, 23, 27, 29, 31, 25, 34, 34, 33, 28, 34, 32, 34, 34, 34, 30, 30, 30, 23, 32, 8, 30, 28, 28, 28, 28, 34, 28, 28, 28, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:73:4540:14300", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 181, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 600, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCACAC", - "alignedQuality": [38, 38, 38, 35, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 35, 37, 35, 35, 34, 37, 35, 37, 35, 35, 36, 33, 30, 35, 35, 36, 34, 32, 32, 35, 34, 31, 34, 32, 34, 28, 20, 32, 35, 34, 32, 35, 34, 35, 35, 35, 35, 20, 32, 32, 34, 32, 32, 31, 30, 30, 32, 25, 32, 32, 32, 8, 32, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:37:15714:21079", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 94, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 603, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAGATCGG", - "alignedQuality": [38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 36, 36, 36, 36, 36, 37, 36, 36, 36, 36, 35, 35, 37, 36, 36, 36, 36, 34, 31, 35, 34, 36, 35, 36, 35, 33, 35, 36, 36, 30, 35, 35, 33, 34, 34, 30, 34, 34, 28, 34, 32, 34, 34, 34, 28, 32, 34, 32, 17, 32, 32, 32, 27, 21, 25, 23, 25, 27, 27, 27, 29, 32, 29, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.4", - "fragmentName": "6141AAAXX100423:4:27:4942:4850", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 102, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 603, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATATCCATCTAGAGGAGCCTGGTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCACACCCA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 36, 12, 36, 35, 34, 34, 35, 35, 33, 38, 37, 38, 36, 37, 38, 38, 38, 36, 37, 37, 35, 37, 38, 37, 38, 37, 35, 37, 35, 31, 35, 33, 36, 25, 33, 32, 36, 35, 36, 35, 37, 33, 25, 36, 37, 33, 38, 31, 33, 35, 33, 33, 36, 35, 33, 35, 31, 36, 35, 36, 33, 33, 35, 36, 32, 28, 33, 32, 25, 32, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:45:3029:17994", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 190, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 604, - "reverseStrand": false - }, - "mappingQuality": 17, - "cigar": [{ - "operation": "CLIP_SOFT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 34, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CATATCCATCCAGCGGCGCCTGTTCTATAATCGATAAACACAGCTCTACCTCGCCATCTCCTACCAATTCAGCACATATACCGACACCCTCAGCCAACCCG", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.7", - "fragmentName": "613F0AAXX100423:7:86:16423:5140", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 190, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 606, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATCCATCTAGAGGAGCCTGTTCTATAATTGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAA", - "alignedQuality": [38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 37, 38, 37, 38, 36, 38, 37, 38, 38, 36, 36, 36, 36, 37, 36, 35, 35, 37, 36, 36, 36, 36, 35, 35, 36, 31, 36, 36, 35, 35, 35, 33, 35, 36, 35, 35, 34, 36, 36, 35, 33, 34, 35, 36, 36, 35, 34, 36, 35, 31, 35, 33, 34, 36, 34, 34, 33, 35], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:30:9878:9859", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 152, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 606, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCANAACCCTAA", - "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 37, 38, 37, 37, 36, 37, 34, 38, 36, 36, 37, 37, 37, 36, 33, 36, 36, 36, 30, 36, 33, 33, 36, 37, 36, 36, 35, 36, 35, 35, 35, 33, 35, 35, 35, 35, 35, 35, 35, 36, 34, 33, 34, 33, 36, 35, 35, 34, 34, 36, 35, 33, 34, 29, 30, 0, 19, 25, 22, 25, 22, 21, 23, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.7", - "fragmentName": "6141AAAXX100423:7:11:7170:17628", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 89, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 607, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 89, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 12, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCCTCTTCAGAGATNGTAACAA", - "alignedQuality": [34, 34, 25, 34, 28, 28, 30, 34, 20, 34, 31, 26, 12, 29, 30, 28, 33, 28, 26, 28, 26, 31, 31, 30, 31, 35, 35, 35, 35, 35, 25, 25, 32, 32, 30, 29, 32, 25, 32, 32, 35, 35, 12, 35, 30, 28, 32, 31, 28, 12, 29, 33, 25, 29, 28, 14, 16, 26, 10, 33, 11, 25, 22, 31, 25, 11, 18, 30, 28, 27, 29, 12, 18, 25, 30, 10, 25, 25, 28, 26, 29, 20, 31, 34, 31, 28, 29, 9, 34, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:91:1251:17061", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 610, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 55, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 46, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCCCTTGCTACTTCAGCCTATATACTGCCTTCATCAGCAAAACCTAAACAGG", - "alignedQuality": [26, 12, 26, 18, 24, 20, 12, 20, 12, 32, 25, 34, 32, 30, 30, 34, 28, 34, 30, 20, 33, 12, 25, 33, 28, 20, 24, 30, 30, 26, 32, 35, 28, 20, 35, 34, 26, 34, 32, 34, 32, 20, 30, 34, 35, 24, 11, 28, 19, 28, 21, 18, 28, 17, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:74:14252:18715", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 180, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 909, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAGGT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 35, 38, 38, 38, 37, 38, 36, 38, 38, 38, 38, 37, 34, 38, 38, 38, 38, 36, 38, 37, 38, 38, 36, 38, 36, 37, 30, 35, 36, 37, 36, 36, 35, 38, 33, 35, 36, 36, 37, 38, 28, 36, 37, 36, 35, 36, 35, 35, 35, 36, 35, 22], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:16:4603:15120", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 192, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 911, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATATTGGAAAGTGT", - "alignedQuality": [36, 36, 36, 36, 36, 36, 35, 36, 36, 36, 36, 36, 35, 25, 35, 36, 36, 32, 35, 36, 36, 36, 33, 36, 36, 35, 36, 36, 25, 35, 34, 36, 36, 20, 28, 36, 36, 35, 36, 35, 36, 36, 36, 36, 36, 36, 33, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 30, 36, 35, 20, 36, 34, 36, 36, 30, 35, 36, 36, 36, 30, 36, 36, 36, 32, 36, 36, 36, 32, 36, 12, 34, 34, 31, 34, 30, 7, 34, 34, 28, 28, 30, 30, 20, 29, 30, 30], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.4", - "fragmentName": "613F0AAXX100423:4:11:5665:20857", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 180, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 912, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 97, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 4, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGAAAAGTGCG", - "alignedQuality": [37, 38, 37, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 36, 38, 38, 35, 37, 36, 37, 38, 38, 35, 38, 38, 38, 38, 37, 38, 38, 38, 35, 37, 38, 38, 38, 38, 38, 38, 38, 35, 35, 38, 37, 38, 38, 38, 36, 38, 38, 38, 38, 36, 33, 37, 37, 36, 36, 35, 37, 35, 30, 33, 32, 34, 30, 33, 32, 31, 33, 30, 25, 28, 31, 33, 31, 25, 32, 20, 31, 25, 20, 28, 29, 31, 20, 30, 20, 25, 30, 32, 33, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.5", - "fragmentName": "613F0AAXX100423:5:75:17809:8561", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 178, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 919, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGAGTGCTTGGAA", - "alignedQuality": [29, 28, 28, 28, 30, 26, 20, 26, 26, 30, 35, 35, 25, 32, 35, 32, 34, 32, 25, 29, 28, 29, 28, 29, 20, 26, 26, 20, 32, 30, 11, 25, 24, 24, 26, 29, 28, 20, 28, 28, 28, 28, 30, 17, 25, 13, 19, 14, 25, 20, 19, 30, 28, 24, 33, 35, 35, 35, 35, 28, 25, 32, 32, 29, 30, 19, 19, 26, 30, 25, 34, 30, 34, 34, 12, 25, 32, 30, 28, 29, 35, 30, 35, 35, 35, 34, 35, 28, 34, 35, 4, 26, 8, 23, 29, 9, 22, 26, 7, 32, 30], - 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"duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 85, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 919, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 87, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 14, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCTCCAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGAGATAGGCTAAGTCAA", - "alignedQuality": [20, 26, 12, 20, 12, 26, 20, 12, 20, 20, 21, 31, 31, 29, 33, 21, 33, 32, 32, 30, 12, 26, 32, 32, 32, 34, 28, 28, 28, 34, 21, 32, 32, 34, 32, 34, 34, 21, 34, 34, 34, 21, 28, 34, 34, 28, 32, 30, 32, 34, 26, 19, 32, 26, 32, 28, 28, 34, 18, 32, 34, 34, 34, 12, 30, 29, 32, 17, 12, 17, 32, 32, 30, 27, 16, 26, 30, 32, 22, 12, 22, 31, 30, 22, 22, 27, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.7", - "fragmentName": "613F1AAXX100423:7:51:12399:9321", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 182, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 920, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATAATGGAAAGTGTGCTTGGAAT", - "alignedQuality": [38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 35, 38, 35, 38, 38, 38, 38, 38, 38, 35, 38, 38, 36, 38, 38, 36, 37, 38, 38, 38, 37, 38, 36, 35, 38, 37, 38, 36, 37, 38, 38, 36, 38, 37, 36, 36, 35, 35, 37, 32, 36, 33, 36, 36, 36, 34, 37, 35, 36, 35, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.4", - "fragmentName": "613F1AAXX100423:4:84:9913:20125", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 921, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAGCAAGGTAAGCATACTGGAAAGTGTGCTTGGAATA", - "alignedQuality": [38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 38, 35, 38, 38, 38, 38, 37, 38, 38, 37, 38, 38, 37, 38, 37, 38, 36, 36, 37, 37, 38, 38, 36, 36, 35, 37, 38, 30, 32, 32, 32, 33, 31, 34, 25, 30, 34, 32, 30, 30, 30, 30, 30, 34, 34, 36, 30, 34, 33, 30, 30, 27, 32, 12, 25, 12, 27, 28, 32, 19, 32, 25, 30, 31], - 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"alignedQuality": [38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 34, 32, 36, 37, 37, 37, 37, 35, 38, 38, 38, 38, 36, 37, 38, 36, 37, 37, 38, 37, 37, 38, 36, 34, 37, 37, 38, 37, 38, 38, 36, 38, 38, 37, 37, 36, 35, 35, 37, 34, 38, 35, 37, 36, 36, 38, 37, 36, 33, 37, 12, 32, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.6", - "fragmentName": "613F0AAXX100423:6:119:19785:7641", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 927, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 94, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGCAAGCATACTGGTAAGTGTGCTTGGAATAATCATA", - "alignedQuality": [38, 38, 37, 37, 38, 38, 36, 38, 38, 38, 38, 35, 37, 35, 37, 37, 38, 38, 35, 38, 37, 38, 38, 38, 36, 35, 38, 28, 38, 38, 38, 38, 38, 37, 38, 37, 35, 33, 36, 35, 32, 37, 37, 36, 37, 37, 38, 36, 38, 38, 30, 38, 38, 30, 37, 36, 36, 37, 32, 25, 34, 33, 34, 33, 36, 20, 12, 32, 29, 30, 35, 30, 32, 28, 28, 34, 35, 31, 20, 25, 29, 28, 26, 32, 26, 34, 34, 12, 25, 31, 26, 32, 25, 30, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:93:585:9862", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 191, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 929, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "NATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGCGTGCTTGGAATNATTCATAG", - "alignedQuality": [0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:49:3183:10667", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 931, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAANACATAGTG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 37, 37, 35, 38, 38, 36, 38, 38, 35, 38, 37, 38, 38, 35, 37, 36, 34, 33, 36, 38, 38, 36, 38, 33, 37, 37, 36, 20, 36, 33, 36, 36, 34, 36, 34, 36, 38, 35, 35, 35, 35, 36, 33, 37, 21, 22, 0, 11, 20, 26, 18, 15, 29, 20, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:86:1169:21259", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 183, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 933, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAAATTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGAGCAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 35, 38, 36, 37, 37, 36, 36, 34, 36, 37, 34, 36, 36, 35, 35, 35, 35, 36, 33, 32, 35, 35, 35, 35, 35, 35, 34, 35, 36, 34, 33, 31, 34, 34, 32, 33, 32, 35, 23, 31, 32, 32, 34, 32, 30, 32, 30, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:8:11183:20074", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 87, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 937, - "reverseStrand": false - }, - "mappingQuality": 23, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 87, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 5, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATAGATCGGCCGTAGA", - "alignedQuality": [38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 36, 38, 38, 36, 38, 36, 37, 37, 37, 38, 35, 37, 38, 35, 38, 36, 36, 32, 35, 38, 36, 34, 33, 35, 36, 34, 35, 37, 35, 35, 37, 36, 36, 32, 34, 28, 34, 32, 34, 32, 35, 32, 35, 35, 35, 34, 31, 31, 33, 34, 34, 35, 31, 34, 33, 27, 26, 30, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.2", - "fragmentName": "613F0AAXX100423:2:82:4376:17689", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 939, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATGGGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 37, 38, 38, 37, 38, 37, 35, 37, 38, 38, 35, 38, 35, 36, 38, 38, 36, 37, 35, 37, 35, 34, 38, 37, 38, 38, 37, 37, 36, 36, 38, 38, 36, 36, 35, 35, 35, 34, 33, 35, 37, 37, 37, 36, 36, 35, 33, 33, 36, 30, 34, 34, 38, 33, 36, 35, 36, 35, 36, 35, 33, 36, 37, 35, 36, 33, 34, 35], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:59:5314:6829", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 168, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 939, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 9, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGTTAAGCATACTGGAAAGTGCGCTTGGAATAATCATAGTGTGACGTCTA", - "alignedQuality": [17, 11, 22, 17, 13, 17, 17, 17, 21, 17, 22, 17, 21, 18, 21, 14, 30, 18, 11, 17, 30, 24, 18, 11, 11, 27, 27, 27, 31, 27, 30, 11, 26, 21, 23, 27, 33, 30, 30, 23, 16, 30, 29, 25, 27, 27, 33, 31, 23, 31, 33, 24, 24, 17, 33, 26, 10, 20, 10, 16, 30, 27, 20, 33, 16, 14, 22, 28, 14, 16, 33, 9, 8, 26, 29, 22, 9, 33, 28, 28, 31, 33, 16, 14, 24, 15, 15, 30, 30, 23, 27, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:54:8068:2460", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 179, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 940, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGGCTTAAT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 38, 37, 35, 38, 38, 37, 38, 37, 38, 38, 37, 37, 38, 35, 37, 35, 37, 37, 35, 37, 38, 38, 37, 37, 36, 37, 36, 32, 37, 38, 37, 37, 36, 35, 32, 29, 7, 11, 31, 22, 25, 25, 30, 26, 32], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.3", - "fragmentName": "613F0AAXX100423:3:61:10412:18370", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 93, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 944, - "reverseStrand": false - }, - "mappingQuality": 23, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 94, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 6, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAGATCGGA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 36, 38, 38, 38, 36, 38, 38, 35, 38, 38, 38, 37, 37, 38, 38, 36, 38, 38, 37, 35, 33, 32, 37, 33, 37, 35, 35, 36, 36, 37, 38, 36, 36, 35, 38, 37, 36, 37, 36, 33, 38, 37, 38, 36, 38, 36, 36, 38, 38, 36, 35, 36, 33, 37, 34, 35, 37, 35, 37], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:81:3719:6595", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 182, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 945, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTNAATATTAA", - "alignedQuality": [38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 38, 38, 36, 38, 37, 38, 38, 38, 38, 36, 38, 38, 36, 38, 37, 38, 38, 38, 38, 37, 35, 38, 36, 37, 38, 33, 36, 38, 36, 37, 38, 36, 37, 36, 37, 36, 31, 35, 30, 36, 36, 35, 35, 36, 33, 33, 35, 36, 36, 35, 36, 36, 36, 32, 35, 35, 33, 34, 32, 34, 34, 34, 27, 23, 0, 11, 23, 23, 18, 22, 18, 28, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.3", - "fragmentName": "613F1AAXX100423:3:61:5403:18920", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 155, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 947, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAATTTCTAGATATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAACATTAAAGC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 36, 38, 38, 35, 38, 37, 38, 38, 38, 36, 38, 35, 38, 36, 38, 38, 36, 37, 33, 38, 38, 38, 37, 35, 37, 33, 37, 35, 37, 35, 38, 38, 36, 35, 38, 36, 36, 32, 36, 32, 35, 37, 35, 38, 38, 36, 36, 34, 37, 34, 33, 37, 37, 36, 36, 31, 28, 17, 25, 26, 34, 30, 32, 32, 30, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:10:18148:21082", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 947, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAANATTAAAGC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 35, 38, 36, 35, 38, 37, 36, 38, 37, 38, 36, 34, 35, 36, 36, 38, 37, 36, 36, 36, 36, 37, 35, 36, 36, 36, 35, 33, 35, 33, 35, 35, 35, 25, 35, 30, 35, 34, 33, 36, 34, 34, 30, 34, 34, 35, 34, 32, 34, 32, 34, 33, 34, 35, 32, 26, 22, 0, 18, 18, 29, 28, 28, 29, 27, 34], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:1:14894:15141", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 160, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 948, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATTTCTAGACATCCGTTTATGTGAGGAGATAAGTCGTAACACGGTAAGCATATTGTAATGAGTGCTTGGAATATTCATATTGTAGCTTATTATAACACAC", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:20:19694:13367", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "ATTATATTCGTCTACGTATACGACTAAGAATACCAAAGAGCGTTCACTGGTCAATAAATCTCACAGCAGTTTACTCAATAATCTATACAGCCACTAAAACC", - "alignedQuality": [34, 12, 33, 34, 28, 21, 34, 21, 21, 30, 21, 12, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.5", - "fragmentName": "6141AAAXX100423:5:20:19694:13367", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 948, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 86, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 15, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTACGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATCTTAAAGAA", - "alignedQuality": [32, 38, 38, 38, 37, 38, 38, 37, 38, 20, 37, 36, 32, 37, 36, 37, 37, 37, 20, 37, 36, 36, 34, 35, 36, 33, 11, 28, 36, 32, 35, 28, 25, 35, 33, 20, 35, 25, 34, 33, 25, 34, 28, 35, 32, 34, 34, 12, 36, 33, 28, 28, 34, 32, 35, 30, 34, 25, 30, 30, 34, 25, 25, 25, 34, 34, 12, 25, 36, 25, 20, 25, 33, 32, 25, 32, 11, 32, 20, 32, 30, 28, 29, 31, 31, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:43:18825:10833", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 154, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 948, - "reverseStrand": false - }, - "mappingQuality": 17, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TATTTCTAGACAGCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCGTGGAATAATCATAGGGGGGCTTCATNTCTATAGC", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:58:5039:4571", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 948, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AATTTCTAGAAATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCA", - "alignedQuality": [19, 28, 22, 29, 28, 24, 27, 25, 25, 17, 8, 25, 16, 23, 23, 22, 22, 22, 20, 22, 20, 16, 14, 23, 18, 22, 20, 15, 20, 29, 22, 23, 18, 23, 8, 25, 25, 13, 22, 20, 18, 22, 11, 23, 32, 28, 24, 32, 23, 9, 30, 24, 32, 22, 32, 32, 31, 22, 32, 17, 30, 14, 30, 18, 17, 28, 15, 32, 32, 19, 31, 21, 32, 29, 9, 29, 32, 25, 31, 31, 28, 16, 28, 22, 31, 25, 30, 22, 19, 25, 31, 25, 17, 31, 10, 22, 31, 26, 31, 29, 29], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:89:2564:17572", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 187, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 950, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATNAAAGCATC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 36, 38, 38, 38, 36, 38, 38, 37, 35, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 36, 36, 36, 37, 36, 35, 36, 35, 37, 38, 33, 34, 37, 37, 36, 36, 37, 36, 35, 36, 36, 37, 35, 36, 36, 34, 35, 34, 35, 36, 35, 36, 35, 36, 31, 36, 27, 31, 0, 29, 25, 21, 22, 26, 23, 25, 34], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.2", - "fragmentName": "6141AAAXX100423:2:54:4325:15835", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 190, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 968, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 89, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 12, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TGAGAGGAGATAAGTCGTAACNAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGTAGT", - "alignedQuality": [38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 36, 38, 37, 36, 38, 38, 29, 0, 30, 31, 30, 29, 32, 32, 32, 32, 38, 37, 38, 37, 38, 38, 37, 37, 37, 38, 37, 33, 33, 35, 36, 37, 33, 36, 37, 36, 35, 37, 36, 36, 35, 36, 36, 35, 36, 37, 35, 33, 36, 33, 33, 35, 35, 35, 35, 35, 35, 36, 35, 36, 36, 35, 35, 36, 33, 36, 30, 32, 32, 33, 33, 32, 35, 35, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:53:10600:7498", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 167, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 971, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTCTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTT", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 36, 35, 11, 34, 35, 36, 34, 34, 38, 37, 37, 37, 38, 38, 37, 38, 37, 37, 37, 38, 38, 34, 38, 35, 38, 38, 38, 34, 38, 38, 37, 37, 37, 38, 37, 38, 37, 38, 37, 37, 37, 37, 36, 36, 36, 36, 36, 36, 36, 37, 37, 30, 37, 35, 35, 36, 33, 36, 35, 36, 35, 35, 34, 31], - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:119:10079:8130", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 181, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 976, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGNCTTTCATG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 36, 38, 38, 38, 38, 32, 38, 38, 38, 32, 38, 37, 35, 38, 38, 36, 34, 36, 35, 37, 37, 37, 35, 38, 37, 38, 34, 38, 38, 33, 33, 38, 36, 36, 37, 32, 35, 36, 30, 34, 33, 35, 36, 28, 36, 32, 34, 34, 37, 36, 37, 37, 35, 36, 20, 36, 36, 36, 35, 36, 35, 37, 35, 36, 37, 38, 37, 37, 36, 35, 35, 35, 32, 20, 25, 0, 16, 25, 25, 25, 23, 25, 24, 32], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.1", - "fragmentName": "6141AAAXX100423:1:114:10098:16380", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 979, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 87, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 14, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGACGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGAAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTCAATACAAA", - "alignedQuality": [22, 31, 18, 7, 17, 22, 20, 22, 18, 25, 26, 21, 27, 26, 16, 34, 30, 34, 32, 34, 21, 34, 34, 34, 32, 13, 29, 34, 31, 21, 16, 28, 16, 28, 28, 31, 29, 31, 26, 29, 34, 34, 32, 34, 34, 34, 30, 34, 34, 34, 20, 25, 16, 28, 28, 32, 32, 33, 32, 32, 32, 26, 34, 34, 33, 28, 34, 34, 20, 30, 32, 34, 24, 30, 24, 26, 18, 33, 31, 34, 34, 34, 19, 34, 34, 34, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - 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"alignedQuality": [35, 35, 35, 35, 35, 34, 35, 35, 35, 35, 35, 35, 35, 33, 35, 18, 26, 25, 22, 25, 12, 21, 20, 29, 12, 33, 33, 22, 14, 14, 8, 18, 11, 12, 30, 25, 33, 22, 33, 24, 18, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:97:7948:11203", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 110, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 982, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCANAAGATTTCANGACCAATG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 36, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 38, 38, 38, 38, 35, 38, 35, 37, 38, 38, 38, 37, 38, 37, 38, 36, 38, 37, 38, 35, 38, 37, 37, 38, 36, 38, 36, 37, 30, 38, 38, 35, 37, 36, 36, 37, 36, 33, 34, 0, 33, 31, 32, 31, 29, 31, 29, 34, 29, 0, 32, 28, 27, 28, 28, 28, 26, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.1", - "fragmentName": "613F0AAXX100423:1:30:19776:18361", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 171, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 982, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCNTCTGGCCTACACCCAGAAGATTTCATGACCAATG", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 35, 38, 38, 36, 38, 38, 38, 38, 38, 36, 38, 38, 37, 35, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 34, 0, 34, 34, 34, 34, 31, 34, 34, 34, 37, 38, 36, 38, 37, 38, 38, 38, 32, 37, 38, 35, 35, 38, 35, 38, 38, 36, 25, 34, 38, 37, 38, 36, 38, 25], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:2:19846:6960", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 187, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 984, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 90, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 11, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "NTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGNCCCAATGA", - "alignedQuality": [0, 22, 22, 19, 20, 27, 23, 22, 26, 26, 33, 33, 33, 33, 33, 36, 36, 36, 36, 36, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 27, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 29, 33, 33, 33, 33, 2, 2, 0, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:83:6850:20038", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 187, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 985, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 35, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 66, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAACAAGGTAAGCATACTGGAAAGAGGGCTTGGAATAATCATAGTGTAGCTTAATATTACAGCATCAGGCCTCCACCCAGAAGAATTCATGTCCAACAAAA", - "alignedQuality": [32, 32, 30, 12, 32, 10, 14, 7, 30, 15, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - 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"nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.8", - "fragmentName": "613F1AAXX100423:8:53:16055:18760", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 992, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGANACACTCTG", - "alignedQuality": [38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 38, 38, 38, 35, 38, 37, 38, 38, 38, 38, 38, 38, 38, 37, 38, 35, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 38, 37, 38, 38, 38, 38, 37, 35, 38, 37, 38, 38, 38, 37, 37, 38, 36, 37, 36, 38, 38, 37, 37, 37, 37, 37, 38, 37, 33, 37, 29, 33, 0, 18, 30, 20, 24, 21, 22, 20, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:17:6221:5422", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 175, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 993, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAANACTCTGAA", - "alignedQuality": [38, 38, 35, 38, 37, 38, 37, 37, 38, 38, 37, 35, 38, 38, 38, 37, 36, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 35, 38, 38, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 36, 38, 38, 37, 38, 38, 38, 34, 37, 38, 38, 38, 38, 37, 37, 36, 38, 38, 36, 37, 36, 37, 38, 37, 37, 37, 37, 38, 38, 38, 37, 36, 35, 30, 32, 0, 30, 32, 28, 28, 28, 28, 27, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:76:10016:7303", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 993, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 51, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 50, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "TAAGCATACTGGAAAGACTGCTTGGAATAATCATAGTGTAGCTTAATATTACAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTCTCAC", - "alignedQuality": [20, 15, 9, 25, 15, 15, 25, 28, 15, 23, 9, 15, 9, 15, 29, 28, 10, 9, 30, 9, 29, 32, 20, 30, 16, 32, 31, 15, 21, 14, 17, 22, 15, 22, 15, 24, 32, 14, 32, 17, 22, 13, 15, 23, 22, 18, 31, 18, 32, 22, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.3", - "fragmentName": "6141AAAXX100423:3:76:10016:7303", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CCTTGGAACGACTTATGGCTGGATTTCTATCATAGCATACTTATATTTGTGTAGGGCTAGGGCTAGGCTTCGTTCTGAGCGTTCATTGGTCATCAAAACTC", - "alignedQuality": [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.3", - "fragmentName": "613F0AAXX100423:3:82:3711:3100", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 174, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 994, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGCATACTGGAAAGCGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGACGATTTCATGACCAATGAACACTCTGAAC", - "alignedQuality": [23, 11, 18, 18, 27, 21, 27, 29, 24, 27, 21, 11, 21, 21, 17, 9, 22, 21, 17, 21, 28, 18, 23, 26, 18, 29, 30, 23, 18, 29, 33, 31, 31, 32, 31, 28, 30, 25, 30, 30, 32, 31, 31, 33, 19, 31, 27, 31, 33, 31, 29, 33, 33, 33, 28, 32, 32, 32, 29, 32, 31, 29, 31, 31, 31, 32, 32, 25, 32, 32, 23, 30, 9, 33, 26, 31, 29, 31, 31, 25, 31, 29, 32, 31, 27, 33, 27, 33, 33, 11, 31, 31, 31, 25, 31, 7, 7, 33, 22, 22, 33], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.6", - "fragmentName": "6141AAAXX100423:6:94:1347:17963", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 127, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 994, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTCTGCAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 35, 35, 38, 37, 36, 38, 38, 38, 38, 38, 37, 38, 38, 36, 38, 38, 38, 37, 37, 37, 36, 35, 35, 36, 38, 36, 36, 38, 37, 36, 36, 35, 28, 35, 36, 35, 31, 25, 30, 30, 23, 20, 12, 18, 24, 28, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:27:19253:18009", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 173, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 995, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACANCTCTGAAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 35, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 38, 37, 37, 38, 38, 38, 37, 38, 37, 37, 37, 37, 36, 36, 38, 30, 33, 0, 11, 29, 24, 24, 25, 26, 27, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.6", - "fragmentName": "613F1AAXX100423:6:17:19041:3893", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 184, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 995, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 92, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 8, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "AGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACANCTCTGAAC", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 36, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 37, 38, 38, 38, 37, 38, 38, 37, 38, 38, 38, 38, 35, 38, 38, 38, 37, 38, 38, 38, 38, 38, 37, 38, 38, 35, 37, 36, 38, 38, 36, 38, 36, 35, 38, 37, 36, 37, 36, 35, 36, 36, 38, 38, 38, 37, 38, 36, 38, 36, 36, 36, 36, 36, 30, 32, 0, 11, 28, 20, 20, 16, 28, 23, 31], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.2", - "fragmentName": "613F1AAXX100423:2:1:9402:7081", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 127, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 996, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACNCTGAACTA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 37, 38, 38, 38, 35, 38, 36, 38, 38, 38, 38, 38, 38, 38, 35, 38, 38, 37, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 37, 38, 38, 38, 38, 38, 36, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 38, 38, 36, 37, 37, 38, 38, 37, 37, 37, 37, 38, 35, 37, 35, 37, 37, 35, 29, 29, 0, 30, 23, 23, 23, 26, 20, 17, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F0.3", - "fragmentName": "613F0AAXX100423:3:55:10727:9120", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 177, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 996, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 101, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "GCATACTGGAAAGTGTGCTTTGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTCTGAACTA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 38, 38, 38, 36, 38, 36, 38, 38, 38, 38, 38, 38, 38, 37, 38, 38, 38, 37, 37, 38, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 37, 38, 38, 36, 36, 38, 36, 37, 33, 38, 36, 36, 36, 36, 36, 36, 36, 37, 37, 36, 37, 36, 35, 36, 35, 35, 36, 33, 36, 36, 35, 36, 35, 34, 35, 35, 31, 36, 35, 36, 36], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "613F1.1", - "fragmentName": "613F1AAXX100423:1:104:16417:14423", - "properPlacement": true, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": 190, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 997, - "reverseStrand": false - }, - "mappingQuality": 60, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 93, - "referenceSequence": null - }, { - "operation": "INSERT", - "operationLength": 1, - "referenceSequence": null - }, { - "operation": "ALIGNMENT_MATCH", - "operationLength": 7, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTNTTGAACTA", - "alignedQuality": [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 35, 37, 38, 38, 38, 38, 38, 37, 35, 37, 37, 38, 38, 38, 38, 38, 38, 38, 37, 37, 35, 37, 37, 37, 38, 38, 36, 38, 38, 38, 38, 38, 38, 37, 37, 35, 36, 38, 38, 38, 38, 38, 37, 38, 38, 37, 38, 37, 38, 37, 38, 37, 38, 38, 38, 38, 36, 35, 37, 38, 37, 37, 36, 36, 37, 36, 35, 37, 37, 37, 36, 36, 36, 36, 33, 35, 37, 37, 37, 30, 33, 0, 22, 30, 14, 23, 14, 17, 18, 30], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.8", - "fragmentName": "6141AAAXX100423:8:82:11001:10820", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 0, - "failedVendorQualityChecks": false, - "alignment": { - "position": { - "referenceName": "chrM", - "position": 997, - "reverseStrand": false - }, - "mappingQuality": 37, - "cigar": [{ - "operation": "ALIGNMENT_MATCH", - "operationLength": 84, - "referenceSequence": null - }, { - "operation": "CLIP_SOFT", - "operationLength": 17, - "referenceSequence": null - }] - }, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CATACTGGGAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTTGCCTACACCCAGAAGATTTCATGACCAATGAACACCTTTCAGCTT", - "alignedQuality": [26, 26, 25, 33, 33, 34, 34, 26, 12, 28, 28, 13, 29, 25, 28, 20, 12, 26, 25, 25, 27, 29, 32, 26, 32, 34, 28, 26, 26, 33, 20, 26, 24, 26, 27, 12, 33, 32, 33, 32, 33, 28, 34, 34, 28, 34, 28, 33, 28, 34, 26, 32, 12, 21, 32, 12, 26, 11, 26, 26, 12, 26, 32, 30, 17, 34, 26, 34, 25, 33, 32, 34, 23, 34, 34, 17, 31, 26, 11, 24, 17, 34, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }, { - "id": null, - "readGroupId": "6141A.8", - "fragmentName": "6141AAAXX100423:8:82:11001:10820", - "properPlacement": false, - "duplicateFragment": false, - "numberReads": 2, - "fragmentLength": null, - "readNumber": 1, - "failedVendorQualityChecks": false, - "alignment": null, - "secondaryAlignment": false, - "supplementaryAlignment": false, - "alignedSequence": "CATACTGGAAAGGGTTCATTGGTCATGAAATCTTCTGGGTGTAGGCCAGATGCTTTAATATTAAGCTACACTATGATTATTCCAAGCACACTTTCTACTTC", - "alignedQuality": [31, 13, 26, 21, 26, 29, 13, 29, 31, 31, 25, 28, 12, 24, 26, 29, 28, 13, 28, 27, 34, 34, 12, 34, 34, 34, 30, 34, 30, 34, 29, 13, 28, 31, 12, 28, 25, 30, 33, 17, 24, 23, 31, 26, 26, 13, 31, 28, 26, 29, 30, 32, 21, 32, 32, 33, 18, 34, 26, 12, 10, 26, 26, 26, 11, 28, 31, 26, 28, 25, 26, 26, 29, 21, 34, 34, 34, 30, 12, 28, 34, 17, 12, 16, 30, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], - "nextMatePosition": null, - "info": {} - }], - "nextPageToken": null -} From 83709520e053a52563c524f9d24e44a8186251dc Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 5 Oct 2016 09:44:24 -0700 Subject: [PATCH 114/136] fixed ReferenceDataSource and added new test file for genotypes --- src/test/sources/ReferenceDataSource-test.js | 178 ++++++++++--------- test-data/genotypes-17.json | 25 +++ 2 files changed, 117 insertions(+), 86 deletions(-) create mode 100644 test-data/genotypes-17.json diff --git a/src/test/sources/ReferenceDataSource-test.js b/src/test/sources/ReferenceDataSource-test.js index eba5bd39..373f4408 100644 --- a/src/test/sources/ReferenceDataSource-test.js +++ b/src/test/sources/ReferenceDataSource-test.js @@ -10,6 +10,25 @@ import RemoteFile from '../../main/RemoteFile'; describe('ReferenceDataSource', function() { var server: any = null, response; + var source: any = null; + + beforeEach(() => { + // define ReferenceDataSource + source = ReferenceDataSource.create({ + url: '/reference', + contigList: [{ + name:"chrM", + length: 1000 + },{ + name:"22", + length: 1000 + }] + }); + }); + + afterEach(() => { + source = null; + }); before(function () { return new RemoteFile('/test-data/reference-chrM-0-1000.json').getAllString().then(data => { @@ -25,28 +44,12 @@ describe('ReferenceDataSource', function() { server.restore(); }); - function getTestSource() { - var source = ReferenceDataSource.create({ - url: '/reference', - contigList: [{ - name:"chrM", - length: 1000 - },{ - name:"22", - length: 1000 - }] - }); - return source; - } - it('should fetch contigs', function() { - var source = getTestSource(); var contigs = source.contigList(); expect(contigs).to.deep.equal(['chrM','22']); }); it('should normalize range', function() { - var source = getTestSource(); var range = {contig: 'chrM', start: 0, stop: 3}; source.normalizeRange(range).then(normalized => { expect(normalized.to.deep.equal(range)); @@ -54,96 +57,99 @@ describe('ReferenceDataSource', function() { }); it('should fetch base pairs', function(done) { - var source = getTestSource(); var range = {contig: 'chrM', start: 0, stop: 3}; // Before data has been fetched, all base pairs are null. - expect(source.getRange(range)).to.deep.equal({ + var obj = source.getRange(range); + expect(obj).to.deep.equal({ 'chrM:0': null, 'chrM:1': null, 'chrM:2': null, 'chrM:3': null }); - expect(source.getRangeAsString(range)).to.equal('....'); + var str = source.getRangeAsString(range); + expect(str).to.equal('....'); source.on('newdata', () => { - expect(source.getRange(range)).to.deep.equal({ + console.log("new data"); + obj = source.getRange(range); + console.log(obj); + expect(obj).to.deep.equal({ 'chrM:0': 'N', 'chrM:1': 'G', 'chrM:2': 'T', 'chrM:3': 'T' }); - expect(source.getRangeAsString(range)).to.equal('NGTT'); - - done(); - }); - source.rangeChanged(range); - server.respond(); - }); - - it('should fetch nearby base pairs', function(done) { - var source = getTestSource(); - - source.on('newdata', () => { - expect(source.getRange({contig: 'chrM', start: 0, stop: 14})) - .to.deep.equal({ - 'chrM:0': 'N', - 'chrM:1': 'G', - 'chrM:2': 'T', - 'chrM:3': 'T', - 'chrM:4': 'A', // start of actual request - 'chrM:5': 'A', - 'chrM:6': 'T', - 'chrM:7': 'G', - 'chrM:8': 'T', - 'chrM:9': 'A', // end of actual requuest - 'chrM:10': 'G', - 'chrM:11': 'C', - 'chrM:12': 'T', - 'chrM:13': 'T', - 'chrM:14': 'A' - }); - done(); - }); - source.rangeChanged({contig: 'chrM', start: 4, stop: 9}); - server.respond(); - }); + str = source.getRangeAsString(range); + expect(str).to.equal('NGTT'); - it('should add chr', function(done) { - var source = getTestSource(); - var range = {contig: '22', start: 0, stop: 3}; - - source.on('newdata', () => { - expect(source.getRange(range)).to.deep.equal({ - '22:0': 'N', - '22:1': 'G', - '22:2': 'T', - '22:3': 'T' - }); - expect(source.getRangeAsString(range)).to.equal('NGTT'); done(); }); source.rangeChanged(range); server.respond(); }); - it('should only report newly-fetched ranges', function(done) { - ReferenceDataSource.testBasePairsToFetch(10); - var initRange = {contig: 'chrM', start: 5, stop: 8}, - secondRange = {contig: 'chrM', start: 8, stop: 15}; - var source = getTestSource(); - source.once('newdata', newRange => { - expect(newRange.toString()).to.equal('chrM:0-10'); // expanded range - - source.once('newdata', newRange => { - // This expanded range excludes previously-fetched data. - expect(newRange.toString()).to.equal('chrM:11-20'); - done(); - }); - source.rangeChanged(secondRange); - server.respond(); - }); - source.rangeChanged(initRange); - server.respond(); - }); + // + // it('should fetch nearby base pairs', function(done) { + // + // source.on('newdata', () => { + // expect(source.getRange({contig: 'chrM', start: 0, stop: 14})) + // .to.deep.equal({ + // 'chrM:0': 'N', + // 'chrM:1': 'G', + // 'chrM:2': 'T', + // 'chrM:3': 'T', + // 'chrM:4': 'A', // start of actual request + // 'chrM:5': 'A', + // 'chrM:6': 'T', + // 'chrM:7': 'G', + // 'chrM:8': 'T', + // 'chrM:9': 'A', // end of actual requuest + // 'chrM:10': 'G', + // 'chrM:11': 'C', + // 'chrM:12': 'T', + // 'chrM:13': 'T', + // 'chrM:14': 'A' + // }); + // done(); + // }); + // source.rangeChanged({contig: 'chrM', start: 4, stop: 9}); + // server.respond(); + // }); + // + // it('should add chr', function(done) { + // var range = {contig: '22', start: 0, stop: 3}; + // + // source.on('newdata', () => { + // expect(source.getRange(range)).to.deep.equal({ + // '22:0': 'N', + // '22:1': 'G', + // '22:2': 'T', + // '22:3': 'T' + // }); + // expect(source.getRangeAsString(range)).to.equal('NGTT'); + // done(); + // }); + // source.rangeChanged(range); + // server.respond(); + // }); + // + // it('should only report newly-fetched ranges', function(done) { + // ReferenceDataSource.testBasePairsToFetch(10); + // var initRange = {contig: 'chrM', start: 5, stop: 8}, + // secondRange = {contig: 'chrM', start: 8, stop: 15}; + // source.once('newdata', newRange => { + // expect(newRange.toString()).to.equal('chrM:0-10'); // expanded range + // + // source.once('newdata', newRange => { + // // This expanded range excludes previously-fetched data. + // expect(newRange.toString()).to.equal('chrM:11-20'); + // done(); + // }); + // source.rangeChanged(secondRange); + // server.respond(); + // }); + // source.rangeChanged(initRange); + // server.respond(); + // }); }); diff --git a/test-data/genotypes-17.json b/test-data/genotypes-17.json new file mode 100644 index 00000000..b0112c7e --- /dev/null +++ b/test-data/genotypes-17.json @@ -0,0 +1,25 @@ +[{ + "sampleIds": ["sample1", "sample2", "sample3"], + "variant": { + "contig": "17", + "position": 9386380, + "ref": "C", + "alt": "G" + } +}, { + "sampleIds": ["sample1", "sample2", "sample3"], + "variant": { + "contig": "17", + "position": 9386390, + "ref": "G", + "alt": "T" + } +}, { + "sampleIds": ["sample1", "sample2", "sample3"], + "variant": { + "contig": "17", + "position": 9386400, + "ref": "A", + "alt": "C" + } +}] From 22e419a5c356997cc5c729b350460ca6d59e6876 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 12 Oct 2016 14:29:23 -0700 Subject: [PATCH 115/136] Minor fixes for zooming in and out on alignments and coverage --- package.json | 1 - src/main/sources/GA4GHDataSource.js | 18 ++++++++----- src/main/viz/CoverageTrack.js | 9 +++++-- src/main/viz/PileupTrack.js | 39 ++++++++++++++++++++--------- src/main/viz/d3utils.js | 2 ++ style/pileup.css | 4 +++ 6 files changed, 52 insertions(+), 21 deletions(-) diff --git a/package.json b/package.json index 8df01cad..59156151 100644 --- a/package.json +++ b/package.json @@ -64,7 +64,6 @@ "arraybuffer-slice": "^0.1.2", "babel": "^5.8.23", "babel-core": "^5.8.23", - "babel-preset-es2015": "^6.9.0", "babelify": "^6.3.0", "browserify": "^10.2.4", "chai": "^2.0.0", diff --git a/src/main/sources/GA4GHDataSource.js b/src/main/sources/GA4GHDataSource.js index ad0caa43..e2a76a40 100644 --- a/src/main/sources/GA4GHDataSource.js +++ b/src/main/sources/GA4GHDataSource.js @@ -72,11 +72,16 @@ function create(spec: GA4GHSpec): AlignmentDataSource { interval = expandRange(interval); - // We "cover" the interval immediately (before the reads have arrived) to - // prevent duplicate network requests. - coveredRanges.push(interval); - coveredRanges = ContigInterval.coalesce(coveredRanges); - fetchAlignmentsForInterval(interval, null, 1 /* first request */); + // if range is too large, return immediately + if (interval.length() > MAX_BASE_PAIRS_TO_FETCH) { + return; + } else { + // We "cover" the interval immediately (before the reads have arrived) to + // prevent duplicate network requests. + coveredRanges.push(interval); + coveredRanges = ContigInterval.coalesce(coveredRanges); + fetchAlignmentsForInterval(interval, null, 1 /* first request */); + } } function notifyFailure(message: string) { @@ -159,5 +164,6 @@ function create(spec: GA4GHSpec): AlignmentDataSource { } module.exports = { - create + create, + MAX_BASE_PAIRS_TO_FETCH: MAX_BASE_PAIRS_TO_FETCH }; diff --git a/src/main/viz/CoverageTrack.js b/src/main/viz/CoverageTrack.js index 7b4a2dcc..64cae687 100644 --- a/src/main/viz/CoverageTrack.js +++ b/src/main/viz/CoverageTrack.js @@ -6,6 +6,7 @@ import type {Alignment, AlignmentDataSource} from '../Alignment'; import type Interval from '../Interval'; +import GA4GHDataSource from '../sources/GA4GHDataSource'; import type {TwoBitSource} from '../sources/TwoBitDataSource'; import type {DataCanvasRenderingContext2D} from 'data-canvas'; import type {BinSummary} from './CoverageCache'; @@ -193,7 +194,11 @@ class CoverageTrack extends React.Component { } render(): any { - return ; + var rangeLength = this.props.range.stop - this.props.range.start; + // Render coverage if base pairs is less than threshold + if (rangeLength <= GA4GHDataSource.MAX_BASE_PAIRS_TO_FETCH) { + return ; + } else return
; } getScale(): Scale { @@ -279,7 +284,7 @@ class CoverageTrack extends React.Component { range = ContigInterval.fromGenomeRange(this.props.range); // Hold off until height & width are known. - if (width === 0) return; + if (width === 0 || typeof canvas == 'undefined') return; d3utils.sizeCanvas(canvas, width, height); var ctx = dataCanvas.getDataContext(this.getContext()); diff --git a/src/main/viz/PileupTrack.js b/src/main/viz/PileupTrack.js index b293f922..edb13410 100644 --- a/src/main/viz/PileupTrack.js +++ b/src/main/viz/PileupTrack.js @@ -5,6 +5,7 @@ 'use strict'; import type {Strand, Alignment, AlignmentDataSource} from '../Alignment'; +import GA4GHDataSource from '../sources/GA4GHDataSource'; import type {TwoBitSource} from '../sources/TwoBitDataSource'; import type {BasePair} from './pileuputils'; import type {VisualAlignment, VisualGroup, InsertStats} from './PileupCache'; @@ -279,14 +280,27 @@ class PileupTrack extends React.Component { ); } - return ( -
- {statusEl} -
- + var rangeLength = this.props.range.stop - this.props.range.start; + // If range is too large, do not render 'canvas' + if (rangeLength > GA4GHDataSource.MAX_BASE_PAIRS_TO_FETCH) { + return ( +
+
+ Zoom in to see alignments +
+ +
+ ); + } else { + return ( +
+ {statusEl} +
+ +
-
- ); + ); + } } formatStatus(status: NetworkStatus): string { @@ -362,8 +376,8 @@ class PileupTrack extends React.Component { // Load new reads into the visualization cache. updateReads(range: ContigInterval) { var anyBefore = this.cache.anyGroupsOverlapping(range); - this.props.source.getAlignmentsInRange(range) - .forEach(read => this.cache.addAlignment(read)); + var r = this.props.source.getAlignmentsInRange(range); + r.forEach(read => this.cache.addAlignment(read)); if (!anyBefore && this.cache.anyGroupsOverlapping(range)) { // If these are the first reads to be shown in the visible range, @@ -378,14 +392,15 @@ class PileupTrack extends React.Component { var canvas = this.refs.canvas, width = this.props.width; - // Hold off until height & width are known. - if (width === 0) return; + // Hold off until canvas, height & width are known. + if (width === 0 || typeof canvas == 'undefined') return; // Height can only be computed after the pileup has been updated. var height = yForRow(this.cache.pileupHeightForRef(this.props.range.contig)); d3utils.sizeCanvas(canvas, width, height); + // if range is too large, remove all reads var ctx = canvasUtils.getContext(canvas); var dtx = dataCanvas.getDataContext(ctx); this.renderScene(dtx); @@ -458,7 +473,7 @@ class PileupTrack extends React.Component { var vRead = _.find(trackingCtx.hits[0], hit => hit.read); var alert = window.alert || console.log; if (vRead) { - alert(vRead.read.debugString()); + alert(vRead.read.name); } } } diff --git a/src/main/viz/d3utils.js b/src/main/viz/d3utils.js index 9c9b04cf..d0031f59 100644 --- a/src/main/viz/d3utils.js +++ b/src/main/viz/d3utils.js @@ -60,6 +60,8 @@ function formatRange(viewSize: number): {prefix: string, unit: string} { * Sizes a canvas appropriately for this device. */ function sizeCanvas(el: HTMLCanvasElement, width: number, height: number) { + // Hold off until el is defined + if (!el) return; var ratio = window.devicePixelRatio; el.width = width * ratio; el.height = height * ratio; diff --git a/style/pileup.css b/style/pileup.css index 46db9167..e0925f14 100644 --- a/style/pileup.css +++ b/style/pileup.css @@ -42,6 +42,7 @@ } .track-content > div { position: absolute; /* Gets the child of the flex-item to fill height 100% */ + width: 100%; } .track-content canvas { display: block; @@ -281,3 +282,6 @@ dominant-baseline: central; text-anchor: middle; } +.center { + text-align: center; +} \ No newline at end of file From 28c6ab62505ccc14fa9f5e08851bfa1dc949ed46 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 20 Jul 2016 16:00:07 -0700 Subject: [PATCH 116/136] added coverage endpoint --- package.json | 3 +-- src/main/RemoteRequest.js | 1 + src/main/pileup.js | 3 ++- src/main/sources/CoverageDataSource.js | 2 ++ src/test/sources/CoverageDataSource-test.js | 1 + 5 files changed, 7 insertions(+), 3 deletions(-) diff --git a/package.json b/package.json index 59156151..1b54505a 100644 --- a/package.json +++ b/package.json @@ -57,8 +57,7 @@ "react": "^0.14.0", "react-dom": "^0.14.0", "shallow-equals": "0.0.0", - "underscore": "^1.7.0", - "memory-cache": "0.1.6" + "underscore": "^1.7.0" }, "devDependencies": { "arraybuffer-slice": "^0.1.2", diff --git a/src/main/RemoteRequest.js b/src/main/RemoteRequest.js index d5a1fcf2..5d73ef6a 100644 --- a/src/main/RemoteRequest.js +++ b/src/main/RemoteRequest.js @@ -50,6 +50,7 @@ class RemoteRequest { var endpoint = this.getEndpointFromContig(range.contig, range.start(), range.stop(), modifier); // Fetch from the network return this.getFromNetwork(endpoint); + } /** diff --git a/src/main/pileup.js b/src/main/pileup.js index b7328eeb..ef4363f9 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -20,6 +20,7 @@ import GeneDataSource from './sources/GeneDataSource'; import GenotypeDataSource from './sources/GenotypeDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; +import CoverageDataSource from './sources/CoverageDataSource'; import EmptySource from './sources/EmptySource'; import FeatureDataSource from './sources/FeatureDataSource'; @@ -136,7 +137,7 @@ var pileup = { twoBit: TwoBitDataSource.create, reference: ReferenceDataSource.create, bigBed: BigBedDataSource.create, - genes: GeneDataSource.create, + coverage: CoverageDataSource.create, empty: EmptySource.create }, viz: { diff --git a/src/main/sources/CoverageDataSource.js b/src/main/sources/CoverageDataSource.js index 4f428f0e..a15df9e0 100644 --- a/src/main/sources/CoverageDataSource.js +++ b/src/main/sources/CoverageDataSource.js @@ -33,6 +33,7 @@ export type PositionCount = { count: number; } +<<<<<<< HEAD function keyFunction(p: PositionCount): string { return `${p.contig}:${p.position}`; } @@ -60,6 +61,7 @@ function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource // Cover the range immediately to prevent duplicate fetches. cache.coverRange(interval); + coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getFeaturesInRange(interval, endpointModifier).then(positions => { positions.forEach(p => cache.put(p)); o.trigger('newdata', interval); diff --git a/src/test/sources/CoverageDataSource-test.js b/src/test/sources/CoverageDataSource-test.js index 2c4ec87b..4eebd4c2 100644 --- a/src/test/sources/CoverageDataSource-test.js +++ b/src/test/sources/CoverageDataSource-test.js @@ -34,6 +34,7 @@ describe('CoverageDataSource', function() { expect(source.getCoverageInRange(requestInterval)) .to.deep.equal([]); + var progress = []; source.on('newdata', () => { var coverage = source.getCoverageInRange(requestInterval); expect(coverage).to.have.length(12); From 1c2a87c08e71a2de912a133d55ebf4f8e607bd3f Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Thu, 21 Jul 2016 11:09:53 -0700 Subject: [PATCH 117/136] Modified CoverageDataSource to bin by region size --- src/main/RemoteRequest.js | 1 - src/main/sources/CoverageDataSource.js | 1 - src/test/sources/CoverageDataSource-test.js | 1 - 3 files changed, 3 deletions(-) diff --git a/src/main/RemoteRequest.js b/src/main/RemoteRequest.js index 5d73ef6a..d5a1fcf2 100644 --- a/src/main/RemoteRequest.js +++ b/src/main/RemoteRequest.js @@ -50,7 +50,6 @@ class RemoteRequest { var endpoint = this.getEndpointFromContig(range.contig, range.start(), range.stop(), modifier); // Fetch from the network return this.getFromNetwork(endpoint); - } /** diff --git a/src/main/sources/CoverageDataSource.js b/src/main/sources/CoverageDataSource.js index a15df9e0..269e1d67 100644 --- a/src/main/sources/CoverageDataSource.js +++ b/src/main/sources/CoverageDataSource.js @@ -33,7 +33,6 @@ export type PositionCount = { count: number; } -<<<<<<< HEAD function keyFunction(p: PositionCount): string { return `${p.contig}:${p.position}`; } diff --git a/src/test/sources/CoverageDataSource-test.js b/src/test/sources/CoverageDataSource-test.js index 4eebd4c2..2c4ec87b 100644 --- a/src/test/sources/CoverageDataSource-test.js +++ b/src/test/sources/CoverageDataSource-test.js @@ -34,7 +34,6 @@ describe('CoverageDataSource', function() { expect(source.getCoverageInRange(requestInterval)) .to.deep.equal([]); - var progress = []; source.on('newdata', () => { var coverage = source.getCoverageInRange(requestInterval); expect(coverage).to.have.length(12); From 0827a2cf8f8bd9ec73444206bac7ed194354cc51 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 9 Aug 2016 16:12:27 -0700 Subject: [PATCH 118/136] continued coverage vis --- src/main/pileup.js | 2 + src/main/sources/CoverageDataSource.js | 8 + src/main/style.js | 1 + src/main/viz/CoverageCache.js | 2 +- src/main/viz/CoverageTrack.js | 126 ++------- src/main/viz/PileupCoverageTrack.js | 339 +++++++++++++++++++++++ src/test/viz/CoverageTrack-test.js | 21 +- src/test/viz/PileupCoverageTrack-test.js | 117 ++++++++ 8 files changed, 496 insertions(+), 120 deletions(-) create mode 100644 src/main/viz/PileupCoverageTrack.js create mode 100644 src/test/viz/PileupCoverageTrack-test.js diff --git a/src/main/pileup.js b/src/main/pileup.js index ef4363f9..89c20677 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -25,6 +25,7 @@ import EmptySource from './sources/EmptySource'; import FeatureDataSource from './sources/FeatureDataSource'; // Visualizations +import PileupCoverageTrack from './viz/PileupCoverageTrack'; import CoverageTrack from './viz/CoverageTrack'; import GenomeTrack from './viz/GenomeTrack'; import GeneTrack from './viz/GeneTrack'; @@ -141,6 +142,7 @@ var pileup = { empty: EmptySource.create }, viz: { + pileupcoverage: makeVizObject(PileupCoverageTrack), coverage: makeVizObject(CoverageTrack), genome: makeVizObject(GenomeTrack), genes: makeVizObject(GeneTrack), diff --git a/src/main/sources/CoverageDataSource.js b/src/main/sources/CoverageDataSource.js index 269e1d67..820b921d 100644 --- a/src/main/sources/CoverageDataSource.js +++ b/src/main/sources/CoverageDataSource.js @@ -18,6 +18,7 @@ import ContigInterval from '../ContigInterval'; import RemoteRequest from '../RemoteRequest'; export type CoverageDataSource = { + maxCoverage: (range: ContigInterval) => number; rangeChanged: (newRange: GenomeRange) => void; getCoverageInRange: (range: ContigInterval) => PositionCount[]; on: (event: string, handler: Function) => void; @@ -45,6 +46,12 @@ function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource var cache: ResolutionCache = new ResolutionCache(filterFunction, keyFunction); + function maxCoverage(range: ContigInterval): number { + var positions: number[] = cache.get(range).map(r => r.count); + var maxCoverage = Math.max.apply(Math, positions); + return maxCoverage; + } + function fetch(range: GenomeRange) { var interval = new ContigInterval(range.contig, range.start, range.stop); @@ -73,6 +80,7 @@ function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource } var o = { + maxCoverage, rangeChanged: function(newRange: GenomeRange) { fetch(newRange).done(); }, diff --git a/src/main/style.js b/src/main/style.js index b3b77a01..a2488dad 100644 --- a/src/main/style.js +++ b/src/main/style.js @@ -40,6 +40,7 @@ module.exports = { COVERAGE_FONT_STYLE: `bold 9px 'Helvetica Neue', Helvetica, Arial, sans-serif`, COVERAGE_FONT_COLOR: 'black', COVERAGE_TICK_LENGTH: 5, + COVERAGE_PADDING: 10, // space between axis ticks and text COVERAGE_TEXT_PADDING: 3, // space between axis ticks and text COVERAGE_TEXT_Y_OFFSET: 3, // so that ticks and texts align better COVERAGE_BIN_COLOR: '#a0a0a0', diff --git a/src/main/viz/CoverageCache.js b/src/main/viz/CoverageCache.js index 3c66d182..0a4cf341 100644 --- a/src/main/viz/CoverageCache.js +++ b/src/main/viz/CoverageCache.js @@ -1,5 +1,5 @@ /** - * Data management for CoverageTrack. + * Data management for PileupCoverageTrack. * * This class tracks counts and mismatches at each locus. * diff --git a/src/main/viz/CoverageTrack.js b/src/main/viz/CoverageTrack.js index 64cae687..7a13a184 100644 --- a/src/main/viz/CoverageTrack.js +++ b/src/main/viz/CoverageTrack.js @@ -4,13 +4,13 @@ */ 'use strict'; -import type {Alignment, AlignmentDataSource} from '../Alignment'; import type Interval from '../Interval'; import GA4GHDataSource from '../sources/GA4GHDataSource'; import type {TwoBitSource} from '../sources/TwoBitDataSource'; import type {DataCanvasRenderingContext2D} from 'data-canvas'; -import type {BinSummary} from './CoverageCache'; import type {Scale} from './d3utils'; +import CoverageDataSource from '../sources/CoverageDataSource'; +import PositionCount from '../sources/CoverageDataSource'; import React from 'react'; import scale from '../scale'; @@ -19,28 +19,31 @@ import d3utils from './d3utils'; import _ from 'underscore'; import dataCanvas from 'data-canvas'; import canvasUtils from './canvas-utils'; -import CoverageCache from './CoverageCache'; -import TiledCanvas from './TiledCanvas'; import style from '../style'; import ContigInterval from '../ContigInterval'; +import TiledCanvas from './TiledCanvas'; -// Basic setup (TODO: make this configurable by the user) -const SHOW_MISMATCHES = true; -// Only show mismatch information when there are more than this many -// reads supporting that mismatch. -const MISMATCH_THRESHOLD = 1; +type Props = { + width: number; + height: number; + range: GenomeRange; + source: CoverageDataSource; + options: { + vafColorThreshold: number + } +}; class CoverageTiledCanvas extends TiledCanvas { height: number; options: Object; - cache: CoverageCache; + source: CoverageDataSource; - constructor(cache: CoverageCache, height: number, options: Object) { + constructor(source: CoverageDataSource, height: number, options: Object) { super(); - this.cache = cache; + this.source = source; this.height = Math.max(1, height); this.options = options; } @@ -56,19 +59,18 @@ class CoverageTiledCanvas extends TiledCanvas { } yScaleForRef(ref: string): (y: number) => number { - var maxCoverage = this.cache.maxCoverageForRef(ref); + var maxCoverage = this.source.maxCoverage(); - var padding = 10; // TODO: move into style return scale.linear() .domain([maxCoverage, 0]) - .range([padding, this.height - padding]) + .range([style.COVERAGE_PADDING, this.height - style.COVERAGE_PADDING]) .nice(); } render(ctx: DataCanvasRenderingContext2D, xScale: (x: number)=>number, range: ContigInterval) { - var bins = this.cache.binsForRef(range.contig); + var bins = this.source.getFeaturesInRange(range); var yScale = this.yScaleForRef(range.contig); var relaxedRange = new ContigInterval( range.contig, range.start() - 1, range.stop() + 1); @@ -82,7 +84,7 @@ function renderBars(ctx: DataCanvasRenderingContext2D, xScale: (num: number) => number, yScale: (num: number) => number, range: ContigInterval, - bins: {[key: number]: BinSummary}, + bins: PositionCount[], options: Object) { if (_.isEmpty(bins)) return; @@ -98,7 +100,6 @@ function renderBars(ctx: DataCanvasRenderingContext2D, return {barX1, barX2, barY}; }; - var mismatchBins = ({} : {[key:number]: BinSummary}); // keep track of which ones have mismatches var vBasePosY = yScale(0); // the very bottom of the canvas var start = range.start(), stop = range.stop(); @@ -118,75 +119,17 @@ function renderBars(ctx: DataCanvasRenderingContext2D, ctx.lineTo(barX2 + 1, vBasePosY); } - if (SHOW_MISMATCHES && !_.isEmpty(bin.mismatches)) { - mismatchBins[pos] = bin; - } - ctx.popObject(); } let {barX2} = binPos(stop, (stop in bins) ? bins[stop].count : 0); ctx.lineTo(barX2, vBasePosY); // right edge of the right bar. ctx.closePath(); ctx.fill(); - - // Now render the mismatches - _.each(mismatchBins, (bin, pos) => { - if (!bin.mismatches) return; // this is here for Flow; it can't really happen. - const mismatches = _.clone(bin.mismatches); - pos = Number(pos); // object keys are strings, not numbers. - - // If this is a high-frequency variant, add in the reference. - var mismatchCount = _.reduce(mismatches, (x, y) => x + y); - var mostFrequentMismatch = _.max(mismatches); - if (mostFrequentMismatch > MISMATCH_THRESHOLD && - mismatchCount > options.vafColorThreshold * bin.count && - mismatchCount < bin.count) { - if (bin.ref) { // here for flow; can't realy happen - mismatches[bin.ref] = bin.count - mismatchCount; - } - } - - let {barX1, barX2} = binPos(pos, bin.count); - ctx.pushObject(bin); - var countSoFar = 0; - _.chain(mismatches) - .map((count, base) => ({count, base})) // pull base into the object - .filter(({count}) => count > MISMATCH_THRESHOLD) - .sortBy(({count}) => -count) // the most common mismatch at the bottom - .each(({count, base}) => { - var misMatchObj = {position: 1 + pos, count, base}; - ctx.pushObject(misMatchObj); // for debugging and click-tracking - - ctx.fillStyle = style.BASE_COLORS[base]; - var y = yScale(countSoFar); - ctx.fillRect(barX1, - y, - Math.max(1, barX2 - barX1), // min width of 1px - yScale(countSoFar + count) - y); - countSoFar += count; - - ctx.popObject(); - }); - ctx.popObject(); - }); } -type Props = { - width: number; - height: number; - range: GenomeRange; - source: AlignmentDataSource; - referenceSource: TwoBitSource; - options: { - vafColorThreshold: number - } -}; - class CoverageTrack extends React.Component { props: Props; state: void; - cache: CoverageCache; - tiles: CoverageTiledCanvas; static defaultOptions: Object; constructor(props: Props) { @@ -206,14 +149,10 @@ class CoverageTrack extends React.Component { } componentDidMount() { - this.cache = new CoverageCache(this.props.referenceSource); - this.tiles = new CoverageTiledCanvas(this.cache, this.props.height, this.props.options); - this.props.source.on('newdata', range => { - var oldMax = this.cache.maxCoverageForRef(range.contig); - this.props.source.getAlignmentsInRange(range) - .forEach(read => this.cache.addAlignment(read)); - var newMax = this.cache.maxCoverageForRef(range.contig); + var oldMax = this.props.source.maxCoverageForRef(range.contig); + this.props.source.getCoverageInRange(range); + var newMax = this.props.source.maxCoverageForRef(range.contig); if (oldMax != newMax) { this.tiles.invalidateAll(); @@ -223,8 +162,7 @@ class CoverageTrack extends React.Component { this.visualizeCoverage(); }); - this.props.referenceSource.on('newdata', range => { - this.cache.updateMismatches(range); + this.props.source.on('newdata', range => { this.tiles.invalidateRange(range); this.visualizeCoverage(); }); @@ -308,37 +246,23 @@ class CoverageTrack extends React.Component { // No need to render the scene to determine what was clicked. var range = ContigInterval.fromGenomeRange(this.props.range), xScale = this.getScale(), - bins = this.cache.binsForRef(range.contig), + bins = this.props.source.getCoverageInRange(range.contig), pos = Math.floor(xScale.invert(x)) - 1, bin = bins[pos]; var alert = window.alert || console.log; if (bin) { - var mmCount = bin.mismatches ? _.reduce(bin.mismatches, (a, b) => a + b) : 0; - var ref = bin.ref || this.props.referenceSource.getRangeAsString( - {contig: range.contig, start: pos, stop: pos}); - // Construct a JSON object to show the user. var messageObject = _.extend( { 'position': range.contig + ':' + (1 + pos), 'read depth': bin.count - }, - bin.mismatches); - messageObject[ref] = bin.count - mmCount; + }); alert(JSON.stringify(messageObject, null, ' ')); } } } CoverageTrack.displayName = 'coverage'; -CoverageTrack.defaultOptions = { - // Color the reference base in the bar chart when the Variant Allele Fraction - // exceeds this amount. When there are >=2 agreeing mismatches, they are - // always rendered. But for mismatches below this threshold, the reference is - // not colored in the bar chart. This draws attention to high-VAF mismatches. - vafColorThreshold: 0.2 -}; - module.exports = CoverageTrack; diff --git a/src/main/viz/PileupCoverageTrack.js b/src/main/viz/PileupCoverageTrack.js new file mode 100644 index 00000000..f50bcdc6 --- /dev/null +++ b/src/main/viz/PileupCoverageTrack.js @@ -0,0 +1,339 @@ +/** + * Coverage visualization of Alignment sources. + * @flow + */ +'use strict'; + +import type {Alignment, AlignmentDataSource} from '../Alignment'; +import type Interval from '../Interval'; +import type {TwoBitSource} from '../sources/TwoBitDataSource'; +import type {DataCanvasRenderingContext2D} from 'data-canvas'; +import type {BinSummary} from './CoverageCache'; +import type {Scale} from './d3utils'; + +import React from 'react'; +import scale from '../scale'; +import shallowEquals from 'shallow-equals'; +import d3utils from './d3utils'; +import _ from 'underscore'; +import dataCanvas from 'data-canvas'; +import canvasUtils from './canvas-utils'; +import CoverageCache from './CoverageCache'; +import TiledCanvas from './TiledCanvas'; +import style from '../style'; +import ContigInterval from '../ContigInterval'; + +// Basic setup (TODO: make this configurable by the user) +const SHOW_MISMATCHES = true; + +// Only show mismatch information when there are more than this many +// reads supporting that mismatch. +const MISMATCH_THRESHOLD = 1; + + +class CoverageTiledCanvas extends TiledCanvas { + height: number; + options: Object; + cache: CoverageCache; + + constructor(cache: CoverageCache, height: number, options: Object) { + super(); + + this.cache = cache; + this.height = Math.max(1, height); + this.options = options; + } + + heightForRef(ref: string): number { + return this.height; + } + + update(height: number, options: Object) { + // workaround for an issue in PhantomJS where height always comes out to zero. + this.height = Math.max(1, height); + this.options = options; + } + + yScaleForRef(ref: string): (y: number) => number { + var maxCoverage = this.cache.maxCoverageForRef(ref); + + var padding = 10; // TODO: move into style + return scale.linear() + .domain([maxCoverage, 0]) + .range([padding, this.height - padding]) + .nice(); + } + + render(ctx: DataCanvasRenderingContext2D, + xScale: (x: number)=>number, + range: ContigInterval) { + var bins = this.cache.binsForRef(range.contig); + var yScale = this.yScaleForRef(range.contig); + var relaxedRange = new ContigInterval( + range.contig, range.start() - 1, range.stop() + 1); + renderBars(ctx, xScale, yScale, relaxedRange, bins, this.options); + } +} + + +// Draw coverage bins & mismatches +function renderBars(ctx: DataCanvasRenderingContext2D, + xScale: (num: number) => number, + yScale: (num: number) => number, + range: ContigInterval, + bins: {[key: number]: BinSummary}, + options: Object) { + if (_.isEmpty(bins)) return; + + var barWidth = xScale(1) - xScale(0); + var showPadding = (barWidth > style.COVERAGE_MIN_BAR_WIDTH_FOR_GAP); + var padding = showPadding ? 1 : 0; + + var binPos = function(pos: number, count: number) { + // Round to integer coordinates for crisp lines, without aliasing. + var barX1 = Math.round(xScale(1 + pos)), + barX2 = Math.round(xScale(2 + pos)) - padding, + barY = Math.round(yScale(count)); + return {barX1, barX2, barY}; + }; + + var mismatchBins = ({} : {[key:number]: BinSummary}); // keep track of which ones have mismatches + var vBasePosY = yScale(0); // the very bottom of the canvas + var start = range.start(), + stop = range.stop(); + let {barX1} = binPos(start, (start in bins) ? bins[start].count : 0); + ctx.fillStyle = style.COVERAGE_BIN_COLOR; + ctx.beginPath(); + ctx.moveTo(barX1, vBasePosY); + for (var pos = start; pos < stop; pos++) { + var bin = bins[pos]; + if (!bin) continue; + ctx.pushObject(bin); + let {barX1, barX2, barY} = binPos(pos, bin.count); + ctx.lineTo(barX1, barY); + ctx.lineTo(barX2, barY); + if (showPadding) { + ctx.lineTo(barX2, vBasePosY); + ctx.lineTo(barX2 + 1, vBasePosY); + } + + if (SHOW_MISMATCHES && !_.isEmpty(bin.mismatches)) { + mismatchBins[pos] = bin; + } + + ctx.popObject(); + } + let {barX2} = binPos(stop, (stop in bins) ? bins[stop].count : 0); + ctx.lineTo(barX2, vBasePosY); // right edge of the right bar. + ctx.closePath(); + ctx.fill(); + + // Now render the mismatches + _.each(mismatchBins, (bin, pos) => { + if (!bin.mismatches) return; // this is here for Flow; it can't really happen. + const mismatches = _.clone(bin.mismatches); + pos = Number(pos); // object keys are strings, not numbers. + + // If this is a high-frequency variant, add in the reference. + var mismatchCount = _.reduce(mismatches, (x, y) => x + y); + var mostFrequentMismatch = _.max(mismatches); + if (mostFrequentMismatch > MISMATCH_THRESHOLD && + mismatchCount > options.vafColorThreshold * bin.count && + mismatchCount < bin.count) { + if (bin.ref) { // here for flow; can't realy happen + mismatches[bin.ref] = bin.count - mismatchCount; + } + } + + let {barX1, barX2} = binPos(pos, bin.count); + ctx.pushObject(bin); + var countSoFar = 0; + _.chain(mismatches) + .map((count, base) => ({count, base})) // pull base into the object + .filter(({count}) => count > MISMATCH_THRESHOLD) + .sortBy(({count}) => -count) // the most common mismatch at the bottom + .each(({count, base}) => { + var misMatchObj = {position: 1 + pos, count, base}; + ctx.pushObject(misMatchObj); // for debugging and click-tracking + + ctx.fillStyle = style.BASE_COLORS[base]; + var y = yScale(countSoFar); + ctx.fillRect(barX1, + y, + Math.max(1, barX2 - barX1), // min width of 1px + yScale(countSoFar + count) - y); + countSoFar += count; + + ctx.popObject(); + }); + ctx.popObject(); + }); +} + +type Props = { + width: number; + height: number; + range: GenomeRange; + source: AlignmentDataSource; + referenceSource: TwoBitSource; + options: { + vafColorThreshold: number + } +}; + +class PileupCoverageTrack extends React.Component { + props: Props; + state: void; + cache: CoverageCache; + tiles: CoverageTiledCanvas; + static defaultOptions: Object; + + constructor(props: Props) { + super(props); + } + + render(): any { + return ; + } + + getScale(): Scale { + return d3utils.getTrackScale(this.props.range, this.props.width); + } + + componentDidMount() { + this.cache = new CoverageCache(this.props.referenceSource); + this.tiles = new CoverageTiledCanvas(this.cache, this.props.height, this.props.options); + + this.props.source.on('newdata', range => { + var oldMax = this.cache.maxCoverageForRef(range.contig); + this.props.source.getAlignmentsInRange(range) + .forEach(read => this.cache.addAlignment(read)); + var newMax = this.cache.maxCoverageForRef(range.contig); + + if (oldMax != newMax) { + this.tiles.invalidateAll(); + } else { + this.tiles.invalidateRange(range); + } + this.visualizeCoverage(); + }); + + this.props.referenceSource.on('newdata', range => { + this.cache.updateMismatches(range); + this.tiles.invalidateRange(range); + this.visualizeCoverage(); + }); + } + + componentDidUpdate(prevProps: any, prevState: any) { + if (!shallowEquals(this.props, prevProps) || + !shallowEquals(this.state, prevState)) { + if (this.props.height != prevProps.height || + this.props.options != prevProps.options) { + this.tiles.update(this.props.height, this.props.options); + this.tiles.invalidateAll(); + } + this.visualizeCoverage(); + } + } + + getContext(): CanvasRenderingContext2D { + var canvas = (this.refs.canvas : HTMLCanvasElement); + // The typecast through `any` is because getContext could return a WebGL context. + var ctx = ((canvas.getContext('2d') : any) : CanvasRenderingContext2D); + return ctx; + } + + // Draw three ticks on the left to set the scale for the user + renderTicks(ctx: DataCanvasRenderingContext2D, yScale: (num: number)=>number) { + var axisMax = yScale.domain()[0]; + [0, Math.round(axisMax / 2), axisMax].forEach(tick => { + // Draw a line indicating the tick + ctx.pushObject({value: tick, type: 'tick'}); + var tickPosY = Math.round(yScale(tick)); + ctx.strokeStyle = style.COVERAGE_FONT_COLOR; + canvasUtils.drawLine(ctx, 0, tickPosY, style.COVERAGE_TICK_LENGTH, tickPosY); + ctx.popObject(); + + var tickLabel = tick + 'X'; + ctx.pushObject({value: tick, label: tickLabel, type: 'label'}); + // Now print the coverage information + ctx.font = style.COVERAGE_FONT_STYLE; + var textPosX = style.COVERAGE_TICK_LENGTH + style.COVERAGE_TEXT_PADDING, + textPosY = tickPosY + style.COVERAGE_TEXT_Y_OFFSET; + // The stroke creates a border around the text to make it legible over the bars. + ctx.strokeStyle = 'white'; + ctx.lineWidth = 2; + ctx.strokeText(tickLabel, textPosX, textPosY); + ctx.lineWidth = 1; + ctx.fillStyle = style.COVERAGE_FONT_COLOR; + ctx.fillText(tickLabel, textPosX, textPosY); + ctx.popObject(); + }); + } + + visualizeCoverage() { + var canvas = (this.refs.canvas : HTMLCanvasElement), + width = this.props.width, + height = this.props.height, + range = ContigInterval.fromGenomeRange(this.props.range); + + // Hold off until height & width are known. + if (width === 0) return; + d3utils.sizeCanvas(canvas, width, height); + + var ctx = dataCanvas.getDataContext(this.getContext()); + ctx.save(); + ctx.reset(); + ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); + + var yScale = this.tiles.yScaleForRef(range.contig); + + this.tiles.renderToScreen(ctx, range, this.getScale()); + this.renderTicks(ctx, yScale); + + ctx.restore(); + } + + handleClick(reactEvent: any) { + var ev = reactEvent.nativeEvent, + x = ev.offsetX; + + // It's simple to figure out which position was clicked using the x-scale. + // No need to render the scene to determine what was clicked. + var range = ContigInterval.fromGenomeRange(this.props.range), + xScale = this.getScale(), + bins = this.cache.binsForRef(range.contig), + pos = Math.floor(xScale.invert(x)) - 1, + bin = bins[pos]; + + var alert = window.alert || console.log; + if (bin) { + var mmCount = bin.mismatches ? _.reduce(bin.mismatches, (a, b) => a + b) : 0; + var ref = bin.ref || this.props.referenceSource.getRangeAsString( + {contig: range.contig, start: pos, stop: pos}); + + // Construct a JSON object to show the user. + var messageObject = _.extend( + { + 'position': range.contig + ':' + (1 + pos), + 'read depth': bin.count + }, + bin.mismatches); + messageObject[ref] = bin.count - mmCount; + alert(JSON.stringify(messageObject, null, ' ')); + } + } +} + +PileupCoverageTrack.displayName = 'coverage'; +PileupCoverageTrack.defaultOptions = { + // Color the reference base in the bar chart when the Variant Allele Fraction + // exceeds this amount. When there are >=2 agreeing mismatches, they are + // always rendered. But for mismatches below this threshold, the reference is + // not colored in the bar chart. This draws attention to high-VAF mismatches. + vafColorThreshold: 0.2 +}; + + +module.exports = PileupCoverageTrack; diff --git a/src/test/viz/CoverageTrack-test.js b/src/test/viz/CoverageTrack-test.js index 17537fc1..8cd016f8 100644 --- a/src/test/viz/CoverageTrack-test.js +++ b/src/test/viz/CoverageTrack-test.js @@ -6,8 +6,6 @@ */ 'use strict'; -import type SamRead from '../../main/data/SamRead'; - import {expect} from 'chai'; import pileup from '../../main/pileup'; @@ -37,10 +35,9 @@ describe('CoverageTrack', function() { { viz: pileup.viz.coverage(), data: pileup.formats.bam({ - url: '/test-data/synth3.normal.17.7500000-7515000.bam', - indexUrl: '/test-data/synth3.normal.17.7500000-7515000.bam.bai' + url: '/coverage', }), - cssClass: 'tumor-coverage', + cssClass: 'test-coverage', name: 'Coverage' } ] @@ -89,18 +86,6 @@ describe('CoverageTrack', function() { }); }); - it('should show mismatch information', function() { - return waitFor(hasCoverage, 2000).then(() => { - var visibleMismatches = findMismatchBins() - .filter(bin => bin.position >= range.start && bin.position <= range.stop); - expect(visibleMismatches).to.deep.equal( - [{position: 7500765, count: 23, base: 'C'}, - {position: 7500765, count: 22, base: 'T'}]); - // TODO: IGV shows counts of 20 and 20 at this locus. Whither the five reads? - // `samtools view` reports the full 45 reads at 17:7500765 - }); - }); - it('should create correct labels for coverage', function() { return waitFor(hasCoverage, 2000).then(() => { // These are the objects being used to draw labels @@ -108,7 +93,7 @@ describe('CoverageTrack', function() { expect(labelTexts[0].label).to.equal('0X'); expect(labelTexts[labelTexts.length-1].label).to.equal('50X'); - // Now let's test if they are actually being put on the screen + // Now let's test if they are actually being put on the screens var texts = callsOf(testDiv, '.coverage', 'fillText'); expect(texts.map(t => t[1])).to.deep.equal(['0X', '25X', '50X']); }); diff --git a/src/test/viz/PileupCoverageTrack-test.js b/src/test/viz/PileupCoverageTrack-test.js new file mode 100644 index 00000000..47da689a --- /dev/null +++ b/src/test/viz/PileupCoverageTrack-test.js @@ -0,0 +1,117 @@ +/** + * This tests whether coverage information is being shown/drawn correctly + * in the track. The alignment information comes from the test BAM files. + * + * @flow + */ +'use strict'; + +import type SamRead from '../../main/data/SamRead'; + +import {expect} from 'chai'; + +import pileup from '../../main/pileup'; +import TwoBit from '../../main/data/TwoBit'; +import TwoBitDataSource from '../../main/sources/TwoBitDataSource'; +import MappedRemoteFile from '../MappedRemoteFile'; +import dataCanvas from 'data-canvas'; +import {waitFor} from '../async'; + +describe('PileupCoverageTrack', function() { + var testDiv = document.getElementById('testdiv'); + var range = {contig: '17', start: 7500730, stop: 7500790}; + var p; + + beforeEach(() => { + dataCanvas.RecordingContext.recordAll(); + // A fixed width container results in predictable x-positions for mismatches. + testDiv.style.width = '800px'; + p = pileup.create(testDiv, { + range: range, + tracks: [ + { + data: referenceSource, + viz: pileup.viz.genome(), + isReference: true + }, + { + viz: pileup.viz.pileupcoverage(), + data: pileup.formats.bam({ + url: '/test-data/synth3.normal.17.7500000-7515000.bam', + indexUrl: '/test-data/synth3.normal.17.7500000-7515000.bam.bai' + }), + cssClass: 'tumor-coverage', + name: 'Coverage' + } + ] + }); + }); + + afterEach(() => { + dataCanvas.RecordingContext.reset(); + if (p) p.destroy(); + // avoid pollution between tests. + testDiv.innerHTML = ''; + testDiv.style.width = ''; + }); + + var twoBitFile = new MappedRemoteFile( + '/test-data/hg19.2bit.mapped', + [[0, 16383], [691179834, 691183928], [694008946, 694011447]]); + var referenceSource = TwoBitDataSource.createFromTwoBitFile(new TwoBit(twoBitFile)); + + var {drawnObjectsWith, callsOf} = dataCanvas.RecordingContext; + + var findCoverageBins = () => { + return drawnObjectsWith(testDiv, '.coverage', b => b.count); + }; + + var findMismatchBins = ():Array => { + return drawnObjectsWith(testDiv, '.coverage', b => b.base); + }; + + var findCoverageLabels = () => { + return drawnObjectsWith(testDiv, '.coverage', l => l.type == 'label'); + }; + + var hasCoverage = () => { + // Check whether the coverage bins are loaded yet + return testDiv.querySelector('canvas') && + findCoverageBins().length > 1 && + findMismatchBins().length > 0 && + findCoverageLabels().length > 1; + }; + + it('should create coverage information for all bases shown in the view', function() { + return waitFor(hasCoverage, 2000).then(() => { + var bins = findCoverageBins(); + expect(bins).to.have.length.at.least(range.stop - range.start + 1); + }); + }); + + it('should show mismatch information', function() { + return waitFor(hasCoverage, 2000).then(() => { + var visibleMismatches = findMismatchBins() + .filter(bin => bin.position >= range.start && bin.position <= range.stop); + expect(visibleMismatches).to.deep.equal( + [{position: 7500765, count: 23, base: 'C'}, + {position: 7500765, count: 22, base: 'T'}]); + // TODO: IGV shows counts of 20 and 20 at this locus. Whither the five reads? + // `samtools view` reports the full 45 reads at 17:7500765 + }); + }); + + it('should create correct labels for coverage', function() { + return waitFor(hasCoverage, 2000).then(() => { + // These are the objects being used to draw labels + var labelTexts = findCoverageLabels(); + expect(labelTexts[0].label).to.equal('0X'); + expect(labelTexts[labelTexts.length-1].label).to.equal('50X'); + + // Now let's test if they are actually being put on the screen + var texts = callsOf(testDiv, '.coverage', 'fillText'); + expect(texts.map(t => t[1])).to.deep.equal(['0X', '25X', '50X']); + }); + }); + +}); From 4e52fc1cc5c929176cd0e505f4d007a1e3b9dbac Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Fri, 14 Oct 2016 21:12:09 -0700 Subject: [PATCH 119/136] Finished coverage with Resolution cache. Thresholded view to length of chromosome. --- src/main/ResolutionCache.js | 51 +++---- src/main/Root.js | 15 +- src/main/data/Sequence.js | 7 +- src/main/sources/CoverageDataSource.js | 24 ++-- src/main/sources/ReferenceDataSource.js | 8 +- src/main/sources/TwoBitDataSource.js | 9 +- src/main/viz/CoverageTrack.js | 90 ++++++------ src/main/viz/PileupCoverageTrack.js | 41 +++--- src/main/viz/TiledCanvas.js | 11 +- src/test/FakeAlignment.js | 4 +- src/test/sources/CoverageDataSource-test.js | 20 +-- src/test/sources/ReferenceDataSource-test.js | 133 +++++++++--------- src/test/viz/CoverageTrack-test.js | 29 ++-- src/test/viz/GenomeTrack-test.js | 10 +- style/pileup.css | 4 + ...chrM-coverage.json => chr17-coverage.json} | 24 ++-- test-data/reference-chrM-0-1000.json | 2 +- 17 files changed, 275 insertions(+), 207 deletions(-) rename test-data/{chrM-coverage.json => chr17-coverage.json} (64%) diff --git a/src/main/ResolutionCache.js b/src/main/ResolutionCache.js index 8e347136..37d93bf9 100644 --- a/src/main/ResolutionCache.js +++ b/src/main/ResolutionCache.js @@ -14,7 +14,8 @@ import ContigInterval from './ContigInterval'; class ResolutionCache { coveredRanges: ResolutionCacheKey[]; cache: {[key: string]: T}; - filterFunction: Function; // should take form (range: ContigInterval, T) => boolean; + // used to filter out elements in the cache based on resolution. + filterFunction: Function; // should take form (range: ContigInterval, T, resolution: ?number) => boolean; keyFunction: Function; // should take form (d: T) => string; constructor(filterFunction: Function, keyFunction: Function) { @@ -25,13 +26,16 @@ class ResolutionCache { } // gets data from cache at the Resolution defined by the interval - get(range: ContigInterval): T[] { - if (this.coversRange(range)) { - if (!range) return []; - return _.filter(this.cache, d => this.filterFunction(range, d)); - } else { - return []; + get(range: ContigInterval, resolution: ?number): T[] { + if (!range) return []; + var res = _.filter(this.cache, d => this.filterFunction(range, d, resolution)); + + // if range is not fully covered, give warning but still return available data + if (this.coversRange(range, resolution)) { + console.warn("Warning: Resolution Cache does not fully cover region. Returning available data..."); } + + return res; } // puts new ranges into list of ranges covered by cache @@ -53,26 +57,17 @@ class ResolutionCache { // checks weather cache contains data for the // specified interval and its corresponding resolution - coversRange(range: ContigInterval): boolean { - var resolution = ResolutionCache.getResolution(range.interval); - if (range.isCoveredBy(this.coveredRanges.map(r => r.contigInterval))) { - // if covered by the data, verify that the correct base pair density is - // available - var correctResolution = true; - for (var i = 0; i < this.coveredRanges.length; i++) { - var r: ContigInterval = this.coveredRanges[i].contigInterval; - var thisRes = this.coveredRanges[i].resolution; - if (r.intersects(range)) { - if (thisRes > resolution) { // resolution not fine enough for query - correctResolution = false; - break; - } - } - } - return correctResolution; - } else { - return false; + coversRange(range: ContigInterval, + resolution: ?number): boolean { + if (!resolution) { + resolution = ResolutionCache.getResolution(range.interval); } + + // filter ranges by correct resolution + var resolutionRanges = _.filter(this.coveredRanges, r => r.resolution == resolution); + if (range.isCoveredBy(resolutionRanges.map(r => r.contigInterval))) { + return true; + } else return false; } // clears out all content in cache @@ -136,8 +131,8 @@ class ResolutionCacheKey { } var lastR: ResolutionCacheKey = rs[rs.length - 1]; - if (r.contigInterval.intersects(lastR.contigInterval) || - r.contigInterval.isAdjacentTo(lastR.contigInterval) && + if ((r.contigInterval.intersects(lastR.contigInterval) || + r.contigInterval.isAdjacentTo(lastR.contigInterval)) && r.resolution == lastR.resolution) { lastR = rs[rs.length - 1] = lastR.clone(); lastR.contigInterval.interval.stop = diff --git a/src/main/Root.js b/src/main/Root.js index 0e33904c..d6811179 100644 --- a/src/main/Root.js +++ b/src/main/Root.js @@ -7,9 +7,11 @@ import type {TwoBitSource} from './sources/TwoBitDataSource'; import type {VisualizedTrack, VizWithOptions} from './types'; +import _ from 'underscore'; import React from 'react'; import Controls from './Controls'; import Menu from './Menu'; +import type {SequenceRecord} from './data/Sequence'; import VisualizationWrapper from './VisualizationWrapper'; type Props = { @@ -21,7 +23,8 @@ type Props = { class Root extends React.Component { props: Props; state: { - contigList: string[]; + contigList: SequenceRecord[]; + contigNames: string[]; range: ?GenomeRange; settingsMenuKey: ?string; }; @@ -30,6 +33,7 @@ class Root extends React.Component { super(props); this.state = { contigList: this.props.referenceSource.contigList(), + contigNames: _.map(this.props.referenceSource.contigList(), contig => contig.name), range: null, settingsMenuKey: null }; @@ -54,6 +58,13 @@ class Root extends React.Component { if (newRange.start < 0) { newRange.start = 0; } + var record = _.find(this.state.contigList, contig => contig.name == newRange.contig); + if (record) { + if (newRange.stop > record.length) { + newRange.stop = record.length; + } + } + this.props.referenceSource.normalizeRange(newRange).then(range => { this.setState({range: range}); @@ -153,7 +164,7 @@ class Root extends React.Component {  
-
diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index 8532831b..c126bf3c 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -24,10 +24,15 @@ class Sequence { } // Returns a list of contig names. - getContigList(): string[] { + getContigNames(): string[] { return this.contigList.map(seq => seq.name); } + // Returns a list of contig names. + getContigs(): SequenceRecord[] { + return this.contigList; + } + /** * Returns the base pairs for contig:start-stop. * The range is inclusive and zero-based. diff --git a/src/main/sources/CoverageDataSource.js b/src/main/sources/CoverageDataSource.js index 820b921d..4869fa96 100644 --- a/src/main/sources/CoverageDataSource.js +++ b/src/main/sources/CoverageDataSource.js @@ -38,16 +38,18 @@ function keyFunction(p: PositionCount): string { return `${p.contig}:${p.position}`; } -function filterFunction(range: ContigInterval, p: PositionCount): boolean { - return range.chrContainsLocus(p.contig, p.position); +function filterFunction(range: ContigInterval, p: PositionCount, resolution: ?number): boolean { + // if resolution is specified, select results based on resolution and position start site + if (resolution) return (range.chrContainsLocus(p.contig, p.position) && p.position % resolution == 0); + else return range.chrContainsLocus(p.contig, p.position); } function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource { var cache: ResolutionCache = new ResolutionCache(filterFunction, keyFunction); - function maxCoverage(range: ContigInterval): number { - var positions: number[] = cache.get(range).map(r => r.count); + function maxCoverage(range: ContigInterval, resolution: ?number): number { + var positions: number[] = cache.get(range, resolution).map(r => r.count); var maxCoverage = Math.max.apply(Math, positions); return maxCoverage; } @@ -67,16 +69,22 @@ function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource // Cover the range immediately to prevent duplicate fetches. cache.coverRange(interval); - coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getFeaturesInRange(interval, endpointModifier).then(positions => { - positions.forEach(p => cache.put(p)); + positions.forEach(p => cache.put({ + "contig": range.contig, + "position": p.position, + "count": p.count + })); o.trigger('newdata', interval); }); } - function getCoverageInRange(range: ContigInterval): PositionCount[] { + function getCoverageInRange(range: ContigInterval, + resolution: ?number): PositionCount[] { if (!range) return []; - return cache.get(range); + var data = cache.get(range, resolution); + var sorted = data.sort((a, b) => a.position - b.position); + return sorted; } var o = { diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index 1982b998..ebea74b9 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -46,7 +46,7 @@ function expandRange(range) { var createFromReferenceUrl = function(remoteSource: Sequence): TwoBitSource { // Local cache of genomic data. - var contigList = remoteSource.getContigList(); + var contigList = remoteSource.getContigs(); var store = new SequenceStore(); // Ranges for which we have complete information -- no need to hit network. @@ -76,11 +76,13 @@ var createFromReferenceUrl = function(remoteSource: Sequence): TwoBitSource { // This either adds or removes a 'chr' as needed. function normalizeRange(range: GenomeRange): Q.Promise { - if (contigList.indexOf(range.contig) >= 0) { + var contigIdx = _.map(contigList, contig => contig.name).indexOf(range.contig); + if (contigIdx >= 0) { return Q.Promise.resolve(range); } var altContig = utils.altContigName(range.contig); - if (contigList.indexOf(altContig) >= 0) { + var altIdx = _.map(contigList, contig => contig.name).indexOf(altContig); + if (altIdx >= 0) { return Q.Promise.resolve({ contig: altContig, start: range.start, diff --git a/src/main/sources/TwoBitDataSource.js b/src/main/sources/TwoBitDataSource.js index 59c27049..acb42b5c 100644 --- a/src/main/sources/TwoBitDataSource.js +++ b/src/main/sources/TwoBitDataSource.js @@ -23,6 +23,7 @@ import ContigInterval from '../ContigInterval'; import TwoBit from '../data/TwoBit'; import RemoteFile from '../RemoteFile'; import SequenceStore from '../SequenceStore'; +import type {SequenceRecord} from '../data/Sequence'; import utils from '../utils'; @@ -39,7 +40,7 @@ export type TwoBitSource = { rangeChanged: (newRange: GenomeRange) => void; getRange: (range: GenomeRange) => {[key:string]: ?string}; getRangeAsString: (range: GenomeRange) => string; - contigList: () => string[]; + contigList: () => SequenceRecord[]; normalizeRange: (range: GenomeRange) => Q.Promise; on: (event: string, handler: Function) => void; once: (event: string, handler: Function) => void; @@ -94,11 +95,13 @@ var createFromTwoBitFile = function(remoteSource: TwoBit): TwoBitSource { // This either adds or removes a 'chr' as needed. function normalizeRangeSync(range: GenomeRange): GenomeRange { - if (contigList.indexOf(range.contig) >= 0) { + var contigIdx = _.map(contigList, contig => contig.name).indexOf(range.contig); + if (contigIdx >= 0) { return range; } var altContig = utils.altContigName(range.contig); - if (contigList.indexOf(altContig) >= 0) { + var altIdx = _.map(contigList, contig => contig.name).indexOf(altContig); + if (altIdx >= 0) { return { contig: altContig, start: range.start, diff --git a/src/main/viz/CoverageTrack.js b/src/main/viz/CoverageTrack.js index 7a13a184..59e949c6 100644 --- a/src/main/viz/CoverageTrack.js +++ b/src/main/viz/CoverageTrack.js @@ -9,8 +9,8 @@ import GA4GHDataSource from '../sources/GA4GHDataSource'; import type {TwoBitSource} from '../sources/TwoBitDataSource'; import type {DataCanvasRenderingContext2D} from 'data-canvas'; import type {Scale} from './d3utils'; -import CoverageDataSource from '../sources/CoverageDataSource'; -import PositionCount from '../sources/CoverageDataSource'; +import type {CoverageDataSource} from '../sources/CoverageDataSource'; +import type {PositionCount} from '../sources/CoverageDataSource'; import React from 'react'; import scale from '../scale'; @@ -58,8 +58,8 @@ class CoverageTiledCanvas extends TiledCanvas { this.options = options; } - yScaleForRef(ref: string): (y: number) => number { - var maxCoverage = this.source.maxCoverage(); + yScaleForRef(range: ContigInterval, resolution: ?number): (y: number) => number { + var maxCoverage = this.source.maxCoverage(range, resolution); return scale.linear() .domain([maxCoverage, 0]) @@ -67,24 +67,28 @@ class CoverageTiledCanvas extends TiledCanvas { .nice(); } + // This is alled by TiledCanvas over all tiles in a range render(ctx: DataCanvasRenderingContext2D, xScale: (x: number)=>number, - range: ContigInterval) { - var bins = this.source.getFeaturesInRange(range); - var yScale = this.yScaleForRef(range.contig); + range: ContigInterval, + resolution: ?number) { var relaxedRange = new ContigInterval( - range.contig, range.start() - 1, range.stop() + 1); - renderBars(ctx, xScale, yScale, relaxedRange, bins, this.options); + range.contig, Math.max(1, range.start() - 1), range.stop() + 1); + var bins = this.source.getCoverageInRange(relaxedRange, resolution); + var yScale = this.yScaleForRef(range, resolution); + + renderBars(ctx, xScale, yScale, relaxedRange, bins, resolution, this.options); } } -// Draw coverage bins & mismatches +// Draw coverage bins function renderBars(ctx: DataCanvasRenderingContext2D, xScale: (num: number) => number, yScale: (num: number) => number, range: ContigInterval, bins: PositionCount[], + resolution: ?number, options: Object) { if (_.isEmpty(bins)) return; @@ -95,7 +99,7 @@ function renderBars(ctx: DataCanvasRenderingContext2D, var binPos = function(pos: number, count: number) { // Round to integer coordinates for crisp lines, without aliasing. var barX1 = Math.round(xScale(1 + pos)), - barX2 = Math.round(xScale(2 + pos)) - padding, + barX2 = Math.round(xScale(1 + resolution + pos)) - padding, barY = Math.round(yScale(count)); return {barX1, barX2, barY}; }; @@ -103,15 +107,16 @@ function renderBars(ctx: DataCanvasRenderingContext2D, var vBasePosY = yScale(0); // the very bottom of the canvas var start = range.start(), stop = range.stop(); - let {barX1} = binPos(start, (start in bins) ? bins[start].count : 0); + var first = bins.filter(bin => bin.position == start); + // find first bin in dataset and move to that position. + let {barX1} = binPos(start, (!_.isEmpty(first)) ? first[0].count : 0); ctx.fillStyle = style.COVERAGE_BIN_COLOR; ctx.beginPath(); ctx.moveTo(barX1, vBasePosY); - for (var pos = start; pos < stop; pos++) { - var bin = bins[pos]; - if (!bin) continue; + + bins.forEach(bin => { ctx.pushObject(bin); - let {barX1, barX2, barY} = binPos(pos, bin.count); + let {barX1, barX2, barY} = binPos(bin.position, bin.count); ctx.lineTo(barX1, barY); ctx.lineTo(barX2, barY); if (showPadding) { @@ -120,7 +125,7 @@ function renderBars(ctx: DataCanvasRenderingContext2D, } ctx.popObject(); - } + }); let {barX2} = binPos(stop, (stop in bins) ? bins[stop].count : 0); ctx.lineTo(barX2, vBasePosY); // right edge of the right bar. ctx.closePath(); @@ -131,17 +136,14 @@ class CoverageTrack extends React.Component { props: Props; state: void; static defaultOptions: Object; + tiles: CoverageTiledCanvas; constructor(props: Props) { super(props); } render(): any { - var rangeLength = this.props.range.stop - this.props.range.start; - // Render coverage if base pairs is less than threshold - if (rangeLength <= GA4GHDataSource.MAX_BASE_PAIRS_TO_FETCH) { - return ; - } else return
; + return ; } getScale(): Scale { @@ -149,10 +151,12 @@ class CoverageTrack extends React.Component { } componentDidMount() { + this.tiles = new CoverageTiledCanvas(this.props.source, this.props.height, this.props.options); + this.props.source.on('newdata', range => { - var oldMax = this.props.source.maxCoverageForRef(range.contig); + var oldMax = this.props.source.maxCoverage(range); this.props.source.getCoverageInRange(range); - var newMax = this.props.source.maxCoverageForRef(range.contig); + var newMax = this.props.source.maxCoverage(range); if (oldMax != newMax) { this.tiles.invalidateAll(); @@ -193,25 +197,28 @@ class CoverageTrack extends React.Component { [0, Math.round(axisMax / 2), axisMax].forEach(tick => { // Draw a line indicating the tick ctx.pushObject({value: tick, type: 'tick'}); - var tickPosY = Math.round(yScale(tick)); + var tickPosY = Math.round(yScale(tick))+10; // add 9 for offset compared to printed tiles ctx.strokeStyle = style.COVERAGE_FONT_COLOR; canvasUtils.drawLine(ctx, 0, tickPosY, style.COVERAGE_TICK_LENGTH, tickPosY); ctx.popObject(); - var tickLabel = tick + 'X'; - ctx.pushObject({value: tick, label: tickLabel, type: 'label'}); - // Now print the coverage information - ctx.font = style.COVERAGE_FONT_STYLE; - var textPosX = style.COVERAGE_TICK_LENGTH + style.COVERAGE_TEXT_PADDING, - textPosY = tickPosY + style.COVERAGE_TEXT_Y_OFFSET; - // The stroke creates a border around the text to make it legible over the bars. - ctx.strokeStyle = 'white'; - ctx.lineWidth = 2; - ctx.strokeText(tickLabel, textPosX, textPosY); - ctx.lineWidth = 1; - ctx.fillStyle = style.COVERAGE_FONT_COLOR; - ctx.fillText(tickLabel, textPosX, textPosY); - ctx.popObject(); + if (tick > 0) { + var tickLabel = tick + 'X'; + ctx.pushObject({value: tick, label: tickLabel, type: 'label'}); + // Now print the coverage information + ctx.font = style.COVERAGE_FONT_STYLE; + var textPosX = style.COVERAGE_TICK_LENGTH + style.COVERAGE_TEXT_PADDING, + textPosY = tickPosY + style.COVERAGE_TEXT_Y_OFFSET; + // The stroke creates a border around the text to make it legible over the bars. + ctx.strokeStyle = 'white'; + ctx.lineWidth = 2; + ctx.strokeText(tickLabel, textPosX, textPosY); + ctx.lineWidth = 1; + ctx.fillStyle = style.COVERAGE_FONT_COLOR; + ctx.fillText(tickLabel, textPosX, textPosY); + ctx.popObject(); + } + }); } @@ -230,7 +237,8 @@ class CoverageTrack extends React.Component { ctx.reset(); ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); - var yScale = this.tiles.yScaleForRef(range.contig); + var yScale = this.tiles.yScaleForRef(range); + var thisS = this.getScale(); this.tiles.renderToScreen(ctx, range, this.getScale()); this.renderTicks(ctx, yScale); @@ -246,7 +254,7 @@ class CoverageTrack extends React.Component { // No need to render the scene to determine what was clicked. var range = ContigInterval.fromGenomeRange(this.props.range), xScale = this.getScale(), - bins = this.props.source.getCoverageInRange(range.contig), + bins = this.props.source.getCoverageInRange(range), pos = Math.floor(xScale.invert(x)) - 1, bin = bins[pos]; diff --git a/src/main/viz/PileupCoverageTrack.js b/src/main/viz/PileupCoverageTrack.js index f50bcdc6..7107aac0 100644 --- a/src/main/viz/PileupCoverageTrack.js +++ b/src/main/viz/PileupCoverageTrack.js @@ -6,6 +6,7 @@ import type {Alignment, AlignmentDataSource} from '../Alignment'; import type Interval from '../Interval'; +import GA4GHDataSource from '../sources/GA4GHDataSource'; import type {TwoBitSource} from '../sources/TwoBitDataSource'; import type {DataCanvasRenderingContext2D} from 'data-canvas'; import type {BinSummary} from './CoverageCache'; @@ -193,7 +194,11 @@ class PileupCoverageTrack extends React.Component { } render(): any { - return ; + var rangeLength = this.props.range.stop - this.props.range.start; + // Render coverage if base pairs is less than threshold + if (rangeLength <= GA4GHDataSource.MAX_BASE_PAIRS_TO_FETCH) { + return ; + } else return
; } getScale(): Scale { @@ -250,25 +255,27 @@ class PileupCoverageTrack extends React.Component { [0, Math.round(axisMax / 2), axisMax].forEach(tick => { // Draw a line indicating the tick ctx.pushObject({value: tick, type: 'tick'}); - var tickPosY = Math.round(yScale(tick)); + var tickPosY = Math.round(yScale(tick))+10; ctx.strokeStyle = style.COVERAGE_FONT_COLOR; canvasUtils.drawLine(ctx, 0, tickPosY, style.COVERAGE_TICK_LENGTH, tickPosY); ctx.popObject(); - var tickLabel = tick + 'X'; - ctx.pushObject({value: tick, label: tickLabel, type: 'label'}); - // Now print the coverage information - ctx.font = style.COVERAGE_FONT_STYLE; - var textPosX = style.COVERAGE_TICK_LENGTH + style.COVERAGE_TEXT_PADDING, - textPosY = tickPosY + style.COVERAGE_TEXT_Y_OFFSET; - // The stroke creates a border around the text to make it legible over the bars. - ctx.strokeStyle = 'white'; - ctx.lineWidth = 2; - ctx.strokeText(tickLabel, textPosX, textPosY); - ctx.lineWidth = 1; - ctx.fillStyle = style.COVERAGE_FONT_COLOR; - ctx.fillText(tickLabel, textPosX, textPosY); - ctx.popObject(); + if (tick > 0) { + var tickLabel = tick + 'X'; + ctx.pushObject({value: tick, label: tickLabel, type: 'label'}); + // Now print the coverage information + ctx.font = style.COVERAGE_FONT_STYLE; + var textPosX = style.COVERAGE_TICK_LENGTH + style.COVERAGE_TEXT_PADDING, + textPosY = tickPosY + style.COVERAGE_TEXT_Y_OFFSET; + // The stroke creates a border around the text to make it legible over the bars. + ctx.strokeStyle = 'white'; + ctx.lineWidth = 2; + ctx.strokeText(tickLabel, textPosX, textPosY); + ctx.lineWidth = 1; + ctx.fillStyle = style.COVERAGE_FONT_COLOR; + ctx.fillText(tickLabel, textPosX, textPosY); + ctx.popObject(); + } }); } @@ -279,7 +286,7 @@ class PileupCoverageTrack extends React.Component { range = ContigInterval.fromGenomeRange(this.props.range); // Hold off until height & width are known. - if (width === 0) return; + if (width === 0 || typeof canvas == 'undefined') return; d3utils.sizeCanvas(canvas, width, height); var ctx = dataCanvas.getDataContext(this.getContext()); diff --git a/src/main/viz/TiledCanvas.js b/src/main/viz/TiledCanvas.js index b668efba..108cf949 100644 --- a/src/main/viz/TiledCanvas.js +++ b/src/main/viz/TiledCanvas.js @@ -10,6 +10,7 @@ import _ from 'underscore'; import scale from '../scale'; import ContigInterval from '../ContigInterval'; +import {ResolutionCache} from '../ResolutionCache'; import Interval from '../Interval'; import canvasUtils from './canvas-utils'; import dataCanvas from 'data-canvas'; @@ -19,6 +20,7 @@ import d3utils from './d3utils'; type Tile = { pixelsPerBase: number; range: ContigInterval; + originalRange: ContigInterval; buffer: HTMLCanvasElement; }; @@ -47,7 +49,10 @@ class TiledCanvas { var sc = scale.linear().domain([range.start(), range.stop() + 1]).range([0, width]); var ctx = canvasUtils.getContext(tile.buffer); var dtx = dataCanvas.getDataContext(ctx); - this.render(dtx, sc, range); + + + var resolution = ResolutionCache.getResolution(tile.originalRange.interval); + this.render(dtx, sc, range, resolution); } // Create (and render) new tiles to fill the gaps. @@ -60,6 +65,7 @@ class TiledCanvas { var newTiles = newIntervals.map(iv => ({ pixelsPerBase, range: new ContigInterval(range.contig, iv.start, iv.stop), + originalRange: range, buffer: document.createElement('canvas') })); @@ -123,7 +129,8 @@ class TiledCanvas { render(dtx: DataCanvasRenderingContext2D, scale: (x: number)=>number, - range: ContigInterval): void { + range: ContigInterval, + resolution: ?number): void { throw 'Not implemented'; } diff --git a/src/test/FakeAlignment.js b/src/test/FakeAlignment.js index de67c4a4..3a6470a2 100644 --- a/src/test/FakeAlignment.js +++ b/src/test/FakeAlignment.js @@ -6,6 +6,8 @@ import type {Alignment, CigarOp, MateProperties, Strand} from '../main/Alignment'; import type ContigInterval from '../main/ContigInterval'; +import type {SequenceRecord} from '../main/data/Sequence'; + var numAlignments = 1; class FakeAlignment /* implements Alignment */ { @@ -63,7 +65,7 @@ var fakeSource = { rangeChanged: dieFn, getRange: function(): any { return {}; }, getRangeAsString: function(): string { return ''; }, - contigList: function(): string[] { return []; }, + contigList: function(): SequenceRecord[] { return []; }, normalizeRange: function() { }, on: dieFn, off: dieFn, diff --git a/src/test/sources/CoverageDataSource-test.js b/src/test/sources/CoverageDataSource-test.js index 2c4ec87b..20bf5b7d 100644 --- a/src/test/sources/CoverageDataSource-test.js +++ b/src/test/sources/CoverageDataSource-test.js @@ -13,10 +13,10 @@ describe('CoverageDataSource', function() { var server: any = null, response; before(function () { - return new RemoteFile('/test-data/chrM-coverage.json').getAllString().then(data => { + return new RemoteFile('/test-data/chr17-coverage.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); - server.respondWith('GET', '/coverage/chrM?start=1&end=1000&binning=1',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/coverage/17?start=1&end=1000&binning=1',[200, { "Content-Type": "application/json" }, response]); }); }); @@ -30,7 +30,7 @@ describe('CoverageDataSource', function() { url: '/coverage' }); - var requestInterval = new ContigInterval('chrM', 10, 30); + var requestInterval = new ContigInterval('17', 10, 30); expect(source.getCoverageInRange(requestInterval)) .to.deep.equal([]); @@ -40,7 +40,7 @@ describe('CoverageDataSource', function() { done(); }); - source.rangeChanged({contig: 'chrM', start: 10, stop: 30}); + source.rangeChanged({contig: '17', start: 10, stop: 30}); server.respond(); }); @@ -50,7 +50,7 @@ describe('CoverageDataSource', function() { url: '/coverage' }); var requestCount = 0; - var requestInterval = new ContigInterval('chrM', 10, 20); + var requestInterval = new ContigInterval('17', 10, 20); expect(source.getCoverageInRange(requestInterval)) .to.deep.equal([]); @@ -63,8 +63,8 @@ describe('CoverageDataSource', function() { done(); }); - source.rangeChanged({contig: 'chrM', start: 1, stop: 30}); - source.rangeChanged({contig: 'chrM', start: 2, stop: 8}); + source.rangeChanged({contig: '17', start: 1, stop: 30}); + source.rangeChanged({contig: '17', start: 2, stop: 8}); server.respond(); @@ -76,7 +76,7 @@ describe('CoverageDataSource', function() { url: '/coverage' }); var requestCount = 0; - var requestInterval = new ContigInterval('chrM', 10, 20); + var requestInterval = new ContigInterval('17', 10, 20); expect(source.getCoverageInRange(requestInterval)) .to.deep.equal([]); @@ -89,8 +89,8 @@ describe('CoverageDataSource', function() { done(); }); - source.rangeChanged({contig: 'chrM', start: 1, stop: 30}); - source.rangeChanged({contig: 'chrM', start: 2, stop: 8}); + source.rangeChanged({contig: '17', start: 1, stop: 30}); + source.rangeChanged({contig: '17', start: 2, stop: 8}); server.respond(); diff --git a/src/test/sources/ReferenceDataSource-test.js b/src/test/sources/ReferenceDataSource-test.js index 373f4408..3f78a42e 100644 --- a/src/test/sources/ReferenceDataSource-test.js +++ b/src/test/sources/ReferenceDataSource-test.js @@ -4,7 +4,7 @@ import {expect} from 'chai'; import sinon from 'sinon'; - +import _ from 'underscore'; import ReferenceDataSource from '../../main/sources/ReferenceDataSource'; import RemoteFile from '../../main/RemoteFile'; @@ -46,6 +46,7 @@ describe('ReferenceDataSource', function() { it('should fetch contigs', function() { var contigs = source.contigList(); + contigs = _.map(contigs, contig => contig.name); expect(contigs).to.deep.equal(['chrM','22']); }); @@ -68,12 +69,13 @@ describe('ReferenceDataSource', function() { 'chrM:3': null }); var str = source.getRangeAsString(range); + console.log(str); expect(str).to.equal('....'); source.on('newdata', () => { console.log("new data"); obj = source.getRange(range); - console.log(obj); + console.log("range", obj); expect(obj).to.deep.equal({ 'chrM:0': 'N', 'chrM:1': 'G', @@ -87,69 +89,70 @@ describe('ReferenceDataSource', function() { }); source.rangeChanged(range); server.respond(); + done(); }); - // - // it('should fetch nearby base pairs', function(done) { - // - // source.on('newdata', () => { - // expect(source.getRange({contig: 'chrM', start: 0, stop: 14})) - // .to.deep.equal({ - // 'chrM:0': 'N', - // 'chrM:1': 'G', - // 'chrM:2': 'T', - // 'chrM:3': 'T', - // 'chrM:4': 'A', // start of actual request - // 'chrM:5': 'A', - // 'chrM:6': 'T', - // 'chrM:7': 'G', - // 'chrM:8': 'T', - // 'chrM:9': 'A', // end of actual requuest - // 'chrM:10': 'G', - // 'chrM:11': 'C', - // 'chrM:12': 'T', - // 'chrM:13': 'T', - // 'chrM:14': 'A' - // }); - // done(); - // }); - // source.rangeChanged({contig: 'chrM', start: 4, stop: 9}); - // server.respond(); - // }); - // - // it('should add chr', function(done) { - // var range = {contig: '22', start: 0, stop: 3}; - // - // source.on('newdata', () => { - // expect(source.getRange(range)).to.deep.equal({ - // '22:0': 'N', - // '22:1': 'G', - // '22:2': 'T', - // '22:3': 'T' - // }); - // expect(source.getRangeAsString(range)).to.equal('NGTT'); - // done(); - // }); - // source.rangeChanged(range); - // server.respond(); - // }); - // - // it('should only report newly-fetched ranges', function(done) { - // ReferenceDataSource.testBasePairsToFetch(10); - // var initRange = {contig: 'chrM', start: 5, stop: 8}, - // secondRange = {contig: 'chrM', start: 8, stop: 15}; - // source.once('newdata', newRange => { - // expect(newRange.toString()).to.equal('chrM:0-10'); // expanded range - // - // source.once('newdata', newRange => { - // // This expanded range excludes previously-fetched data. - // expect(newRange.toString()).to.equal('chrM:11-20'); - // done(); - // }); - // source.rangeChanged(secondRange); - // server.respond(); - // }); - // source.rangeChanged(initRange); - // server.respond(); - // }); + + it('should fetch nearby base pairs', function(done) { + + source.on('newdata', () => { + expect(source.getRange({contig: 'chrM', start: 0, stop: 14})) + .to.deep.equal({ + 'chrM:0': 'N', + 'chrM:1': 'G', + 'chrM:2': 'T', + 'chrM:3': 'T', + 'chrM:4': 'A', // start of actual request + 'chrM:5': 'A', + 'chrM:6': 'T', + 'chrM:7': 'G', + 'chrM:8': 'T', + 'chrM:9': 'A', // end of actual requuest + 'chrM:10': 'G', + 'chrM:11': 'C', + 'chrM:12': 'T', + 'chrM:13': 'T', + 'chrM:14': 'A' + }); + done(); + }); + source.rangeChanged({contig: 'chrM', start: 4, stop: 9}); + server.respond(); + }); + + it('should add chr', function(done) { + var range = {contig: '22', start: 0, stop: 3}; + + source.on('newdata', () => { + expect(source.getRange(range)).to.deep.equal({ + '22:0': 'N', + '22:1': 'G', + '22:2': 'T', + '22:3': 'T' + }); + expect(source.getRangeAsString(range)).to.equal('NGTT'); + done(); + }); + source.rangeChanged(range); + server.respond(); + }); + + it('should only report newly-fetched ranges', function(done) { + ReferenceDataSource.testBasePairsToFetch(10); + var initRange = {contig: 'chrM', start: 5, stop: 8}, + secondRange = {contig: 'chrM', start: 8, stop: 15}; + source.once('newdata', newRange => { + expect(newRange.toString()).to.equal('chrM:0-10'); // expanded range + + source.once('newdata', newRange => { + // This expanded range excludes previously-fetched data. + expect(newRange.toString()).to.equal('chrM:11-20'); + done(); + }); + source.rangeChanged(secondRange); + server.respond(); + }); + source.rangeChanged(initRange); + server.respond(); + }); }); diff --git a/src/test/viz/CoverageTrack-test.js b/src/test/viz/CoverageTrack-test.js index 8cd016f8..3c4adbbd 100644 --- a/src/test/viz/CoverageTrack-test.js +++ b/src/test/viz/CoverageTrack-test.js @@ -8,6 +8,9 @@ import {expect} from 'chai'; +import sinon from 'sinon'; + +import RemoteFile from '../../main/RemoteFile'; import pileup from '../../main/pileup'; import TwoBit from '../../main/data/TwoBit'; import TwoBitDataSource from '../../main/sources/TwoBitDataSource'; @@ -17,9 +20,24 @@ import {waitFor} from '../async'; describe('CoverageTrack', function() { var testDiv = document.getElementById('testdiv'); - var range = {contig: '17', start: 7500730, stop: 7500790}; + var range = {contig: '17', start: 0, stop: 100}; var p; + var server: any = null, response; + + before(function () { + return new RemoteFile('/test-data/chr17-coverage.json').getAllString().then(data => { + response = data; + server = sinon.fakeServer.create(); + server.respondWith('GET', '/coverage/17?start=1&end=1000&binning=1',[200, { "Content-Type": "application/json" }, response]); + }); + }); + + after(function () { + server.restore(); + }); + + beforeEach(() => { dataCanvas.RecordingContext.recordAll(); // A fixed width container results in predictable x-positions for mismatches. @@ -34,10 +52,10 @@ describe('CoverageTrack', function() { }, { viz: pileup.viz.coverage(), - data: pileup.formats.bam({ + data: pileup.formats.coverage({ url: '/coverage', }), - cssClass: 'test-coverage', + cssClass: 'coverage', name: 'Coverage' } ] @@ -63,10 +81,6 @@ describe('CoverageTrack', function() { return drawnObjectsWith(testDiv, '.coverage', b => b.count); }; - var findMismatchBins = ():Array => { - return drawnObjectsWith(testDiv, '.coverage', b => b.base); - }; - var findCoverageLabels = () => { return drawnObjectsWith(testDiv, '.coverage', l => l.type == 'label'); }; @@ -75,7 +89,6 @@ describe('CoverageTrack', function() { // Check whether the coverage bins are loaded yet return testDiv.querySelector('canvas') && findCoverageBins().length > 1 && - findMismatchBins().length > 0 && findCoverageLabels().length > 1; }; diff --git a/src/test/viz/GenomeTrack-test.js b/src/test/viz/GenomeTrack-test.js index 0af362b7..f68f5002 100644 --- a/src/test/viz/GenomeTrack-test.js +++ b/src/test/viz/GenomeTrack-test.js @@ -54,7 +54,7 @@ describe('GenomeTrack', function() { it('should tolerate non-chr ranges', function() { var p = pileup.create(testDiv, { - range: {contig: '17', start: 7500730, stop: 7500790}, + range: {contig: 'chr17', start: 7500730, stop: 7500790}, tracks: [ { data: referenceSource, @@ -95,7 +95,7 @@ describe('GenomeTrack', function() { it('should zoom from huge zoom out', function() { var p = pileup.create(testDiv, { - range: { contig: '17', start: 0, stop: 114529884 }, + range: { contig: 'chr17', start: 0, stop: 114529884 }, tracks: [{ data: referenceSource, viz: pileup.viz.genome(), @@ -116,7 +116,7 @@ describe('GenomeTrack', function() { return waitFor(referenceTrackLoaded, 2000).then(() => { //in global view we shouldn't see reference track expect(hasReference()).to.be.false; - p.setRange({contig: '17', start: 7500725, stop: 7500775}); + p.setRange({contig: 'chr17', start: 7500725, stop: 7500775}); }).delay(300).then(() => { //after zoom in we should see reference track expect(hasReference()).to.be.true; @@ -127,7 +127,7 @@ describe('GenomeTrack', function() { it('should zoom in and out', function() { var p = pileup.create(testDiv, { - range: {contig: '17', start: 7500725, stop: 7500775}, + range: {contig: 'chr17', start: 7500725, stop: 7500775}, tracks: [ { data: referenceSource, @@ -170,7 +170,7 @@ describe('GenomeTrack', function() { it('should accept user-entered locations', function() { var p = pileup.create(testDiv, { - range: {contig: '17', start: 7500725, stop: 7500775}, + range: {contig: 'chr17', start: 7500725, stop: 7500775}, tracks: [ { data: referenceSource, diff --git a/style/pileup.css b/style/pileup.css index e0925f14..049cb3cc 100644 --- a/style/pileup.css +++ b/style/pileup.css @@ -20,11 +20,15 @@ .track-label { flex: 0 0 100px; /* fixed-width track labels */ text-align: right; + overflow: hidden; + text-overflow: ellipsis; font-size: 0.9em; position: relative; /* make this an offset parent for positioning the label. */ } .track-label > span { padding-right: 5px; + overflow: hidden; + text-overflow: ellipsis; } /* bottom-justify these track labels */ .track.reference .track-label > span, diff --git a/test-data/chrM-coverage.json b/test-data/chr17-coverage.json similarity index 64% rename from test-data/chrM-coverage.json rename to test-data/chr17-coverage.json index caaeab28..36a533f0 100644 --- a/test-data/chrM-coverage.json +++ b/test-data/chr17-coverage.json @@ -1,49 +1,49 @@ [{ - "contig": "chrM", + "contig": "17", "position": 10, "count": 50 }, { - "contig": "chrM", + "contig": "17", "position": 11, "count": 52 }, { - "contig": "chrM", + "contig": "17", "position": 12, "count": 54 }, { - "contig": "chrM", + "contig": "17", "position": 13, "count": 56 }, { - "contig": "chrM", + "contig": "17", "position": 14, "count": 58 }, { - "contig": "chrM", + "contig": "17", "position": 15, "count": 58 }, { - "contig": "chrM", + "contig": "17", "position": 16, "count": 58 }, { - "contig": "chrM", + "contig": "17", "position": 17, "count": 58 }, { - "contig": "chrM", + "contig": "17", "position": 18, "count": 68 }, { - "contig": "chrM", + "contig": "17", "position": 19, "count": 72 }, { - "contig": "chrM", + "contig": "17", "position": 20, "count": 75 }, { - "contig": "chrM", + "contig": "17", "position": 21, "count": 62 }] diff --git a/test-data/reference-chrM-0-1000.json b/test-data/reference-chrM-0-1000.json index 95699648..99d342cf 100644 --- a/test-data/reference-chrM-0-1000.json +++ b/test-data/reference-chrM-0-1000.json @@ -1 +1 @@ -"NGTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAAATATTAAGCAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATTAAAATCCAACTTATATGTGAAAATTCATTGTTAGGACCTAAACTCAATAACGAAAGTAATTCTAGTCATTTATAATACACGACAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAAAACTATTTGCCAGAGAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAACGTTAGGTCAAGGTGTAGCCAATGAAATGGGAAGAAATGGGCTACATTTTCTTATAAAAGAACATTACTATACCCTTTATGAAACTAAAGGACTAAGGAGGATTTAGTAGTAAATTAAGAATAGAGAGCTTAATTGAATTGAGCAATGAAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCAT" +"NGTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGATAATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTAAACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCTTAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAAATATTAAGCAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATTAAAATCCAACTTATATGTGAAAATTCATTGTTAGGACCTAAACTCAATAACGAAAGTAATTCTAGTCATTTATAATACACGACAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAAAACTATTTGCCAGAGAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAACGTTAGGTCAAGGTGTAGCCAATGAAATGGGAAGAAATGGGCTACATTTTCTTATAAAAGAACATTACTATACCCTTTATGAAACTAAAGGACTAAGGAGGATTTAGTAGTAAATTAAGAATAGAGAGCTTAATTGAATTGAGCAATGAAGTACGCACACACCGCCCGTCACCCTCCTCAAATTAAATTAAACTTAACATAATTAATTTCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCATCTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTCTGAACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATAAATCAAAACATTTATCCTACTAAAAGTATTGGAGAAAGAAATTCGTACATCTAGGAGCTATAGAACTAGTACCGCAAGGGAAAGATGAAAGACTAATTAAAAGTAAGAACAAGCAAAGATTAAACCTTGTACCTTTTGCATAATGAACTAACTAGAAAACTTCTAACTAAAAGAATTACAGCTAGAAACCCCGAAACCAAACGAGCTACCTAAAAACAATTTTATGAATCAACTCGTCTATGTGGCAAAATAGTGAGAAGATTTTTAGGTAGAGGTGAAAAGCCTAACGAGCTTGGTGATAGCTGGTTACCCAAAAAATGAATTTAAGTTCAATTTTAAACTTGCTAAAAAAACAACAAAATCAAAAAGTAAGTTTAGATTATAGCCAAAAGAGGGACAGCTCTTCTGGAACGGAAAAAACCTTTAATAGTGAATAATTAACAAAACAGCTTTTAACCATTGTAGGCCTAAAAGCAGCCACCAATAAAGAAAGCGTTCAAGCTCAACATAAAATTTCAATTAATTCCATAATTTACACCAACTTCCTAAACTTAAAATTGGGTTAATCTATAACTTTATAGATGCAACACTGTTAGTATGAGTAACAAGAATTCCAATTCTCCAGGCATACGCGTATAACAACTCGGATAACCATTGTTAGTTAATCAGACTATAGGCAATAATCACACTATAAATAATCCACCTATAACTTCTCTGTTAACCCAACACCGGAATGCCTAAAGGAAAGATCCAAAAAGATAAAAGGAACTCGGCAAACAAGAACCCCGCCTGTTTACCAAAAACATCACCTCTAGCATTACAAGTATTAGAGGCACTGCCTGCCCAGTGACTAAAGTTTAACGGCCGCGGTATCCTGACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAATTAGGGACTAGCATGAACGGCTAAACGAGGGTCCAACTGTCTCTTATCTTTAATCAGTGAAATTGACCTTTCAGTGAAGAGGCTGAAATATAATAATAAGACGAGAAGACCCTATGGAGCTTAAATTATATAACTTATCTATTTAATTTATTAAACCTAATGGCCCAAAAACTATAGTATAAGTTTGAAATTTCGGTTGGGGTGACCTCGGAGAATAAAAAATCCTCCGAATGATTATAACCTAGACTTACAAGTCAAAGTAAAATCAACATATCTTATTGACCCAGATATATTTTGATCAACGGACCAAGTTACCCTAGGGATAACAGCGCAATCCTATTTAAGAGTTCATATCGACAATTAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCAATGGTGTAGAAGCTATTAATGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGCAATCCAGGTCGGTTTCTATCTATTTACGATTTCTCCCAGTACGAAAGGACAAGAGAAATAGAGCCACCTTACAAATAAGCGCTCTCAACTTAATTTATGAATAAAATCTAAATAAAATATATACGTACACCCTCTAACCTAGAGAAGGTTATTAGGGTGGCAGAGCCAGGAAATTGCGTAAGACTTAAAACCTTGTTCCCAGAGGTTCAAATCCTCTCCCTAATAGTGTTCTTTATTAATATCCTAACACTCCTCGTCCCCATTCTAATCGCCATAGCCTTCCTAACATTAGTAGAACGCAAAATCTTAGGGTACATACAACTACGAAAAGGCCCTAACATTGTTGGTCCATACGGCATTTTACAACCATTTGCAGACGCCATAAAATTATTTATAAAAGAACCAATACGCCCTTTAACAACCTCTATATCCTTATTTATTATTGCACCTACCCTATCACTCACACTAGCATTAAGTCTATGAGTTCCCCTACCAATACCACACCCATTAATTAATTTAAACCTAGGGATTTTATTTATTTTAGCAACATCTAGCCTATCAGTTTACTCCATTCTATGATCAGGATGAGCCTCAAACTCCAAATACTCACTATTCGGAGCTTTACGAGCCGTAGCCCAAACAATTTCATATGAAGTAACCATAGCTATTATCCTTTTATCAGTTCTATTAATAAATGGATCCTACTCTCTACAAACACTTATTACAACCCAAGAACACATATGATTACTTCTGCCAGCCTGACCCATAGCCATAATATGATTTATCTCAACCCTAGCAGAAACAAACCGGGCCCCCTTCGACCTGACAGAAGGAGAATCAGAATTAGTATCAGGGTTTAACGTAGAATACGCAGCCGGCCCATTCGCGTTATTCTTTATAGCAGAGTACACTAACATTATTCTAATAAACGCCCTAACAACTATTATCTTCCTAGGACCCCTATACTATATCAATTTACCAGAACTCTACTCAACTAACTTCATAATAGAAGCTCTACTACTATCATCAACATTCCTATGGATCCGAGCATCTTATCCACGCTTCCGTTACGATCAACTTATACATCTTCTATGAAAAAACTTTCTACCCCTAACACTAGCATTATGTATGTGACATATTTCTTTACCAATTTTTACAGCGGGAGTACCACCATACATATAGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATTATAGAGGTTCAAGCCCTCTTATTTCTAGGACAATAGGAATTGAACCTACACTTAAGAATTCAAAATTCTCCGTGCTACCTAAACACCTTATCCTAATAGTAAGGTCAGCTAATTAAGCTATCGGGCCCATACCCCGAAAACGTTGGTTTAAATCCTTCCCGTACTAATAAATCCTATCACCCTTGCCATCATCTACTTCACAATCTTCTTAGGTCCTGTAATCACAATATCCAGCACCAACCTAATACTAATATGAGTAGGCCTGGAATTCAGCCTACTAGCAATTATCCCCATACTAATCAACAAAAAAAACCCACGATCAACTGAAGCAGCAACAAAATACTTCGTCACACAAGCAACAGCCTCAATAATTATCCTCCTGGCCATCGTACTCAACTATAAACAACTAGGAACATGAATATTTCAACAACAAACAAACGGTCTTATCCTTAACATAACATTAATAGCCCTATCCATAAAACTAGGCCTCGCCCCATTCCACTTCTGATTACCAGAAGTAACTCAAGGGATCCCACTGCACATAGGACTTATTCTTCTTACATGACAAAAAATTGCTCCCCTATCAATTTTAATTCAAATTTACCCGCTACTCAACTCTACTATCATTTTAATACTAGCAATTACTTCTATTTTCATAGGGGCATGAGGAGGACTTAACCAAACACAAATACGAAAAATTATAGCCTATTCATCAATTGCCCACATAGGATGAATATTAGCAATTCTTCCTTACAACCCATCCCTCACTCTACTCAACCTCATAATCTATATTATTCTTACAGCCCCTATATTCATAGCACTTATACTAAATAACTCTATAACCATCAACTCAATCTCACTTCTATGAAATAAAACTCCAGCAATACTAACTATAATCTCACTGATATTACTATCCCTAGGAGGCCTTCCACCACTAACAGGATTCTTACCAAAATGAATTATCATCACAGAACTTATAAAAAACAACTGTCTAATTATAGCAACACTCATAGCAATAATAGCTCTACTAAACCTATTCTTTTATACTCGCCTAATTTATTCCACTTCACTAACAATATTTCCAACCAACAATAACTCAAAAATAATAACTCACCAAACAAAAACTAAACCCAACCTAATATTTTCCACCCTAGCTATCATAAGCACAATAACCCTACCCCTAGCCCCCCAACTAATTACCTAGAAGTTTAGGATATACTAGTCCGCGAGCCTTCAAAGCCCTAAGAAAACACACAAGTTTAACTTCTGATAAGGACTGTAAGACTTCATCCTACATCTATTGAATGCAAATCAATTGCTTTAATTAAGCTAAGACCTCAACTAGATTGGCAGGAATTAAACCTACGAAAATTTAGTTAACAGCTAAATACCCTATTACTGGCTTCAATCTACTTCTACCGCCGAAAAAAAAAAATGGCGGTAGAAGTCTTAGTAGAGATTTCTCTACACCTTCGAATTTGCAATTCGACATGAATATCACCTTAAGACCTCTGGTAAAAAGAGGATTTAAACCTCTGTGTTTAGATTTACAGTCTAATGCTTACTCAGCCATTTTACCTATGTTCATTAATCGTTGATTATTCTCAACCAATCACAAAGATATCGGAACCCTCTATCTACTATTCGGAGCCTGAGCGGGAATAGTGGGTACTGCACTAAGTATTTTAATTCGAGCAGAATTAGGTCAACCAGGTGCACTTTTAGGAGATGACCAAATTTACAATGTTATCGTAACTGCCCATGCTTTTGTTATAATTTTCTTCATAGTAATACCAATAATAATTGGAGGCTTTGGAAACTGACTTGTCCCACTAATAATCGGAGCCCCAGATATAGCATTCCCACGAATAAATAATATAAGTTTTTGACTCCTACCACCATCATTTCTCCTTCTCCTAGCATCATCAATAGTAGAAGCAGGAGCAGGAACAGGATGAACAGTCTACCCACCTCTAGCCGGAAATCTAGCCCATGCAGGAGCATCAGTAGACCTAACAATTTTCTCCCTTCATTTAGCTGGAGTGTCATCTATTTTAGGTGCAATTAATTTTATTACCACTATTATCAACATGAAACCCCCAGCCATAACACAGTATCAAACTCCACTATTTGTCTGATCCGTACTTATTACAGCCGTACTGCTCCTATTATCACTACCAGTGCTAGCCGCAGGCATTACTATACTACTAACAGACCGCAACCTAAACACAACTTTCTTTGATCCCGCTGGAGGAGGGGACCCAATTCTCTACCAGCATCTGTTCTGATTCTTTGGGCACCCAGAAGTTTATATTCTTATCCTCCCAGGATTTGGAATTATTTCACATGTAGTTACTTACTACTCCGGAAAAAAAGAACCTTTCGGCTATATAGGAATAGTATGAGCAATAATGTCTATTGGCTTTCTAGGCTTTATTGTATGAGCCCACCACATATTCACAGTAGGATTAGATGTAGACACACGAGCTTACTTTACATCAGCCACTATAATTATCGCAATTCCTACCGGTGTCAAAGTATTTAGCTGACTTGCAACCCTACACGGAGGTAATATTAAATGATCTCCAGCTATACTATGAGCCTTAGGCTTTATTTTCTTATTTACAGTTGGTGGTCTAACCGGAATTGTTTTATCCAACTCATCCCTTGACATCGTGCTTCACGATACATACTATGTAGTAGCCCATTTCCACTATGTTCTATCAATGGGAGCAGTGTTTGCTATCATAGCAGGATTTGTTCACTGATTCCCATTATTTTCAGGCTTCACCCTAGATGACACATGAGCAAAAGCCCACTTCGCCATCATATTCGTAGGAGTAAACATAACATTCTTCCCTCAACATTTCCTGGGCCTTTCAGGAATACCACGACGCTACTCAGACTACCCAGATGCTTACACCACATGAAACACTGTCTCTTCTATAGGATCATTTATTTCACTAACAGCTGTTCTCATCATGATCTTTATAATTTGAGAGGCCTTTGCTTCAAAACGAGAAGTAATATCAGTATCGTATGCTTCAACAAATTTAGAATGACTTCATGGCTGCCCTCCACCATATCACACATTCGAGGAACCAACCTATGTAAAAGTAAAATAAGAAAGGAAGGAATCGAACCCCCTAAAATTGGTTTCAAGCCAATCTCATATCCTATATGTCTTTCTCAATAAGATATTAGTAAAATCAATTACATAACTTTGTCAAAGTTAAATTATAGATCAATAATCTATATATCTTATATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTAATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTATATCATCTCGCTAATATTAACAACAAAACTAACACATACAAGCACAATAGATGCACAAGAAGTTGAAACCATTTGAACTATTCTACCAGCTGTAATCCTTATCATAATTGCTCTCCCCTCTCTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATAGGGCACCAATGATACTGAAGCTACGAATATACTGACTATGAAGACCTATGCTTTGATTCATATATAATCCCAACAAACGACCTAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAACCGAGTCGTTCTGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCCAGGCCGACTAAATCAAGCAACAGTAACATCAAACCGACCAGGGTTATTCTATGGCCAATGCTCTGAAATTTGTGGATCTAACCATAGCTTTATGCCCATTGTCCTAGAAATGGTTCCACTAAAATATTTCGAAAACTGATCTGCTTCAATAATTTAATTTCACTATGAAGCTAAGAGCGTTAACCTTTTAAGTTAAAGTTAGAGACCTTAAAATCTCCATAGTGATATGCCACAACTAGATACATCAACATGATTTATCACAATTATCTCATCAATAATTACCCTATTTATCTTATTTCAACTAAAAGTCTCATCACAAACATTCCCACTGGCACCTTCACCAAAATCACTAACAACCATAAAAGTAAAAACCCCTTGAGAATTAAAATGAACGAAAATCTATTTGCCTCATTCATTACCCCAACAATAATAGGATTCCCAATCGTTGTAGCCATCATTATATTTCCTTCAATCCTATTCCCATCCTCAAAACGCCTAATCAACAACCGTCTCCATTCTTTCCAACACTGACTAGTTAAACTTATTATCAAACAAATAATGCTAATCCACACACCAAAAGGACGAACATGAACCCTAATAATTGTTTCCCTAATCATATTTATTGGATCAACAAATCTCCTAGGCCTTTTACCACATACATTTACACCTACTACCCAACTATCCATAAATCTAAGTATAGCCATTCCACTATGAGCTGGAGCCGTAATTACAGGCTTCCGACACAAACTAAAAAGCTCACTTGCCCACTTCCTTCCACAAGGAACTCCAATTTCACTAATTCCAATACTTATTATTATTGAAACAATTAGCCTATTTATTCAACCAATGGCATTAGCAGTCCGGCTTACAGCTAACATTACTGCAGGACACTTATTAATACACCTAATCGGAGGAGCTACTCTAGTATTAATAAATATTAGCCCACCAACAGCTACCATTACATTTATTATTTTACTTCTACTCACAATTCTAGAATTTGCAGTAGCATTAATTCAAGCCTACGTATTCACCCTCCTAGTAAGCCTATATCTACATGATAATACATAATGACCCACCAAACTCATGCATATCACATAGTTAATCCAAGTCCATGACCATTAACTGGAGCCTTTTCAGCCCTCCTTCTAACATCAGGTCTAGTAATATGATTTCACTATAATTCAATTACACTATTAACCCTTGGCCTACTCACCAATATCCTCACAATATATCAATGATGACGAGACGTAATTCGTGAAGGAACCTACCAAGGCCACCACACTCCTATTGTACAAAAAGGACTACGATATGGTATAATTCTATTCATCGTCTCGGAAGTATTTTTCTTTGCAGGATTCTTCTGAGCGTTCTATCATTCTAGCCTCGTACCAACACATGATCTAGGAGGCTGCTGACCTCCAACAGGAATTTCACCACTTAACCCTCTAGAAGTCCCACTACTTAATACTTCAGTACTTCTAGCATCAGGTGTTTCAATTACATGAGCTCATCATAGCCTTATAGAAGGTAAACGAAACCACATAAATCAAGCCCTACTAATTACCATTATACTAGGACTTTACTTCACCATCCTCCAAGCTTCAGAATACTTTGAAACATCATTCTCCATTTCAGATGGTATCTATGGTTCTACATTCTTCATGGCTACTGGATTCCATGGACTCCATGTAATTATTGGATCAACATTCCTTATTGTTTGCCTACTACGACAACTAAAATTTCACTTCACATCAAAACATCACTTCGGATTTGAAGCCGCAGCATGATACTGACATTTTGTAGACGTAGTCTGACTTTTCCTATACGTCTCCATTTATTGATGAGGATCTTACTCCCTTAGTATAATTAATATAACTGACTTCCAATTAGTAGATTCTGAATAAACCCAGAAGAGAGTAATTAACCTGTACACTGTTATCTTCATTAATATTTTATTATCCCTAACGCTAATTCTAGTTGCATTCTGACTCCCCCAAATAAATCTGTACTCAGAAAAAGCAAATCCATATGAATGCGGATTCGACCCTACAAGCTCTGCACGTCTACCATTCTCAATAAAATTTTTCTTGGTAGCAATTACATTTCTATTATTTGACCTAGAAATTGCTCTTCTACTTCCACTACCATGAGCAATTCAAACAATTAAAACCTCTACTATAATAATTATAGCCTTTATTCTAGTCACAATTCTATCTCTAGGCCTAGCATATGAATGAACACAAAAAGGATTAGAATGAACAGAGTAAATGGTAATTAGTTTAAAAAAAATTAATGATTTCGACTCATTAGATTATGATGATGTTCATAATTACCAATATGCCATCTACCTTCTTCAACCTCACCATAGCCTTCTCACTATCACTTCTAGGGACACTTATATTTCGCTCTCACCTAATATCCACATTACTATGCCTGGAAGGCATAGTATTATCCTTATTTA" From 094d2dc59700599d0db470fb934203fa11ee405a Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 1 Nov 2016 23:36:25 -0700 Subject: [PATCH 120/136] completed coverage tracks and binning --- src/main/RemoteRequest.js | 20 ++-- src/main/ResolutionCache.js | 32 +++-- src/main/data/FeatureEndpoint.js | 2 +- src/main/data/GeneEndpoint.js | 7 +- src/main/data/GenotypeEndpoint.js | 6 +- src/main/data/Sequence.js | 5 +- src/main/data/VariantEndpoint.js | 2 +- src/main/pileup.js | 1 - src/main/sources/CoverageDataSource.js | 53 ++++++--- src/main/sources/FeatureDataSource.js | 5 +- src/main/sources/GeneDataSource.js | 2 +- src/main/sources/GenotypeDataSource.js | 2 +- src/main/sources/ReferenceDataSource.js | 2 +- src/main/sources/VariantDataSource.js | 7 +- src/main/viz/CoverageTrack.js | 116 +++++++++++++------ src/main/viz/PileupTrack.js | 21 +--- src/main/viz/TiledCanvas.js | 3 +- src/main/viz/pileuputils.js | 17 +++ src/test/RemoteRequest-test.js | 2 +- src/test/sources/ReferenceDataSource-test.js | 1 - style/pileup.css | 6 +- test-data/chr17-coverage.json | 42 ++++--- 22 files changed, 226 insertions(+), 128 deletions(-) diff --git a/src/main/RemoteRequest.js b/src/main/RemoteRequest.js index d5a1fcf2..f362c670 100644 --- a/src/main/RemoteRequest.js +++ b/src/main/RemoteRequest.js @@ -10,6 +10,7 @@ import Q from 'q'; import ContigInterval from './ContigInterval'; var BASE_PAIRS_PER_FETCH = 1000; +var MONSTER_REQUEST = 5000000; class RemoteRequest { url: string; @@ -43,7 +44,7 @@ class RemoteRequest { var length = range.stop() - range.start(); if (length <= 0) { return Q.reject(`Requested <0 interval (${length}) from ${this.url}`); - } else if (length > 5000000) { + } else if (length > MONSTER_REQUEST) { throw `Monster request: Won't fetch ${length} sized ranges from ${this.url}`; } // get endpoint @@ -61,9 +62,9 @@ class RemoteRequest { xhr.responseType = 'json'; xhr.setRequestHeader('Content-Type', 'application/json'); - return this.promiseXHR(xhr).then(json => { - // extract response from promise - return json[0]; + return this.promiseXHR(xhr).then(e => { + // send back response and status + return e[0]; }); } @@ -76,14 +77,14 @@ class RemoteRequest { // Wrapper to convert XHRs to Promises. // The promised values are the response (e.g. an ArrayBuffer) and the Event. - promiseXHR(xhr: XMLHttpRequest): Q.Promise<[any, Event]> { + promiseXHR(xhr: XMLHttpRequest): Q.Promise<[any]> { var url = this.url; var deferred = Q.defer(); xhr.addEventListener('load', function(e) { if (this.status >= 400) { deferred.reject(`Request for ${url} failed with status: ${this.status} ${this.statusText}`); } else { - deferred.resolve([this.response, e]); + deferred.resolve([this]); } }); xhr.addEventListener('error', function(e) { @@ -95,4 +96,9 @@ class RemoteRequest { } } -module.exports = RemoteRequest; +module.exports = { + RemoteRequest, + MONSTER_REQUEST: MONSTER_REQUEST +}; + +//module.exports = RemoteRequest; diff --git a/src/main/ResolutionCache.js b/src/main/ResolutionCache.js index 37d93bf9..d9ee0626 100644 --- a/src/main/ResolutionCache.js +++ b/src/main/ResolutionCache.js @@ -11,11 +11,16 @@ import _ from 'underscore'; import Interval from './Interval'; import ContigInterval from './ContigInterval'; +type ResolutionObject = { + resolution: number; + object: T; +} + class ResolutionCache { coveredRanges: ResolutionCacheKey[]; - cache: {[key: string]: T}; + cache: {[key: string]: ResolutionObject}; // used to filter out elements in the cache based on resolution. - filterFunction: Function; // should take form (range: ContigInterval, T, resolution: ?number) => boolean; + filterFunction: Function; // should take form (range: ContigInterval, T) => boolean; keyFunction: Function; // should take form (d: T) => string; constructor(filterFunction: Function, keyFunction: Function) { @@ -28,11 +33,13 @@ class ResolutionCache { // gets data from cache at the Resolution defined by the interval get(range: ContigInterval, resolution: ?number): T[] { if (!range) return []; - var res = _.filter(this.cache, d => this.filterFunction(range, d, resolution)); - - // if range is not fully covered, give warning but still return available data - if (this.coversRange(range, resolution)) { - console.warn("Warning: Resolution Cache does not fully cover region. Returning available data..."); + var res = {}; + if (!resolution) { + res = _.map(_.filter(this.cache, d => this.filterFunction(range, d.object)), + obj => obj.object); + } else { + res = _.map(_.filter(this.cache, d => this.filterFunction(range, d.object) && d.resolution == resolution), + obj => obj.object); } return res; @@ -48,10 +55,17 @@ class ResolutionCache { } // puts data in cache - put(value: T) { + put(value: T, resolution: ?number) { + if (!resolution) { + resolution = 1; + } + var resObject = { + resolution: resolution, + object: value + }; var key = this.keyFunction(value); if (!this.cache[key]) { - this.cache[key] = value; + this.cache[key] = resObject; } } diff --git a/src/main/data/FeatureEndpoint.js b/src/main/data/FeatureEndpoint.js index d0de28f3..321953c7 100644 --- a/src/main/data/FeatureEndpoint.js +++ b/src/main/data/FeatureEndpoint.js @@ -7,7 +7,7 @@ import Q from 'q'; import ContigInterval from '../ContigInterval'; -import type RemoteRequest from '../RemoteRequest'; +import type {RemoteRequest} from '../RemoteRequest'; export type Feature = { id: string; diff --git a/src/main/data/GeneEndpoint.js b/src/main/data/GeneEndpoint.js index a63f954a..b1ab5f68 100644 --- a/src/main/data/GeneEndpoint.js +++ b/src/main/data/GeneEndpoint.js @@ -7,7 +7,7 @@ import Q from 'q'; import type {Gene} from '../sources/BigBedDataSource'; -import type RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; import Interval from '../Interval'; import ContigInterval from '../../main/ContigInterval'; @@ -49,8 +49,9 @@ class GeneEndpoint { } getGenesInRange(range: ContigInterval): Q.Promise { - return this.remoteRequest.get(range).then(object => { - var d = extractGenes(object); + return this.remoteRequest.get(range).then(e => { + var genes = e.response; + var d = extractGenes(genes); return d; }); } diff --git a/src/main/data/GenotypeEndpoint.js b/src/main/data/GenotypeEndpoint.js index d5c04431..f29fe048 100644 --- a/src/main/data/GenotypeEndpoint.js +++ b/src/main/data/GenotypeEndpoint.js @@ -7,7 +7,7 @@ import ContigInterval from '../ContigInterval'; import Q from 'q'; -import type RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; import type {Variant} from './vcf'; export type Genotype = { @@ -23,8 +23,8 @@ class GenotypeEndpoint { } getFeaturesInRange(range: ContigInterval): Q.Promise { - return this.remoteRequest.get(range).then(object => { - return object; + return this.remoteRequest.get(range).then(e => { + return e.response; }); } } diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index c126bf3c..1edcc0c5 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -7,7 +7,7 @@ import Q from 'q'; import ContigInterval from '../ContigInterval'; -import type RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; export type SequenceRecord = { name: string; @@ -44,7 +44,8 @@ class Sequence { if (start > stop) { throw `Requested a range with start > stop (${start}, ${stop})`; } - return this.remoteRequest.get(range).then(sequence => { + return this.remoteRequest.get(range).then(e => { + var sequence = e.response; var d = sequence.substring(start, (stop-start + 1)); return d; }); diff --git a/src/main/data/VariantEndpoint.js b/src/main/data/VariantEndpoint.js index cf6447c0..1222c817 100644 --- a/src/main/data/VariantEndpoint.js +++ b/src/main/data/VariantEndpoint.js @@ -7,7 +7,7 @@ import ContigInterval from '../ContigInterval'; import Q from 'q'; -import type RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; import type {Variant} from './vcf'; class VariantEndpoint { diff --git a/src/main/pileup.js b/src/main/pileup.js index 89c20677..3b8d55b0 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -16,7 +16,6 @@ import ReferenceDataSource from './sources/ReferenceDataSource'; import BigBedDataSource from './sources/BigBedDataSource'; import VcfDataSource from './sources/VcfDataSource'; import VariantDataSource from './sources/VariantDataSource'; -import GeneDataSource from './sources/GeneDataSource'; import GenotypeDataSource from './sources/GenotypeDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; diff --git a/src/main/sources/CoverageDataSource.js b/src/main/sources/CoverageDataSource.js index 4869fa96..e2f00fc7 100644 --- a/src/main/sources/CoverageDataSource.js +++ b/src/main/sources/CoverageDataSource.js @@ -15,7 +15,7 @@ import _ from 'underscore'; import {Events} from 'backbone'; import {ResolutionCache} from '../ResolutionCache'; import ContigInterval from '../ContigInterval'; -import RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; export type CoverageDataSource = { maxCoverage: (range: ContigInterval) => number; @@ -30,24 +30,29 @@ var BASE_PAIRS_PER_FETCH = 1000; export type PositionCount = { contig: string; - position: number; + start: number; + end: number; count: number; } function keyFunction(p: PositionCount): string { - return `${p.contig}:${p.position}`; + return `${p.contig}:${p.start}-${p.end}`; } -function filterFunction(range: ContigInterval, p: PositionCount, resolution: ?number): boolean { - // if resolution is specified, select results based on resolution and position start site - if (resolution) return (range.chrContainsLocus(p.contig, p.position) && p.position % resolution == 0); - else return range.chrContainsLocus(p.contig, p.position); +function filterFunction(range: ContigInterval, p: PositionCount): boolean { + return range.chrContainsLocus(p.contig, p.start); } function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource { var cache: ResolutionCache = new ResolutionCache(filterFunction, keyFunction); + function notifyFailure(message: string) { + o.trigger('networkfailure', message); + o.trigger('networkdone'); + console.warn(message); + } + function maxCoverage(range: ContigInterval, resolution: ?number): number { var positions: number[] = cache.get(range, resolution).map(r => r.count); var maxCoverage = Math.max.apply(Math, positions); @@ -64,18 +69,32 @@ function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource } // modify endpoint to calculate coverage using binning - var basePairsPerBin = ResolutionCache.getResolution(interval.interval); - var endpointModifier = `binning=${basePairsPerBin}`; + var resolution = ResolutionCache.getResolution(interval.interval); + var endpointModifier = `binning=${resolution}`; // Cover the range immediately to prevent duplicate fetches. cache.coverRange(interval); - return remoteSource.getFeaturesInRange(interval, endpointModifier).then(positions => { - positions.forEach(p => cache.put({ - "contig": range.contig, - "position": p.position, - "count": p.count - })); - o.trigger('newdata', interval); + var numRequests = 1; + o.trigger('networkprogress', {numRequests}); + return remoteSource.getFeaturesInRange(interval, endpointModifier).then(json => { + var response = json.response; + if (json.status >= 400) { + notifyFailure(json.status + ' ' + json.statusText + ' ' + JSON.stringify(response)); + } else { + if (response.errorCode) { + notifyFailure('Error from CoverageDataSource: ' + JSON.stringify(response)); + } else { + // add new data to cache + response.forEach(p => cache.put({ + "contig": range.contig, + "start": p.start, + "end": p.end, + "count": p.count + }, resolution)); + o.trigger('newdata', interval); + } + } + o.trigger('networkdone'); }); } @@ -83,7 +102,7 @@ function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource resolution: ?number): PositionCount[] { if (!range) return []; var data = cache.get(range, resolution); - var sorted = data.sort((a, b) => a.position - b.position); + var sorted = data.sort((a, b) => a.start - b.start); return sorted; } diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index b84ea697..91617513 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -20,7 +20,7 @@ import _ from 'underscore'; import {Events} from 'backbone'; import ContigInterval from '../ContigInterval'; -import RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; import FeatureEndpoint from '../data/FeatureEndpoint'; import type {Feature} from '../data/FeatureEndpoint'; @@ -78,7 +78,8 @@ function createFromFeatureUrl(remoteSource: FeatureEndpoint): FeatureDataSource // "Cover" the range immediately to prevent duplicate fetches. coveredRanges.push(interval); coveredRanges = ContigInterval.coalesce(coveredRanges); - return remoteSource.getFeaturesInRange(interval).then(features => { + return remoteSource.getFeaturesInRange(interval).then(e => { + var features = e.response; features.forEach(feature => addFeature(feature)); o.trigger('newdata', interval); }); diff --git a/src/main/sources/GeneDataSource.js b/src/main/sources/GeneDataSource.js index 1a027bdd..a0795167 100644 --- a/src/main/sources/GeneDataSource.js +++ b/src/main/sources/GeneDataSource.js @@ -10,7 +10,7 @@ import {Events} from 'backbone'; import ContigInterval from '../ContigInterval'; import Interval from '../Interval'; import type { BigBedSource, Gene } from './BigBedDataSource'; -import RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; import GeneEndpoint from '../data/GeneEndpoint'; var BASE_PAIRS_PER_FETCH = 5000; diff --git a/src/main/sources/GenotypeDataSource.js b/src/main/sources/GenotypeDataSource.js index c32274b3..5d581fc2 100644 --- a/src/main/sources/GenotypeDataSource.js +++ b/src/main/sources/GenotypeDataSource.js @@ -22,7 +22,7 @@ import _ from 'underscore'; import {Events} from 'backbone'; import ContigInterval from '../ContigInterval'; -import RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; import GenotypeEndpoint from '../data/GenotypeEndpoint'; export type GenotypeDataSource = { diff --git a/src/main/sources/ReferenceDataSource.js b/src/main/sources/ReferenceDataSource.js index ebea74b9..ff63d954 100644 --- a/src/main/sources/ReferenceDataSource.js +++ b/src/main/sources/ReferenceDataSource.js @@ -24,7 +24,7 @@ import Sequence from '../data/Sequence'; import type {SequenceRecord} from '../data/Sequence'; import SequenceStore from '../SequenceStore'; import type {TwoBitSource} from './TwoBitDataSource'; -import RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; import utils from '../utils'; diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index d7d13649..ed9a4c66 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -23,7 +23,7 @@ import {Events} from 'backbone'; import ContigInterval from '../ContigInterval'; import type {VcfDataSource} from './VcfDataSource'; -import RemoteRequest from '../RemoteRequest'; +import {RemoteRequest} from '../RemoteRequest'; import VariantEndpoint from '../data/VariantEndpoint'; var BASE_PAIRS_PER_FETCH = 1000; @@ -67,8 +67,9 @@ function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { // "Cover" the range immediately to prevent duplicate fetches. coveredRanges.push(interval); coveredRanges = ContigInterval.coalesce(coveredRanges); - return remoteSource.getFeaturesInRange(interval).then(object => { - object.forEach(variant => addVariant(variant)); + return remoteSource.getFeaturesInRange(interval).then(e => { + var variants = e.response; + variants.forEach(variant => addVariant(variant)); o.trigger('newdata', interval); }); } diff --git a/src/main/viz/CoverageTrack.js b/src/main/viz/CoverageTrack.js index 59e949c6..8fbe0a1a 100644 --- a/src/main/viz/CoverageTrack.js +++ b/src/main/viz/CoverageTrack.js @@ -5,11 +5,12 @@ 'use strict'; import type Interval from '../Interval'; -import GA4GHDataSource from '../sources/GA4GHDataSource'; import type {TwoBitSource} from '../sources/TwoBitDataSource'; import type {DataCanvasRenderingContext2D} from 'data-canvas'; import type {Scale} from './d3utils'; import type {CoverageDataSource} from '../sources/CoverageDataSource'; +import type {VizProps} from '../VisualizationWrapper'; +import RemoteRequest from '../RemoteRequest'; import type {PositionCount} from '../sources/CoverageDataSource'; import React from 'react'; @@ -22,17 +23,8 @@ import canvasUtils from './canvas-utils'; import style from '../style'; import ContigInterval from '../ContigInterval'; import TiledCanvas from './TiledCanvas'; - - -type Props = { - width: number; - height: number; - range: GenomeRange; - source: CoverageDataSource; - options: { - vafColorThreshold: number - } -}; +import type {State, NetworkStatus} from './pileuputils'; +import {formatStatus} from './pileuputils'; class CoverageTiledCanvas extends TiledCanvas { @@ -42,7 +34,6 @@ class CoverageTiledCanvas extends TiledCanvas { constructor(source: CoverageDataSource, height: number, options: Object) { super(); - this.source = source; this.height = Math.max(1, height); this.options = options; @@ -71,12 +62,18 @@ class CoverageTiledCanvas extends TiledCanvas { render(ctx: DataCanvasRenderingContext2D, xScale: (x: number)=>number, range: ContigInterval, + originalRange: ?ContigInterval, resolution: ?number) { var relaxedRange = new ContigInterval( range.contig, Math.max(1, range.start() - 1), range.stop() + 1); var bins = this.source.getCoverageInRange(relaxedRange, resolution); - var yScale = this.yScaleForRef(range, resolution); + // if original range is not set, use tiled range which is a subset of originalRange + if (!originalRange) { + originalRange = range; + } + + var yScale = this.yScaleForRef(originalRange, resolution); renderBars(ctx, xScale, yScale, relaxedRange, bins, resolution, this.options); } } @@ -92,58 +89,98 @@ function renderBars(ctx: DataCanvasRenderingContext2D, options: Object) { if (_.isEmpty(bins)) return; + // make sure bins are sorted by position + bins = _.sortBy(bins, x => x.start); + var barWidth = xScale(1) - xScale(0); var showPadding = (barWidth > style.COVERAGE_MIN_BAR_WIDTH_FOR_GAP); var padding = showPadding ? 1 : 0; - var binPos = function(pos: number, count: number) { + var binPos = function(ps: PositionCount) { // Round to integer coordinates for crisp lines, without aliasing. - var barX1 = Math.round(xScale(1 + pos)), - barX2 = Math.round(xScale(1 + resolution + pos)) - padding, - barY = Math.round(yScale(count)); + var barX1 = Math.round(xScale(ps.start)), + barX2 = Math.max(barX1 + 2, Math.round(xScale(ps.end)) - padding), // make sure bar is >= 1px + barY = Math.round(yScale(ps.count)); return {barX1, barX2, barY}; }; var vBasePosY = yScale(0); // the very bottom of the canvas var start = range.start(), stop = range.stop(); - var first = bins.filter(bin => bin.position == start); - // find first bin in dataset and move to that position. - let {barX1} = binPos(start, (!_.isEmpty(first)) ? first[0].count : 0); + + // go to the first bin in dataset (specified by the smallest start position) ctx.fillStyle = style.COVERAGE_BIN_COLOR; ctx.beginPath(); - ctx.moveTo(barX1, vBasePosY); bins.forEach(bin => { ctx.pushObject(bin); - let {barX1, barX2, barY} = binPos(bin.position, bin.count); - ctx.lineTo(barX1, barY); - ctx.lineTo(barX2, barY); - if (showPadding) { - ctx.lineTo(barX2, vBasePosY); - ctx.lineTo(barX2 + 1, vBasePosY); - } + let {barX1, barX2, barY} = binPos(bin); + ctx.moveTo(barX1, vBasePosY); // start at bottom left of bar + ctx.lineTo(barX1, barY); // left edge of bar + ctx.lineTo(barX2, barY); // top of bar + ctx.lineTo(barX2, vBasePosY); // right edge of the right bar. ctx.popObject(); }); - let {barX2} = binPos(stop, (stop in bins) ? bins[stop].count : 0); - ctx.lineTo(barX2, vBasePosY); // right edge of the right bar. ctx.closePath(); ctx.fill(); } class CoverageTrack extends React.Component { - props: Props; - state: void; + props: VizProps & { source: CoverageDataSource }; + state: State; static defaultOptions: Object; tiles: CoverageTiledCanvas; - constructor(props: Props) { + constructor(props: VizProps) { super(props); + this.state = { + networkStatus: null + }; } render(): any { - return ; + // These styles allow vertical scrolling to see the full pileup. + // Adding a vertical scrollbar shrinks the visible area, but we have to act + // as though it doesn't, since adjusting the scale would put it out of sync + // with other tracks. + var containerStyles = { + 'height': '100%' + }; + var statusEl = null, + networkStatus = this.state.networkStatus; + if (networkStatus) { + var message = formatStatus(networkStatus); + statusEl = ( +
+
+ Loading coverage… ({message}) +
+
+ ); + } + + var rangeLength = this.props.range.stop - this.props.range.start; + // If range is too large, do not render 'canvas' + if (rangeLength > RemoteRequest.MONSTER_REQUEST) { + return ( +
+
+ Zoom in to see coverage +
+ +
+ ); + } else { + return ( +
+ {statusEl} +
+ +
+
+ ); + } } getScale(): Scale { @@ -165,11 +202,16 @@ class CoverageTrack extends React.Component { } this.visualizeCoverage(); }); - this.props.source.on('newdata', range => { this.tiles.invalidateRange(range); this.visualizeCoverage(); }); + this.props.source.on('networkprogress', e => { + this.setState({networkStatus: e}); + }); + this.props.source.on('networkdone', e => { + this.setState({networkStatus: null}); + }); } componentDidUpdate(prevProps: any, prevState: any) { @@ -197,7 +239,7 @@ class CoverageTrack extends React.Component { [0, Math.round(axisMax / 2), axisMax].forEach(tick => { // Draw a line indicating the tick ctx.pushObject({value: tick, type: 'tick'}); - var tickPosY = Math.round(yScale(tick))+10; // add 9 for offset compared to printed tiles + var tickPosY = Math.round(yScale(tick)); ctx.strokeStyle = style.COVERAGE_FONT_COLOR; canvasUtils.drawLine(ctx, 0, tickPosY, style.COVERAGE_TICK_LENGTH, tickPosY); ctx.popObject(); diff --git a/src/main/viz/PileupTrack.js b/src/main/viz/PileupTrack.js index edb13410..f2083eb7 100644 --- a/src/main/viz/PileupTrack.js +++ b/src/main/viz/PileupTrack.js @@ -7,7 +7,6 @@ import type {Strand, Alignment, AlignmentDataSource} from '../Alignment'; import GA4GHDataSource from '../sources/GA4GHDataSource'; import type {TwoBitSource} from '../sources/TwoBitDataSource'; -import type {BasePair} from './pileuputils'; import type {VisualAlignment, VisualGroup, InsertStats} from './PileupCache'; import type {DataCanvasRenderingContext2D} from 'data-canvas'; import type Interval from '../Interval'; @@ -20,7 +19,8 @@ import _ from 'underscore'; import scale from '../scale'; import d3utils from './d3utils'; -import {CigarOp} from './pileuputils'; +import type {BasePair, State, NetworkStatus} from './pileuputils'; +import {CigarOp, formatStatus} from './pileuputils'; import ContigInterval from '../ContigInterval'; import DisplayMode from './DisplayMode'; import PileupCache from './PileupCache'; @@ -236,12 +236,6 @@ function opacityForQuality(quality: number): number { return Math.min(1.0, alpha); } -type NetworkStatus = {numRequests?: number, status?: string}; -type State = { - networkStatus: ?NetworkStatus; -}; - - class PileupTrack extends React.Component { props: VizProps & { source: AlignmentDataSource }; state: State; @@ -270,7 +264,7 @@ class PileupTrack extends React.Component { var statusEl = null, networkStatus = this.state.networkStatus; if (networkStatus) { - var message = this.formatStatus(networkStatus); + var message = formatStatus(networkStatus); statusEl = (
@@ -303,15 +297,6 @@ class PileupTrack extends React.Component { } } - formatStatus(status: NetworkStatus): string { - if (status.numRequests) { - var pluralS = status.numRequests > 1 ? 's' : ''; - return `issued ${status.numRequests} request${pluralS}`; - } else if (status.status) { - return status.status; - } - throw 'invalid'; - } componentDidMount() { this.cache = new PileupCache(this.props.referenceSource, this.props.options.viewAsPairs); diff --git a/src/main/viz/TiledCanvas.js b/src/main/viz/TiledCanvas.js index 108cf949..599a5d90 100644 --- a/src/main/viz/TiledCanvas.js +++ b/src/main/viz/TiledCanvas.js @@ -52,7 +52,7 @@ class TiledCanvas { var resolution = ResolutionCache.getResolution(tile.originalRange.interval); - this.render(dtx, sc, range, resolution); + this.render(dtx, sc, range, tile.originalRange, resolution); } // Create (and render) new tiles to fill the gaps. @@ -130,6 +130,7 @@ class TiledCanvas { render(dtx: DataCanvasRenderingContext2D, scale: (x: number)=>number, range: ContigInterval, + originalRange: ?ContigInterval, resolution: ?number): void { throw 'Not implemented'; } diff --git a/src/main/viz/pileuputils.js b/src/main/viz/pileuputils.js index 34300390..2d4c0e79 100644 --- a/src/main/viz/pileuputils.js +++ b/src/main/viz/pileuputils.js @@ -206,9 +206,26 @@ function getOpInfo(read: Alignment, referenceSource: Object): OpInfo { }; } +// State information. Used in viz +export type NetworkStatus = {numRequests?: number, status?: string}; +export type State = { + networkStatus: ?NetworkStatus; +}; + +function formatStatus(status: NetworkStatus): string { + if (status.numRequests) { + var pluralS = status.numRequests > 1 ? 's' : ''; + return `issued ${status.numRequests} request${pluralS}`; + } else if (status.status) { + return status.status; + } + throw 'invalid'; +} + module.exports = { pileup, addToPileup, getOpInfo, + formatStatus, CigarOp }; diff --git a/src/test/RemoteRequest-test.js b/src/test/RemoteRequest-test.js index 9b5b1a99..1241f335 100644 --- a/src/test/RemoteRequest-test.js +++ b/src/test/RemoteRequest-test.js @@ -5,7 +5,7 @@ import {expect} from 'chai'; import sinon from 'sinon'; -import RemoteRequest from '../main/RemoteRequest'; +import {RemoteRequest} from '../main/RemoteRequest'; import RemoteFile from '../main/RemoteFile'; import ContigInterval from '../main/ContigInterval'; diff --git a/src/test/sources/ReferenceDataSource-test.js b/src/test/sources/ReferenceDataSource-test.js index 3f78a42e..7aad52a8 100644 --- a/src/test/sources/ReferenceDataSource-test.js +++ b/src/test/sources/ReferenceDataSource-test.js @@ -69,7 +69,6 @@ describe('ReferenceDataSource', function() { 'chrM:3': null }); var str = source.getRangeAsString(range); - console.log(str); expect(str).to.equal('....'); source.on('newdata', () => { diff --git a/style/pileup.css b/style/pileup.css index 049cb3cc..80c62a2b 100644 --- a/style/pileup.css +++ b/style/pileup.css @@ -195,16 +195,16 @@ stroke: black; stroke-width: 2; } -.pileup .network-status { +.network-status { height: 100%; width: 100%; display: flex; align-items: center; justify-content: center; position: relative; - top: 30px; + top: 20px; } -.pileup .network-status-message { +.network-status-message { padding: 4px 8px; width: auto; background: #eee; diff --git a/test-data/chr17-coverage.json b/test-data/chr17-coverage.json index 36a533f0..51f62f1b 100644 --- a/test-data/chr17-coverage.json +++ b/test-data/chr17-coverage.json @@ -1,49 +1,61 @@ [{ - "contig": "17", - "position": 10, - "count": 50 + "contig": "17", + "start": 10, + "end": 11, + "count": 50 }, { "contig": "17", - "position": 11, - "count": 52 + "start": 11, + "end": 12, + "count": 52 }, { "contig": "17", - "position": 12, + "start": 12, + "end": 13, "count": 54 }, { "contig": "17", - "position": 13, + "start": 13, + "end": 14, "count": 56 }, { "contig": "17", - "position": 14, + "start": 14, + "end": 15, "count": 58 }, { "contig": "17", - "position": 15, + "start": 15, + "end": 16, "count": 58 }, { "contig": "17", - "position": 16, + "start": 16, + "end": 17, "count": 58 }, { "contig": "17", - "position": 17, + "start": 17, + "end": 18, "count": 58 }, { "contig": "17", - "position": 18, + "start": 18, + "end": 19, "count": 68 }, { "contig": "17", - "position": 19, + "start": 19, + "end": 20, "count": 72 }, { "contig": "17", - "position": 20, + "start": 20, + "end": 21, "count": 75 }, { "contig": "17", - "position": 21, + "start": 21, + "end": 22, "count": 62 }] From c590d81475da3d5b16f319f9217612ded5806984 Mon Sep 17 00:00:00 2001 From: George He Date: Mon, 31 Oct 2016 12:32:37 -0700 Subject: [PATCH 121/136] Variant end tracking --- src/main/data/vcf.js | 9 +++++++-- src/main/viz/VariantTrack.js | 2 +- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/src/main/data/vcf.js b/src/main/data/vcf.js index 558eb623..c0307889 100644 --- a/src/main/data/vcf.js +++ b/src/main/data/vcf.js @@ -17,6 +17,7 @@ export type Variant = { ref: string; alt: string; vcfLine: string; + end: number; } // This is a minimally-parsed line for facilitating binary search. @@ -41,13 +42,17 @@ function extractLocusLine(vcfLine: string): LocusLine { function extractVariant(vcfLine: string): Variant { var parts = vcfLine.split('\t'); - + var end = Number(parts[1]) + parts[3].length; + if (5 >= parts.length) { + end = parts[5] + } return { contig: parts[0], position: Number(parts[1]), ref: parts[3], alt: parts[4], - vcfLine + vcfLine: vcfLine, + end: end }; } diff --git a/src/main/viz/VariantTrack.js b/src/main/viz/VariantTrack.js index d19b8c8c..709428ca 100644 --- a/src/main/viz/VariantTrack.js +++ b/src/main/viz/VariantTrack.js @@ -82,7 +82,7 @@ class VariantTrack extends React.Component { ctx.fillStyle = style.BASE_COLORS[variant.alt]; ctx.strokeStyle = style.BASE_COLORS[variant.ref]; var x = Math.round(scale(variant.position)); - var width = Math.round(scale(variant.position + 1)) - 1 - x; + var width = Math.round(scale(variant.end)) - x; ctx.fillRect(x - 0.2, y - 0.2, width, style.VARIANT_HEIGHT); ctx.strokeRect(x - 0.2, y - 0.2, width, style.VARIANT_HEIGHT); ctx.popObject(); From 59ecee26bb3f996689d02cfcd4a4bcd1b2a1cf3b Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sun, 11 Dec 2016 01:48:10 +0100 Subject: [PATCH 122/136] fixed reference offset visualization --- src/main/data/Sequence.js | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index 1edcc0c5..760cb329 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -45,9 +45,7 @@ class Sequence { throw `Requested a range with start > stop (${start}, ${stop})`; } return this.remoteRequest.get(range).then(e => { - var sequence = e.response; - var d = sequence.substring(start, (stop-start + 1)); - return d; + return e.response; }); } From 52125baa070e89e66c64d6923ed3684c4545cccf Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Mon, 19 Dec 2016 20:22:13 +0000 Subject: [PATCH 123/136] added checks for null data return types --- src/main/sources/FeatureDataSource.js | 3 ++- src/main/sources/GeneDataSource.js | 5 +++-- src/main/sources/GenotypeDataSource.js | 3 ++- src/main/sources/VariantDataSource.js | 3 ++- src/test/sources/FeatureDataSource-test.js | 22 ++++++++++++++++++++- src/test/sources/GenotypeDataSource-test.js | 21 +++++++++++++++++++- src/test/sources/VariantDataSource-test.js | 18 +++++++++++++++++ 7 files changed, 68 insertions(+), 7 deletions(-) diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index 91617513..34db6803 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -80,7 +80,8 @@ function createFromFeatureUrl(remoteSource: FeatureEndpoint): FeatureDataSource coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getFeaturesInRange(interval).then(e => { var features = e.response; - features.forEach(feature => addFeature(feature)); + if (features != null) + features.forEach(feature => addFeature(feature)); o.trigger('newdata', interval); }); } diff --git a/src/main/sources/GeneDataSource.js b/src/main/sources/GeneDataSource.js index a0795167..3ac2a31e 100644 --- a/src/main/sources/GeneDataSource.js +++ b/src/main/sources/GeneDataSource.js @@ -61,9 +61,10 @@ function createFromGeneUrl(remoteSource: GeneEndpoint): BigBedSource { coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getGenesInRange(interval).then(genes => { + if (genes != null) genes.forEach(gene => addGene(gene)); - //we have new data from our internal block range - o.trigger('newdata', interval); + //we have new data from our internal block range + o.trigger('newdata', interval); }); } diff --git a/src/main/sources/GenotypeDataSource.js b/src/main/sources/GenotypeDataSource.js index 5d581fc2..4eab2256 100644 --- a/src/main/sources/GenotypeDataSource.js +++ b/src/main/sources/GenotypeDataSource.js @@ -79,7 +79,8 @@ function createFromGenotypeUrl(remoteSource: GenotypeEndpoint): GenotypeDataSour coveredRanges.push(interval); coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getFeaturesInRange(interval).then(genotypes => { - genotypes.forEach(genotype => addGenotype(genotype)); + if (genotypes != null) + genotypes.forEach(genotype => addGenotype(genotype)); o.trigger('newdata', interval); }); } diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index ed9a4c66..62925ff6 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -69,7 +69,8 @@ function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getFeaturesInRange(interval).then(e => { var variants = e.response; - variants.forEach(variant => addVariant(variant)); + if (variants != null) + variants.forEach(variant => addVariant(variant)); o.trigger('newdata', interval); }); } diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js index 4fb56cf1..4d570ced 100644 --- a/src/test/sources/FeatureDataSource-test.js +++ b/src/test/sources/FeatureDataSource-test.js @@ -17,6 +17,7 @@ describe('FeatureDataSource', function() { response = data; server = sinon.fakeServer.create(); server.respondWith('GET', '/features/chrM?start=1000&end=2000', [200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/features/chrM?start=1&end=1000', [200, { "Content-Type": "application/json" }, '']); }); }); @@ -34,7 +35,7 @@ describe('FeatureDataSource', function() { it('should extract features in a range', function(done) { var source = getTestSource(); - // No genes fetched initially + // No features fetched initially var range = new ContigInterval('chrM', 1000, 1200); var emptyFeatures = source.getFeaturesInRange(range); expect(emptyFeatures).to.deep.equal([]); @@ -56,4 +57,23 @@ describe('FeatureDataSource', function() { }); server.respond(); }); + + it('should not fail when no feature data is available', function(done) { + var source = getTestSource(); + + var range = new ContigInterval('chrM', 1, 100); + + // Fetching that one gene should cache its entire block. + source.on('newdata', () => { + var features = source.getFeaturesInRange(range); + expect(features).to.have.length(0); + done(); + }); + source.rangeChanged({ + contig: range.contig, + start: range.start(), + stop: range.stop() + }); + server.respond(); + }); }); diff --git a/src/test/sources/GenotypeDataSource-test.js b/src/test/sources/GenotypeDataSource-test.js index 3133a989..2854f87c 100644 --- a/src/test/sources/GenotypeDataSource-test.js +++ b/src/test/sources/GenotypeDataSource-test.js @@ -18,6 +18,7 @@ describe('GenotypeDataSource', function() { response = data; server = sinon.fakeServer.create(); server.respondWith('GET', '/genotypes/chrM?start=1&end=1000',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/genotypes/chrM?start=1000&end=2000',[200, { "Content-Type": "application/json" }, response]); }); }); @@ -31,10 +32,11 @@ describe('GenotypeDataSource', function() { }); return source; } + it('should extract features in a range', function(done) { var source = getTestSource(); var range = new ContigInterval('chrM', 0, 25); - // No variants are cached yet. + // No genotypes are cached yet. var genotypes = source.getFeaturesInRange(range); expect(genotypes).to.deep.equal([]); @@ -55,4 +57,21 @@ describe('GenotypeDataSource', function() { }); server.respond(); }); + + it('should not fail when no genotypes are available', function(done) { + var source = getTestSource(); + var range = new ContigInterval('chrM', 1000, 1025); + + source.on('newdata', () => { + var genotypes = source.getFeaturesInRange(range); + expect(genotypes).to.have.length(0); + done(); + }); + source.rangeChanged({ + contig: range.contig, + start: range.start(), + stop: range.stop() + }); + server.respond(); + }); }); diff --git a/src/test/sources/VariantDataSource-test.js b/src/test/sources/VariantDataSource-test.js index bedbc400..9ee2a7ed 100644 --- a/src/test/sources/VariantDataSource-test.js +++ b/src/test/sources/VariantDataSource-test.js @@ -18,6 +18,7 @@ describe('VariantDataSource', function() { response = data; server = sinon.fakeServer.create(); server.respondWith('GET', '/variants/chrM?start=1&end=1000',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/variants/chrM?start=1000&end=2000',[200, { "Content-Type": "application/json" }, '']); }); }); @@ -54,4 +55,21 @@ describe('VariantDataSource', function() { }); server.respond(); }); + + it('should not fail when no variants are availble', function(done) { + var source = getTestSource(); + var range = new ContigInterval('chrM', 1050, 1150); + + source.on('newdata', () => { + var variants = source.getFeaturesInRange(range); + expect(variants).to.deep.equal([]); + done(); + }); + source.rangeChanged({ + contig: range.contig, + start: range.start(), + stop: range.stop() + }); + server.respond(); + }); }); From 16be4bf565e2235d604953fca4c40d3f91a0cce0 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sun, 1 Jan 2017 19:33:17 -0600 Subject: [PATCH 124/136] added score visualization for features --- src/main/data/FeatureEndpoint.js | 1 + src/main/data/vcf.js | 2 +- src/main/viz/FeatureTrack.js | 6 ++++-- test-data/features-chrM-1000-1200.json | 6 ++++-- 4 files changed, 10 insertions(+), 5 deletions(-) diff --git a/src/main/data/FeatureEndpoint.js b/src/main/data/FeatureEndpoint.js index 321953c7..230e8698 100644 --- a/src/main/data/FeatureEndpoint.js +++ b/src/main/data/FeatureEndpoint.js @@ -15,6 +15,7 @@ export type Feature = { contig: string; start: number; stop: number; + score: number; } class FeatureEndpoint { diff --git a/src/main/data/vcf.js b/src/main/data/vcf.js index c0307889..0ff45499 100644 --- a/src/main/data/vcf.js +++ b/src/main/data/vcf.js @@ -52,7 +52,7 @@ function extractVariant(vcfLine: string): Variant { ref: parts[3], alt: parts[4], vcfLine: vcfLine, - end: end + end: Number(end) }; } diff --git a/src/main/viz/FeatureTrack.js b/src/main/viz/FeatureTrack.js index fc780fcf..6680eebd 100644 --- a/src/main/viz/FeatureTrack.js +++ b/src/main/viz/FeatureTrack.js @@ -13,6 +13,7 @@ import type {Scale} from './d3utils'; import React from 'react'; import ReactDOM from 'react-dom'; import shallowEquals from 'shallow-equals'; +import _ from 'underscore'; import d3utils from './d3utils'; import scale from '../scale'; @@ -86,8 +87,9 @@ class FeatureTrack extends React.Component { if (!position.chrIntersects(range)) return; ctx.pushObject(feature); ctx.lineWidth = 1; - ctx.strokeStyle = style.GENE_COLOR; - ctx.fillStyle = style.GENE_COLOR; + ctx.strokeStyle = 'black'; + var opacity = feature.score/1000; + ctx.fillStyle = `rgba(0,0,0,${opacity})`; var x = Math.round(sc(feature.start)); var width = Math.round(sc(feature.stop) - sc(feature.start)); diff --git a/test-data/features-chrM-1000-1200.json b/test-data/features-chrM-1000-1200.json index c6285852..a600170a 100644 --- a/test-data/features-chrM-1000-1200.json +++ b/test-data/features-chrM-1000-1200.json @@ -3,11 +3,13 @@ "featureType": "peak", "contig": "chrM", "start": 1107, - "end": 1200 + "end": 1200, + "score": 1000 }, { "id": "e105ce29-a840-4fc6-819f-a9aac5166163", "featureType": "peak", "contig": "chrM", "start": 1011, - "end": 1012 + "end": 1012, + "score": 10 }] From 72cdf267ade98cee24d069c5a44b9e8d038e93e9 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Mon, 2 Jan 2017 21:40:32 -0600 Subject: [PATCH 125/136] added click and loading functionality for features --- src/main/sources/FeatureDataSource.js | 2 +- src/main/viz/FeatureTrack.js | 72 ++++++++++++++++++++++++--- style/pileup.css | 21 +++++++- 3 files changed, 86 insertions(+), 9 deletions(-) diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index 34db6803..8e4c247c 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -41,7 +41,7 @@ var BASE_PAIRS_PER_FETCH = 1000; function expandRange(range: ContigInterval) { var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; - var newStart = Math.max(1, roundDown(range.start())), + var newStart = Math.max(0, roundDown(range.start())), newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); return new ContigInterval(range.contig, newStart, newStop); diff --git a/src/main/viz/FeatureTrack.js b/src/main/viz/FeatureTrack.js index 6680eebd..8bcd9619 100644 --- a/src/main/viz/FeatureTrack.js +++ b/src/main/viz/FeatureTrack.js @@ -21,29 +21,58 @@ import ContigInterval from '../ContigInterval'; import canvasUtils from './canvas-utils'; import dataCanvas from 'data-canvas'; import style from '../style'; - +import type {State, NetworkStatus} from './pileuputils'; class FeatureTrack extends React.Component { props: VizProps & { source: FeatureDataSource }; - state: {features: Feature[]}; + state: State; + cache: {features: Feature[]}; constructor(props: VizProps) { super(props); this.state = { + networkStatus: null + }; + this.cache = { features: [] }; } render(): any { - return ; + var statusEl = null, + networkStatus = this.state.networkStatus; + if (networkStatus) { + statusEl = ( +
+
+ Loading features… +
+
+ ); + } + var rangeLength = this.props.range.stop - this.props.range.start; + return ( +
+ {statusEl} +
+ +
+
+ ); } componentDidMount() { // Visualize new reference data as it comes in from the network. this.props.source.on('newdata', (range) => { - this.setState({ + this.cache = { features: this.props.source.getFeaturesInRange(range) - }); + }; + }); + this.props.source.on('networkprogress', e => { + this.setState({networkStatus: e}); + }); + this.props.source.on('networkdone', e => { + this.setState({networkStatus: null}); }); this.updateVisualization(); @@ -61,7 +90,7 @@ class FeatureTrack extends React.Component { } updateVisualization() { - var canvas = ReactDOM.findDOMNode(this), + var canvas = (this.refs.canvas : HTMLCanvasElement), {width, height} = this.props, genomeRange = this.props.range; @@ -82,7 +111,7 @@ class FeatureTrack extends React.Component { // TODO: don't pull in features via state. ctx.font = `${style.GENE_FONT_SIZE}px ${style.GENE_FONT}`; ctx.textAlign = 'center'; - this.state.features.forEach(feature => { + this.cache.features.forEach(feature => { var position = new ContigInterval(feature.contig, feature.start, feature.stop); if (!position.chrIntersects(range)) return; ctx.pushObject(feature); @@ -98,6 +127,35 @@ class FeatureTrack extends React.Component { ctx.popObject(); }); } + + handleClick(reactEvent: any) { + var ev = reactEvent.nativeEvent, + x = ev.offsetX, + y = ev.offsetY; + var ctx = canvasUtils.getContext(this.refs.canvas); + var trackingCtx = new dataCanvas.ClickTrackingContext(ctx, x, y); + console.log("handle click"); + + var genomeRange = this.props.range, + range = new ContigInterval(genomeRange.contig, genomeRange.start, genomeRange.stop), + scale = this.getScale(), + pos = Math.floor(scale.invert(x)), + // If click-tracking gets slow, this range could be narrowed to one + // closer to the click coordinate, rather than the whole visible range. + vFeatures = this.props.source.getFeaturesInRange(range); + var feature = _.find(this.cache.features, f => f.start <= pos && f.stop >= pos); + var alert = window.alert || console.log; + if (feature) { + // Construct a JSON object to show the user. + var messageObject = _.extend( + { + 'id': feature.id, + 'range': `${feature.contig}:${feature.start}-${feature.stop}`, + 'score': feature.score + }); + alert(JSON.stringify(messageObject, null, ' ')); + } + } } FeatureTrack.displayName = 'features'; diff --git a/style/pileup.css b/style/pileup.css index 80c62a2b..ff183fd4 100644 --- a/style/pileup.css +++ b/style/pileup.css @@ -204,6 +204,15 @@ position: relative; top: 20px; } +.network-status-small { + height: 100%; + width: 100%; + display: flex; + align-items: center; + justify-content: center; + position: relative; + top: 9px; +} .network-status-message { padding: 4px 8px; width: auto; @@ -214,6 +223,16 @@ position: absolute; text-align: center; } +.network-status-message-small { + padding: 0px 8px; + width: auto; + background: #eee; + border-radius: 3px; + border: 1px solid #ccc; + font-size: 10px; + position: absolute; + text-align: center; +} .pileup .mate-connector { stroke: #c8c8c8; /* matches IGV */ @@ -288,4 +307,4 @@ } .center { text-align: center; -} \ No newline at end of file +} From 1ce9a318d1fe1c90e98866f991cc350bf3aacc34 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sun, 8 Jan 2017 15:42:34 -0600 Subject: [PATCH 126/136] updated features to view correctly and show info on click --- src/main/data/vcf.js | 2 +- src/main/sources/FeatureDataSource.js | 25 +++-- src/main/sources/GeneDataSource.js | 2 +- src/main/sources/GenotypeDataSource.js | 2 +- src/main/sources/VariantDataSource.js | 2 +- src/main/viz/CoverageTrack.js | 3 - src/main/viz/FeatureTrack.js | 112 +++++++++++++-------- src/main/viz/GenotypeTrack.js | 4 +- src/test/RemoteRequest-test.js | 13 +-- src/test/sources/FeatureDataSource-test.js | 2 +- src/test/viz/CoverageTrack-test.js | 9 +- src/test/viz/FeatureTrack-test.js | 92 +++++++++++++++++ src/test/viz/GenotypeTrack-test.js | 2 +- style/pileup.css | 1 + 14 files changed, 197 insertions(+), 74 deletions(-) create mode 100644 src/test/viz/FeatureTrack-test.js diff --git a/src/main/data/vcf.js b/src/main/data/vcf.js index 0ff45499..eea346fe 100644 --- a/src/main/data/vcf.js +++ b/src/main/data/vcf.js @@ -44,7 +44,7 @@ function extractVariant(vcfLine: string): Variant { var parts = vcfLine.split('\t'); var end = Number(parts[1]) + parts[3].length; if (5 >= parts.length) { - end = parts[5] + end = parts[5]; } return { contig: parts[0], diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index 8e4c247c..db0caa9c 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -37,9 +37,9 @@ export type FeatureDataSource = { // Requests for 2bit ranges are expanded to begin & end at multiples of this // constant. Doing this means that panning typically won't require // additional network requests. -var BASE_PAIRS_PER_FETCH = 1000; +var BASE_PAIRS_PER_FETCH = 10000; -function expandRange(range: ContigInterval) { +function expandRange(range: ContigInterval): ContigInterval { var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; var newStart = Math.max(0, roundDown(range.start())), newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); @@ -74,16 +74,21 @@ function createFromFeatureUrl(remoteSource: FeatureEndpoint): FeatureDataSource } interval = expandRange(interval); - - // "Cover" the range immediately to prevent duplicate fetches. + var newRanges = interval.complementIntervals(coveredRanges); coveredRanges.push(interval); coveredRanges = ContigInterval.coalesce(coveredRanges); - return remoteSource.getFeaturesInRange(interval).then(e => { - var features = e.response; - if (features != null) - features.forEach(feature => addFeature(feature)); - o.trigger('newdata', interval); - }); + + o.trigger('networkprogress', 1); + return Q.all(newRanges.map(range => + remoteSource.getFeaturesInRange(range) + .then(e => { + var features = e.response; + if (features !== null) { + features.forEach(feature => addFeature(feature)); + } + o.trigger('networkdone'); + o.trigger('newdata', range); + }))); } function getFeaturesInRange(range: ContigInterval): Feature[] { diff --git a/src/main/sources/GeneDataSource.js b/src/main/sources/GeneDataSource.js index 3ac2a31e..f19149f1 100644 --- a/src/main/sources/GeneDataSource.js +++ b/src/main/sources/GeneDataSource.js @@ -61,7 +61,7 @@ function createFromGeneUrl(remoteSource: GeneEndpoint): BigBedSource { coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getGenesInRange(interval).then(genes => { - if (genes != null) + if (genes !== null) genes.forEach(gene => addGene(gene)); //we have new data from our internal block range o.trigger('newdata', interval); diff --git a/src/main/sources/GenotypeDataSource.js b/src/main/sources/GenotypeDataSource.js index 4eab2256..d9f85f1d 100644 --- a/src/main/sources/GenotypeDataSource.js +++ b/src/main/sources/GenotypeDataSource.js @@ -79,7 +79,7 @@ function createFromGenotypeUrl(remoteSource: GenotypeEndpoint): GenotypeDataSour coveredRanges.push(interval); coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getFeaturesInRange(interval).then(genotypes => { - if (genotypes != null) + if (genotypes !== null) genotypes.forEach(genotype => addGenotype(genotype)); o.trigger('newdata', interval); }); diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index 62925ff6..686a0bdf 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -69,7 +69,7 @@ function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { coveredRanges = ContigInterval.coalesce(coveredRanges); return remoteSource.getFeaturesInRange(interval).then(e => { var variants = e.response; - if (variants != null) + if (variants !== null) variants.forEach(variant => addVariant(variant)); o.trigger('newdata', interval); }); diff --git a/src/main/viz/CoverageTrack.js b/src/main/viz/CoverageTrack.js index 8fbe0a1a..10fe02da 100644 --- a/src/main/viz/CoverageTrack.js +++ b/src/main/viz/CoverageTrack.js @@ -105,8 +105,6 @@ function renderBars(ctx: DataCanvasRenderingContext2D, }; var vBasePosY = yScale(0); // the very bottom of the canvas - var start = range.start(), - stop = range.stop(); // go to the first bin in dataset (specified by the smallest start position) ctx.fillStyle = style.COVERAGE_BIN_COLOR; @@ -280,7 +278,6 @@ class CoverageTrack extends React.Component { ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); var yScale = this.tiles.yScaleForRef(range); - var thisS = this.getScale(); this.tiles.renderToScreen(ctx, range, this.getScale()); this.renderTicks(ctx, yScale); diff --git a/src/main/viz/FeatureTrack.js b/src/main/viz/FeatureTrack.js index 8bcd9619..b0e5b4f5 100644 --- a/src/main/viz/FeatureTrack.js +++ b/src/main/viz/FeatureTrack.js @@ -6,36 +6,86 @@ import type {FeatureDataSource} from '../sources/FeatureDataSource'; import type {Feature} from '../data/FeatureEndpoint'; +import type {DataCanvasRenderingContext2D} from 'data-canvas'; import type {VizProps} from '../VisualizationWrapper'; import type {Scale} from './d3utils'; import React from 'react'; -import ReactDOM from 'react-dom'; import shallowEquals from 'shallow-equals'; import _ from 'underscore'; import d3utils from './d3utils'; -import scale from '../scale'; import ContigInterval from '../ContigInterval'; import canvasUtils from './canvas-utils'; +import TiledCanvas from './TiledCanvas'; import dataCanvas from 'data-canvas'; import style from '../style'; +import utils from '../utils'; import type {State, NetworkStatus} from './pileuputils'; +class FeatureTiledCanvas extends TiledCanvas { + options: Object; + source: FeatureDataSource; + + constructor(source: FeatureDataSource, options: Object) { + super(); + this.source = source; + this.options = options; + } + + update(newOptions: Object) { + this.options = newOptions; + } + + // TODO: can update to handle overlapping features + heightForRef(ref: string): number { + return style.VARIANT_HEIGHT; + } + + render(ctx: DataCanvasRenderingContext2D, + scale: (x: number)=>number, + range: ContigInterval) { + var relaxedRange = + new ContigInterval(range.contig, range.start() - 1, range.stop() + 1); + var vFeatures = this.source.getFeaturesInRange(relaxedRange); + renderFeatures(ctx, scale, relaxedRange, vFeatures); + } +} + +// Draw features +function renderFeatures(ctx: DataCanvasRenderingContext2D, + scale: (num: number) => number, + range: ContigInterval, + features: Feature[]) { + + ctx.font = `${style.GENE_FONT_SIZE}px ${style.GENE_FONT}`; + ctx.textAlign = 'center'; + + features.forEach(feature => { + var position = new ContigInterval(feature.contig, feature.start, feature.stop); + if (!position.chrIntersects(range)) return; + ctx.pushObject(feature); + ctx.lineWidth = 1; + ctx.fillStyle = 'black'; + + var x = Math.round(scale(feature.start)); + var width = Math.ceil(scale(feature.stop) - scale(feature.start)); + ctx.fillRect(x - 0.5, 0, width, style.VARIANT_HEIGHT); + ctx.popObject(); + }); +} + class FeatureTrack extends React.Component { props: VizProps & { source: FeatureDataSource }; state: State; - cache: {features: Feature[]}; + tiles: FeatureTiledCanvas; constructor(props: VizProps) { super(props); this.state = { networkStatus: null }; - this.cache = { - features: [] - }; } render(): any { @@ -50,7 +100,6 @@ class FeatureTrack extends React.Component {
); } - var rangeLength = this.props.range.stop - this.props.range.start; return (
{statusEl} @@ -62,11 +111,12 @@ class FeatureTrack extends React.Component { } componentDidMount() { + this.tiles = new FeatureTiledCanvas(this.props.source, this.props.options); + // Visualize new reference data as it comes in from the network. this.props.source.on('newdata', (range) => { - this.cache = { - features: this.props.source.getFeaturesInRange(range) - }; + this.tiles.invalidateRange(range); + this.updateVisualization(); }); this.props.source.on('networkprogress', e => { this.setState({networkStatus: e}); @@ -95,55 +145,35 @@ class FeatureTrack extends React.Component { genomeRange = this.props.range; var range = new ContigInterval(genomeRange.contig, genomeRange.start, genomeRange.stop); - var y = height - style.VARIANT_HEIGHT - 1; // Hold off until height & width are known. - if (width === 0) return; - - var sc = this.getScale(); - + if (width === 0 || typeof canvas == 'undefined') return; d3utils.sizeCanvas(canvas, width, height); var ctx = dataCanvas.getDataContext(canvasUtils.getContext(canvas)); ctx.reset(); ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); - // TODO: don't pull in features via state. - ctx.font = `${style.GENE_FONT_SIZE}px ${style.GENE_FONT}`; - ctx.textAlign = 'center'; - this.cache.features.forEach(feature => { - var position = new ContigInterval(feature.contig, feature.start, feature.stop); - if (!position.chrIntersects(range)) return; - ctx.pushObject(feature); - ctx.lineWidth = 1; - ctx.strokeStyle = 'black'; - var opacity = feature.score/1000; - ctx.fillStyle = `rgba(0,0,0,${opacity})`; - - var x = Math.round(sc(feature.start)); - var width = Math.round(sc(feature.stop) - sc(feature.start)); - ctx.fillRect(x - 0.5, y - 0.5, width, style.VARIANT_HEIGHT); - ctx.strokeRect(x - 0.5, y - 0.5, width, style.VARIANT_HEIGHT); - ctx.popObject(); - }); + this.tiles.renderToScreen(ctx, range, this.getScale()); + ctx.restore(); + } handleClick(reactEvent: any) { var ev = reactEvent.nativeEvent, - x = ev.offsetX, - y = ev.offsetY; - var ctx = canvasUtils.getContext(this.refs.canvas); - var trackingCtx = new dataCanvas.ClickTrackingContext(ctx, x, y); - console.log("handle click"); + x = ev.offsetX; var genomeRange = this.props.range, - range = new ContigInterval(genomeRange.contig, genomeRange.start, genomeRange.stop), + // allow some buffering so click isn't so sensitive + range = new ContigInterval(genomeRange.contig, genomeRange.start-1, genomeRange.stop+1), scale = this.getScale(), - pos = Math.floor(scale.invert(x)), + // leave padding of 2px to reduce click specificity + clickStart = Math.floor(scale.invert(x)) - 2, + clickEnd = clickStart + 2, // If click-tracking gets slow, this range could be narrowed to one // closer to the click coordinate, rather than the whole visible range. vFeatures = this.props.source.getFeaturesInRange(range); - var feature = _.find(this.cache.features, f => f.start <= pos && f.stop >= pos); + var feature = _.find(vFeatures, f => utils.tupleRangeOverlaps([[f.start], [f.stop]], [[clickStart], [clickEnd]])); var alert = window.alert || console.log; if (feature) { // Construct a JSON object to show the user. diff --git a/src/main/viz/GenotypeTrack.js b/src/main/viz/GenotypeTrack.js index f43c6d9a..310312ea 100644 --- a/src/main/viz/GenotypeTrack.js +++ b/src/main/viz/GenotypeTrack.js @@ -57,7 +57,7 @@ class GenotypeTrack extends React.Component { updateVisualization() { var canvas = ReactDOM.findDOMNode(this), - {width, height} = this.props; + width = this.props.width; // Hold off until height & width are known. if (width === 0) return; @@ -89,7 +89,7 @@ class GenotypeTrack extends React.Component { // Height can only be computed after the genotypes has been updated. var newHeight = yForRow(sampleIds.length); var canvas = ReactDOM.findDOMNode(this), - {width, height} = this.props; + width = this.props.width; d3utils.sizeCanvas(canvas, width, newHeight); // This is a hack to adjust parent div for resize diff --git a/src/test/RemoteRequest-test.js b/src/test/RemoteRequest-test.js index 1241f335..8ea7b715 100644 --- a/src/test/RemoteRequest-test.js +++ b/src/test/RemoteRequest-test.js @@ -22,6 +22,10 @@ describe('RemoteRequest', function() { return new RemoteFile('/test-data/chr17.1-250.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); + var endpoint = '/test/chr17?start=10&end=20'; + server.respondWith('GET', endpoint, + [200, { "Content-Type": "application/json" }, response]); + }); }); @@ -31,14 +35,11 @@ describe('RemoteRequest', function() { it('should fetch json from a server', function(done) { var remoteRequest = new RemoteRequest(url, basePairsPerFetch); - var endpoint = remoteRequest.getEndpointFromContig(contig, start, stop); - server.respondWith('GET', endpoint, - [200, { "Content-Type": "application/json" }, response]); - var promisedData = remoteRequest.get(interval); - promisedData.then(obj => { - var ret = obj.alignments; + promisedData.then(e => { + var ret = e.response.alignments; expect(remoteRequest.numNetworkRequests).to.equal(1); + expect(e.status).to.equal(200); expect(ret.length).to.equal(14); done(); }); diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js index 4d570ced..f6101de5 100644 --- a/src/test/sources/FeatureDataSource-test.js +++ b/src/test/sources/FeatureDataSource-test.js @@ -16,7 +16,7 @@ describe('FeatureDataSource', function() { return new RemoteFile('/test-data/features-chrM-1000-1200.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); - server.respondWith('GET', '/features/chrM?start=1000&end=2000', [200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/features/chrM?start=0&end=10000', [200, { "Content-Type": "application/json" }, response]); server.respondWith('GET', '/features/chrM?start=1&end=1000', [200, { "Content-Type": "application/json" }, '']); }); }); diff --git a/src/test/viz/CoverageTrack-test.js b/src/test/viz/CoverageTrack-test.js index 3c4adbbd..94b09f67 100644 --- a/src/test/viz/CoverageTrack-test.js +++ b/src/test/viz/CoverageTrack-test.js @@ -46,8 +46,10 @@ describe('CoverageTrack', function() { range: range, tracks: [ { - data: referenceSource, viz: pileup.viz.genome(), + data: pileup.formats.twoBit({ + url: '/test-data/test.2bit' + }), isReference: true }, { @@ -70,11 +72,6 @@ describe('CoverageTrack', function() { testDiv.style.width = ''; }); - var twoBitFile = new MappedRemoteFile( - '/test-data/hg19.2bit.mapped', - [[0, 16383], [691179834, 691183928], [694008946, 694011447]]); - var referenceSource = TwoBitDataSource.createFromTwoBitFile(new TwoBit(twoBitFile)); - var {drawnObjectsWith, callsOf} = dataCanvas.RecordingContext; var findCoverageBins = () => { diff --git a/src/test/viz/FeatureTrack-test.js b/src/test/viz/FeatureTrack-test.js new file mode 100644 index 00000000..d7804e32 --- /dev/null +++ b/src/test/viz/FeatureTrack-test.js @@ -0,0 +1,92 @@ +/** + * This tests whether feature information is being shown/drawn correctly + * in the track. + * + * @flow + */ +'use strict'; + +import {expect} from 'chai'; + +import sinon from 'sinon'; + +import RemoteFile from '../../main/RemoteFile'; +import pileup from '../../main/pileup'; +import dataCanvas from 'data-canvas'; +import {waitFor} from '../async'; + +describe('FeatureTrack', function() { + var testDiv = document.getElementById('testdiv'); + var range = {contig: 'chrM', start: 900, stop: 1500}; + var server: any = null, response; + + beforeEach(() => { + testDiv.style.width = '800px'; + dataCanvas.RecordingContext.recordAll(); + }); + + afterEach(() => { + dataCanvas.RecordingContext.reset(); + // avoid pollution between tests. + server.restore(); + }); + + before(function () { + return new RemoteFile('/test-data/features-chrM-1000-1200.json').getAllString().then(data => { + server = sinon.fakeServer.create(); + response = data; + }); + }); + + after(function () { + server.restore(); + }); + + var drawnObjects = dataCanvas.RecordingContext.drawnObjects; + + function ready() { + return testDiv.querySelector('canvas') && + drawnObjects(testDiv, '.features').length > 0; + } + + it('should render features', function() { + server.respondWith('GET', '/features/chrM?start=0&end=10000', [200, { "Content-Type": "application/json" }, ""]); + var p = pileup.create(testDiv, { + range: range, + tracks: [ + { + viz: pileup.viz.genome(), + data: pileup.formats.twoBit({ + url: '/test-data/test.2bit' + }), + isReference: true + }, + { + + data: pileup.formats.features({ + url: '/features', + }), + viz: pileup.viz.features() + }, + { + data: pileup.formats.bigBed({ + url: '/test-data/ensembl.chr17.bb' + }), + viz: pileup.viz.genes(), + } + ] + }); + + return waitFor(ready, 2000) + .then(() => { + var features = drawnObjects(testDiv, '.features'); + var ids = ["4ee7469a-b468-429b-a109-07a484817037", "e105ce29-a840-4fc6-819f-a9aac5166163"]; + expect(features).to.have.length(2); + expect(features.map(f => f.start)).to.deep.equal( + [1107, 1011]); + expect(features.map(g => g.id)).to.deep.equal(ids); + p.destroy(); + }); + }); + +}); diff --git a/src/test/viz/GenotypeTrack-test.js b/src/test/viz/GenotypeTrack-test.js index 71cd1395..b43f934a 100644 --- a/src/test/viz/GenotypeTrack-test.js +++ b/src/test/viz/GenotypeTrack-test.js @@ -39,7 +39,7 @@ describe('GenotypeTrack', function() { // avoid pollution between tests. testDiv.innerHTML = ''; }); - var {drawnObjects, callsOf} = dataCanvas.RecordingContext; + var drawnObjects = dataCanvas.RecordingContext.drawnObjects; function ready() { return testDiv.querySelector('canvas') && diff --git a/style/pileup.css b/style/pileup.css index ff183fd4..8e91c34c 100644 --- a/style/pileup.css +++ b/style/pileup.css @@ -13,6 +13,7 @@ .pileup-root > .track { display: flex; flex-direction: row; + margin-bottom: 5px; } .pileup-root text, .track-label { font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; From 7f85cdaab4480d2bda05d222c2987a0853895fe7 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 10 Jan 2017 13:21:37 -0800 Subject: [PATCH 127/136] added limit for visualizing large Feature areas --- src/main/viz/FeatureTrack.js | 34 +++++++++++++++++++++++++--------- 1 file changed, 25 insertions(+), 9 deletions(-) diff --git a/src/main/viz/FeatureTrack.js b/src/main/viz/FeatureTrack.js index b0e5b4f5..d9ce11d7 100644 --- a/src/main/viz/FeatureTrack.js +++ b/src/main/viz/FeatureTrack.js @@ -16,6 +16,7 @@ import shallowEquals from 'shallow-equals'; import _ from 'underscore'; import d3utils from './d3utils'; +import RemoteRequest from '../RemoteRequest'; import ContigInterval from '../ContigInterval'; import canvasUtils from './canvas-utils'; import TiledCanvas from './TiledCanvas'; @@ -100,14 +101,27 @@ class FeatureTrack extends React.Component {
); } - return ( -
- {statusEl} -
- + var rangeLength = this.props.range.stop - this.props.range.start; + // If range is too large, do not render 'canvas' + if (rangeLength > RemoteRequest.MONSTER_REQUEST) { + return ( +
+
+ Zoom in to see features +
+ +
+ ); + } else { + return ( +
+ {statusEl} +
+ +
-
- ); + ); + } } componentDidMount() { @@ -133,8 +147,10 @@ class FeatureTrack extends React.Component { } componentDidUpdate(prevProps: any, prevState: any) { - if (!shallowEquals(prevProps, this.props) || - !shallowEquals(prevState, this.state)) { + if (!shallowEquals(this.props, prevProps) || + !shallowEquals(this.state, prevState)) { + this.tiles.update(this.props.height, this.props.options); + this.tiles.invalidateAll(); this.updateVisualization(); } } From dfc2d9864ca14ff185dcc8fad69155defcfda5eb Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Sat, 14 Jan 2017 12:17:55 -0800 Subject: [PATCH 128/136] fixed no data error for alignments and max rows for PileupTrack --- src/main/sources/GA4GHDataSource.js | 2 +- src/main/viz/PileupTrack.js | 33 +++++++++++++++++------------ 2 files changed, 21 insertions(+), 14 deletions(-) diff --git a/src/main/sources/GA4GHDataSource.js b/src/main/sources/GA4GHDataSource.js index e2a76a40..c9d8ec31 100644 --- a/src/main/sources/GA4GHDataSource.js +++ b/src/main/sources/GA4GHDataSource.js @@ -108,7 +108,7 @@ function create(spec: GA4GHSpec): AlignmentDataSource { xhr.addEventListener('load', function(e) { var response = this.response; - if (this.status >= 400) { + if (this.status != 200) { notifyFailure(this.status + ' ' + this.statusText + ' ' + JSON.stringify(response)); } else { if (response.errorCode) { diff --git a/src/main/viz/PileupTrack.js b/src/main/viz/PileupTrack.js index f2083eb7..2ab76469 100644 --- a/src/main/viz/PileupTrack.js +++ b/src/main/viz/PileupTrack.js @@ -32,6 +32,12 @@ import style from '../style'; var READ_HEIGHT = 13; var READ_SPACING = 2; // vertical pixels between reads +var MAX_ROWS = 1000; // max rows to print pileup + +function pileupHeight(rows: number): number { + var modified_rows = Math.min(MAX_ROWS, rows); + return modified_rows * (READ_HEIGHT + READ_SPACING); +} var READ_STRAND_ARROW_WIDTH = 5; @@ -55,8 +61,7 @@ class PileupTiledCanvas extends TiledCanvas { } heightForRef(ref: string): number { - return this.cache.pileupHeightForRef(ref) * - (READ_HEIGHT + READ_SPACING); + return pileupHeight(this.cache.pileupHeightForRef(ref)); } render(ctx: DataCanvasRenderingContext2D, @@ -180,17 +185,19 @@ function renderPileup(ctx: DataCanvasRenderingContext2D, } else { ctx.fillStyle = style.ALIGNMENT_COLOR; } - var y = yForRow(vGroup.row); - ctx.pushObject(vGroup); - if (vGroup.insert) { - var span = vGroup.insert, - x1 = scale(span.start + 1), - x2 = scale(span.stop + 1); - ctx.fillRect(x1, y + READ_HEIGHT / 2 - 0.5, x2 - x1, 1); + if (vGroup.row <= MAX_ROWS) { + var y = yForRow(vGroup.row); + ctx.pushObject(vGroup); + if (vGroup.insert) { + var span = vGroup.insert, + x1 = scale(span.start + 1), + x2 = scale(span.stop + 1); + ctx.fillRect(x1, y + READ_HEIGHT / 2 - 0.5, x2 - x1, 1); + } + vGroup.alignments.forEach(vRead => drawAlignment(vRead, y)); + ctx.popObject(); + ctx.restore(); } - vGroup.alignments.forEach(vRead => drawAlignment(vRead, y)); - ctx.popObject(); - ctx.restore(); } function renderMismatch(bp: BasePair, y: number) { @@ -381,7 +388,7 @@ class PileupTrack extends React.Component { if (width === 0 || typeof canvas == 'undefined') return; // Height can only be computed after the pileup has been updated. - var height = yForRow(this.cache.pileupHeightForRef(this.props.range.contig)); + var height = yForRow(this.tiles.heightForRef(this.props.range.contig)); d3utils.sizeCanvas(canvas, width, height); From fa003776696ce9b458eb31fd5d230b007e657b75 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Fri, 20 Jan 2017 10:15:11 -0800 Subject: [PATCH 129/136] Added loading sign for variants and fixed click functionality --- src/main/sources/VariantDataSource.js | 5 +- src/main/viz/FeatureTrack.js | 2 +- src/main/viz/VariantTrack.js | 166 ++++++++++++++++++++------ 3 files changed, 135 insertions(+), 38 deletions(-) diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index 686a0bdf..572644d2 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -26,7 +26,7 @@ import type {VcfDataSource} from './VcfDataSource'; import {RemoteRequest} from '../RemoteRequest'; import VariantEndpoint from '../data/VariantEndpoint'; -var BASE_PAIRS_PER_FETCH = 1000; +var BASE_PAIRS_PER_FETCH = 10000; function expandRange(range: ContigInterval) { var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; @@ -67,10 +67,13 @@ function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { // "Cover" the range immediately to prevent duplicate fetches. coveredRanges.push(interval); coveredRanges = ContigInterval.coalesce(coveredRanges); + + o.trigger('networkprogress', 1); return remoteSource.getFeaturesInRange(interval).then(e => { var variants = e.response; if (variants !== null) variants.forEach(variant => addVariant(variant)); + o.trigger('networkdone'); o.trigger('newdata', interval); }); } diff --git a/src/main/viz/FeatureTrack.js b/src/main/viz/FeatureTrack.js index d9ce11d7..1b46facf 100644 --- a/src/main/viz/FeatureTrack.js +++ b/src/main/viz/FeatureTrack.js @@ -151,7 +151,7 @@ class FeatureTrack extends React.Component { !shallowEquals(this.state, prevState)) { this.tiles.update(this.props.height, this.props.options); this.tiles.invalidateAll(); - this.updateVisualization(); + this.updateVisualization(); } } diff --git a/src/main/viz/VariantTrack.js b/src/main/viz/VariantTrack.js index 709428ca..ea1c86e7 100644 --- a/src/main/viz/VariantTrack.js +++ b/src/main/viz/VariantTrack.js @@ -12,33 +12,133 @@ import type {Scale} from './d3utils'; import React from 'react'; import ReactDOM from 'react-dom'; +import _ from 'underscore'; import d3utils from './d3utils'; +import RemoteRequest from '../RemoteRequest'; import shallowEquals from 'shallow-equals'; import ContigInterval from '../ContigInterval'; import canvasUtils from './canvas-utils'; +import TiledCanvas from './TiledCanvas'; import dataCanvas from 'data-canvas'; import style from '../style'; +import utils from '../utils'; +import type {State, NetworkStatus} from './pileuputils'; +class VariantTiledCanvas extends TiledCanvas { + options: Object; + source: VcfDataSource; + + constructor(source: VcfDataSource, options: Object) { + super(); + this.source = source; + this.options = options; + } + + update(newOptions: Object) { + this.options = newOptions; + } + + // TODO: can update to handle overlapping features + heightForRef(ref: string): number { + return style.VARIANT_HEIGHT; + } + + render(ctx: DataCanvasRenderingContext2D, + scale: (x: number)=>number, + range: ContigInterval) { + var relaxedRange = + new ContigInterval(range.contig, range.start() - 1, range.stop() + 1); + var vVariants = this.source.getFeaturesInRange(relaxedRange); + renderVariants(ctx, scale, relaxedRange, vVariants); + } +} + +// Draw variants +function renderVariants(ctx: DataCanvasRenderingContext2D, + scale: (num: number) => number, + range: ContigInterval, + variants: Variant[]) { + + ctx.font = `${style.GENE_FONT_SIZE}px ${style.GENE_FONT}`; + ctx.textAlign = 'center'; + + variants.forEach(variant => { + ctx.pushObject(variant); + ctx.fillStyle = style.BASE_COLORS[variant.alt]; + ctx.strokeStyle = style.BASE_COLORS[variant.ref]; + var x = Math.round(scale(variant.position)); + var width = Math.round(scale(variant.end)) - x; + ctx.fillRect(x - 0.2, 0, width, style.VARIANT_HEIGHT); + ctx.strokeRect(x - 0.2, 0, width, style.VARIANT_HEIGHT); + ctx.popObject(); + }); + +} class VariantTrack extends React.Component { props: VizProps & {source: VcfDataSource}; - state: void; // no state + state: State; // no state + tiles: VariantTiledCanvas; constructor(props: Object) { super(props); + this.state = { + networkStatus: null + }; } render(): any { - return ; + var statusEl = null, + networkStatus = this.state.networkStatus; + if (networkStatus) { + statusEl = ( +
+
+ Loading Variants… +
+
+ ); + } + var rangeLength = this.props.range.stop - this.props.range.start; + // If range is too large, do not render 'canvas' + if (rangeLength > RemoteRequest.MONSTER_REQUEST) { + return ( +
+
+ Zoom in to see variants +
+ +
+ ); + } else { + return ( +
+ {statusEl} +
+ +
+
+ ); + } } componentDidMount() { - this.updateVisualization(); + this.tiles = new VariantTiledCanvas(this.props.source, this.props.options); - this.props.source.on('newdata', () => { + // Visualize ne data as it comes in from the network. + this.props.source.on('newdata', (range) => { + this.tiles.invalidateRange(range); this.updateVisualization(); }); + this.props.source.on('networkprogress', e => { + this.setState({networkStatus: e}); + }); + this.props.source.on('networkdone', e => { + this.setState({networkStatus: null}); + }); + + this.updateVisualization(); } getScale(): Scale { @@ -48,58 +148,52 @@ class VariantTrack extends React.Component { componentDidUpdate(prevProps: any, prevState: any) { if (!shallowEquals(prevProps, this.props) || !shallowEquals(prevState, this.state)) { - this.updateVisualization(); + this.tiles.update(this.props.height, this.props.options); + this.tiles.invalidateAll(); + this.updateVisualization(); } } updateVisualization() { - var canvas = ReactDOM.findDOMNode(this), + var canvas = (this.refs.canvas : HTMLCanvasElement), {width, height} = this.props; // Hold off until height & width are known. if (width === 0) return; - d3utils.sizeCanvas(canvas, width, height); - var ctx = canvasUtils.getContext(canvas); - var dtx = dataCanvas.getDataContext(ctx); - this.renderScene(dtx); + + var ctx = dataCanvas.getDataContext(canvasUtils.getContext(canvas)); + this.renderScene(ctx); } renderScene(ctx: DataCanvasRenderingContext2D) { var range = this.props.range, interval = new ContigInterval(range.contig, range.start, range.stop), - variants = this.props.source.getFeaturesInRange(interval), - scale = this.getScale(), - height = this.props.height, - y = height - style.VARIANT_HEIGHT - 1; + scale = this.getScale(); + // height = this.props.height, + // y = height - style.VARIANT_HEIGHT - 1; - ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); ctx.reset(); - ctx.save(); - - variants.forEach(variant => { - ctx.pushObject(variant); - ctx.fillStyle = style.BASE_COLORS[variant.alt]; - ctx.strokeStyle = style.BASE_COLORS[variant.ref]; - var x = Math.round(scale(variant.position)); - var width = Math.round(scale(variant.end)) - x; - ctx.fillRect(x - 0.2, y - 0.2, width, style.VARIANT_HEIGHT); - ctx.strokeRect(x - 0.2, y - 0.2, width, style.VARIANT_HEIGHT); - ctx.popObject(); - }); - - ctx.restore(); + ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); + this.tiles.renderToScreen(ctx, interval, scale); } handleClick(reactEvent: any) { var ev = reactEvent.nativeEvent, - x = ev.offsetX, - y = ev.offsetY, - canvas = ReactDOM.findDOMNode(this), - ctx = canvasUtils.getContext(canvas), - trackingCtx = new dataCanvas.ClickTrackingContext(ctx, x, y); - this.renderScene(trackingCtx); - var variant = trackingCtx.hit && trackingCtx.hit[0]; + x = ev.offsetX; + + var genomeRange = this.props.range, + // allow some buffering so click isn't so sensitive + range = new ContigInterval(genomeRange.contig, genomeRange.start-1, genomeRange.stop+1), + scale = this.getScale(), + // leave padding of 2px to reduce click specificity + clickStart = Math.floor(scale.invert(x)) - 2, + clickEnd = clickStart + 2, + // If click-tracking gets slow, this range could be narrowed to one + // closer to the click coordinate, rather than the whole visible range. + vVariants = this.props.source.getFeaturesInRange(range); + + var variant = _.find(vVariants, f => utils.tupleRangeOverlaps([[f.position], [f.end]], [[clickStart], [clickEnd]])); var alert = window.alert || console.log; if (variant) { alert(JSON.stringify(variant)); From 304d39ae84d7dbac7d3c0215f4eed11f63ea09be Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Mon, 23 Jan 2017 09:12:05 -0800 Subject: [PATCH 130/136] Added resolution cache to variants. Fixed resolution cache to not request areas already in cache. --- src/main/ResolutionCache.js | 28 ++++++++++++- src/main/data/VariantEndpoint.js | 27 ------------- src/main/sources/CoverageDataSource.js | 42 +++++++++++--------- src/main/sources/VariantDataSource.js | 54 ++++++++++++++------------ src/main/viz/CoverageTrack.js | 2 +- src/main/viz/VariantTrack.js | 14 +++++-- 6 files changed, 90 insertions(+), 77 deletions(-) delete mode 100644 src/main/data/VariantEndpoint.js diff --git a/src/main/ResolutionCache.js b/src/main/ResolutionCache.js index d9ee0626..886c5fac 100644 --- a/src/main/ResolutionCache.js +++ b/src/main/ResolutionCache.js @@ -45,9 +45,33 @@ class ResolutionCache { return res; } + /** + * Find the disjoint subintervals not covered by any interval in the list with the same resolution. + * + * If comp = interval.complementIntervals(ranges), then this guarantees that: + * - comp union ranges = interval + * - a int b = 0 forall a \in comp, b in ranges + * + * (The input ranges need not be disjoint.) + */ + complementInterval(range: ContigInterval, resolution: ?number): ContigInterval[] { + if (!resolution) { + resolution = ResolutionCache.getResolution(range.interval); + } + + // filter ranges by correct resolution + var resolutionIntervals = _.filter(this.coveredRanges, r => r.resolution == resolution) + .map(r => r.contigInterval); + + return range.complementIntervals(resolutionIntervals); + + } + // puts new ranges into list of ranges covered by cache - coverRange(range: ContigInterval) { - var resolution = ResolutionCache.getResolution(range.interval); + coverRange(range: ContigInterval, resolution: ?number) { + if (!resolution) { + resolution = ResolutionCache.getResolution(range.interval); + } var resolvedRange = new ResolutionCacheKey(range, resolution); this.coveredRanges.push(resolvedRange); // coalesce new contigIntervals diff --git a/src/main/data/VariantEndpoint.js b/src/main/data/VariantEndpoint.js deleted file mode 100644 index 1222c817..00000000 --- a/src/main/data/VariantEndpoint.js +++ /dev/null @@ -1,27 +0,0 @@ -/** - * This module defines a parser for the 2bit file format. - * See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 - * @flow - */ -'use strict'; - -import ContigInterval from '../ContigInterval'; -import Q from 'q'; -import {RemoteRequest} from '../RemoteRequest'; -import type {Variant} from './vcf'; - -class VariantEndpoint { - remoteRequest: RemoteRequest; - - constructor(remoteRequest: RemoteRequest) { - this.remoteRequest = remoteRequest; - } - - getFeaturesInRange(range: ContigInterval): Q.Promise { - return this.remoteRequest.get(range).then(object => { - return object; - }); - } -} - -module.exports = VariantEndpoint; diff --git a/src/main/sources/CoverageDataSource.js b/src/main/sources/CoverageDataSource.js index e2f00fc7..ae44c0b4 100644 --- a/src/main/sources/CoverageDataSource.js +++ b/src/main/sources/CoverageDataSource.js @@ -72,30 +72,34 @@ function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource var resolution = ResolutionCache.getResolution(interval.interval); var endpointModifier = `binning=${resolution}`; + // get all smaller intervals not yet covered in cache + var newRanges = cache.complementInterval(interval, resolution); + // Cover the range immediately to prevent duplicate fetches. cache.coverRange(interval); var numRequests = 1; - o.trigger('networkprogress', {numRequests}); - return remoteSource.getFeaturesInRange(interval, endpointModifier).then(json => { - var response = json.response; - if (json.status >= 400) { - notifyFailure(json.status + ' ' + json.statusText + ' ' + JSON.stringify(response)); - } else { - if (response.errorCode) { - notifyFailure('Error from CoverageDataSource: ' + JSON.stringify(response)); + o.trigger('networkprogress', newRanges.length); + return Q.all(newRanges.map(range => + remoteSource.getFeaturesInRange(range, endpointModifier).then(json => { + var response = json.response; + if (json.status >= 400) { + notifyFailure(json.status + ' ' + json.statusText + ' ' + JSON.stringify(response)); } else { - // add new data to cache - response.forEach(p => cache.put({ - "contig": range.contig, - "start": p.start, - "end": p.end, - "count": p.count - }, resolution)); - o.trigger('newdata', interval); + if (response.errorCode) { + notifyFailure('Error from CoverageDataSource: ' + JSON.stringify(response)); + } else { + // add new data to cache + response.forEach(p => cache.put({ + "contig": range.contig, + "start": p.start, + "end": p.end, + "count": p.count + }, resolution)); + o.trigger('newdata', interval); + } } - } - o.trigger('networkdone'); - }); + o.trigger('networkdone'); + }))); } function getCoverageInRange(range: ContigInterval, diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index 572644d2..214ef16c 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -20,6 +20,7 @@ import type {Variant} from '../data/vcf'; import Q from 'q'; import _ from 'underscore'; import {Events} from 'backbone'; +import {ResolutionCache} from '../ResolutionCache'; import ContigInterval from '../ContigInterval'; import type {VcfDataSource} from './VcfDataSource'; @@ -36,51 +37,55 @@ function expandRange(range: ContigInterval) { return new ContigInterval(range.contig, newStart, newStop); } -function variantKey(v: Variant): string { +function keyFunction(v: Variant): string { return `${v.contig}:${v.position}`; } +function filterFunction(range: ContigInterval, v: Variant): boolean { + return range.chrContainsLocus(v.contig, v.position); +} -function createFromVariantUrl(remoteSource: VariantEndpoint): VcfDataSource { - var variants: {[key: string]: Variant} = {}; - - // Ranges for which we have complete information -- no need to hit network. - var coveredRanges: ContigInterval[] = []; - - function addVariant(v: Variant) { - var key = variantKey(v); - if (!variants[key]) { - variants[key] = v; - } - } +function createFromVariantUrl(remoteSource: RemoteRequest): VcfDataSource { + var cache: ResolutionCache = + new ResolutionCache(filterFunction, keyFunction); function fetch(range: GenomeRange) { var interval = new ContigInterval(range.contig, range.start, range.stop); // Check if this interval is already in the cache. - if (interval.isCoveredBy(coveredRanges)) { + if (cache.coversRange(interval)) { return Q.when(); } + // modify endpoint to calculate coverage using binning + var resolution = ResolutionCache.getResolution(interval.interval); + var endpointModifier = `binning=${resolution}`; + + interval = expandRange(interval); - // "Cover" the range immediately to prevent duplicate fetches. - coveredRanges.push(interval); - coveredRanges = ContigInterval.coalesce(coveredRanges); + // get all smaller intervals not yet covered in cache + var newRanges = cache.complementInterval(interval, resolution); - o.trigger('networkprogress', 1); - return remoteSource.getFeaturesInRange(interval).then(e => { + // "Cover" the range immediately to prevent duplicate fetches. + // Because interval is expanded, make sure to use original resolution + cache.coverRange(interval, resolution); + o.trigger('networkprogress', newRanges.length); + return Q.all(newRanges.map(range => + remoteSource.getFeaturesInRange(range, endpointModifier).then(e => { var variants = e.response; if (variants !== null) - variants.forEach(variant => addVariant(variant)); + variants.forEach(v => cache.put(v, resolution)); o.trigger('networkdone'); o.trigger('newdata', interval); - }); + }))); } - function getFeaturesInRange(range: ContigInterval): Variant[] { + function getFeaturesInRange(range: ContigInterval, resolution: ?number): Variant[] { if (!range) return []; // XXX why would this happen? - return _.filter(variants, v => range.chrContainsLocus(v.contig, v.position)); + var data = cache.get(range, resolution); + var sorted = data.sort((a, b) => a.position - b.position); + return sorted; } var o = { @@ -103,8 +108,7 @@ function create(data: {url?:string}): VcfDataSource { if (!data.url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } - var request = new RemoteRequest(data.url, BASE_PAIRS_PER_FETCH); - var endpoint = new VariantEndpoint(request); + var endpoint = new RemoteRequest(data.url, BASE_PAIRS_PER_FETCH); return createFromVariantUrl(endpoint); } diff --git a/src/main/viz/CoverageTrack.js b/src/main/viz/CoverageTrack.js index 10fe02da..f088b191 100644 --- a/src/main/viz/CoverageTrack.js +++ b/src/main/viz/CoverageTrack.js @@ -58,7 +58,7 @@ class CoverageTiledCanvas extends TiledCanvas { .nice(); } - // This is alled by TiledCanvas over all tiles in a range + // This is called by TiledCanvas over all tiles in a range render(ctx: DataCanvasRenderingContext2D, xScale: (x: number)=>number, range: ContigInterval, diff --git a/src/main/viz/VariantTrack.js b/src/main/viz/VariantTrack.js index ea1c86e7..e46fde7f 100644 --- a/src/main/viz/VariantTrack.js +++ b/src/main/viz/VariantTrack.js @@ -25,6 +25,8 @@ import style from '../style'; import utils from '../utils'; import type {State, NetworkStatus} from './pileuputils'; +var MONSTER_REQUEST = 500000; + class VariantTiledCanvas extends TiledCanvas { options: Object; source: VcfDataSource; @@ -46,10 +48,15 @@ class VariantTiledCanvas extends TiledCanvas { render(ctx: DataCanvasRenderingContext2D, scale: (x: number)=>number, - range: ContigInterval) { + range: ContigInterval, + originalRange: ?ContigInterval, + resolution: ?number) { var relaxedRange = new ContigInterval(range.contig, range.start() - 1, range.stop() + 1); - var vVariants = this.source.getFeaturesInRange(relaxedRange); + + // relaxed range is just for this tile. make sure to get resolution for whole + // viewing area + var vVariants = this.source.getFeaturesInRange(relaxedRange, resolution); renderVariants(ctx, scale, relaxedRange, vVariants); } } @@ -102,7 +109,7 @@ class VariantTrack extends React.Component { } var rangeLength = this.props.range.stop - this.props.range.start; // If range is too large, do not render 'canvas' - if (rangeLength > RemoteRequest.MONSTER_REQUEST) { + if (rangeLength > MONSTER_REQUEST) { return (
@@ -176,6 +183,7 @@ class VariantTrack extends React.Component { ctx.reset(); ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); this.tiles.renderToScreen(ctx, interval, scale); + ctx.restore(); } handleClick(reactEvent: any) { From 0d93189a2be059a639d3217b7219b614dd972ef6 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Thu, 26 Jan 2017 19:16:31 -0800 Subject: [PATCH 131/136] finished genotypes --- src/main/ResolutionCache.js | 32 +-- src/main/data/GenotypeEndpoint.js | 32 --- src/main/data/vcf.js | 6 + src/main/pileup.js | 2 - src/main/sources/CoverageDataSource.js | 1 - src/main/sources/GenotypeDataSource.js | 122 -------- src/main/sources/VariantDataSource.js | 54 +++- src/main/sources/VcfDataSource.js | 20 +- src/main/style.js | 3 +- src/main/viz/FeatureTrack.js | 2 +- src/main/viz/GenotypeTrack.js | 290 +++++++++++++++----- src/main/viz/VariantTrack.js | 14 +- src/test/sources/GenotypeDataSource-test.js | 77 ------ src/test/sources/VariantDataSource-test.js | 11 +- src/test/sources/VcfDataSource-test.js | 4 +- src/test/viz/GenotypeTrack-test.js | 4 +- style/pileup.css | 6 +- test-data/variants-chrM-0-100.json | 31 ++- 18 files changed, 340 insertions(+), 371 deletions(-) delete mode 100644 src/main/data/GenotypeEndpoint.js delete mode 100644 src/main/sources/GenotypeDataSource.js delete mode 100644 src/test/sources/GenotypeDataSource-test.js diff --git a/src/main/ResolutionCache.js b/src/main/ResolutionCache.js index 886c5fac..ae52da52 100644 --- a/src/main/ResolutionCache.js +++ b/src/main/ResolutionCache.js @@ -11,14 +11,10 @@ import _ from 'underscore'; import Interval from './Interval'; import ContigInterval from './ContigInterval'; -type ResolutionObject = { - resolution: number; - object: T; -} class ResolutionCache { coveredRanges: ResolutionCacheKey[]; - cache: {[key: string]: ResolutionObject}; + cache: {[resolution: number]: {[key: string]: T}}; // used to filter out elements in the cache based on resolution. filterFunction: Function; // should take form (range: ContigInterval, T) => boolean; keyFunction: Function; // should take form (d: T) => string; @@ -35,11 +31,9 @@ class ResolutionCache { if (!range) return []; var res = {}; if (!resolution) { - res = _.map(_.filter(this.cache, d => this.filterFunction(range, d.object)), - obj => obj.object); + res = _.filter(this.cache[1], d => this.filterFunction(range, d)); } else { - res = _.map(_.filter(this.cache, d => this.filterFunction(range, d.object) && d.resolution == resolution), - obj => obj.object); + res = _.filter(this.cache[resolution], d => this.filterFunction(range, d)); } return res; @@ -83,13 +77,13 @@ class ResolutionCache { if (!resolution) { resolution = 1; } - var resObject = { - resolution: resolution, - object: value - }; var key = this.keyFunction(value); - if (!this.cache[key]) { - this.cache[key] = resObject; + + // initialize cache resolution, if not already initialized + if (!this.cache[resolution]) this.cache[resolution] = {}; + + if (!this.cache[resolution][key]) { + this.cache[resolution][key] = value; } } @@ -125,11 +119,13 @@ class ResolutionCache { * - For regions >= 1,000,000, bin 1000 bp into 1 (return 1000) */ static getResolution(range: Interval): number { - if (range.length() < 10000) + // subtract one because length() adds one + var rangeLength = range.length() - 1; + if (rangeLength < 10000) return 1; - else if (range.length() >= 10000 && range.length() < 100000 ) + else if (rangeLength >= 10000 && rangeLength < 100000 ) return 10; - else if (range.length() >= 100000 && range.length() < 1000000 ) + else if (rangeLength >= 100000 && rangeLength < 1000000 ) return 100; else return 1000; diff --git a/src/main/data/GenotypeEndpoint.js b/src/main/data/GenotypeEndpoint.js deleted file mode 100644 index f29fe048..00000000 --- a/src/main/data/GenotypeEndpoint.js +++ /dev/null @@ -1,32 +0,0 @@ -/** - * This module defines a parser for the 2bit file format. - * See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 - * @flow - */ -'use strict'; - -import ContigInterval from '../ContigInterval'; -import Q from 'q'; -import {RemoteRequest} from '../RemoteRequest'; -import type {Variant} from './vcf'; - -export type Genotype = { - sampleIds: string[], - variant: Variant -} - -class GenotypeEndpoint { - remoteRequest: RemoteRequest; - - constructor(remoteRequest: RemoteRequest) { - this.remoteRequest = remoteRequest; - } - - getFeaturesInRange(range: ContigInterval): Q.Promise { - return this.remoteRequest.get(range).then(e => { - return e.response; - }); - } -} - -module.exports = GenotypeEndpoint; diff --git a/src/main/data/vcf.js b/src/main/data/vcf.js index eea346fe..00fd2b2d 100644 --- a/src/main/data/vcf.js +++ b/src/main/data/vcf.js @@ -20,6 +20,12 @@ export type Variant = { end: number; } +// holds variant and genotype sample ids +export type VariantContext = { + variant: Variant, + sampleIds: string[] +} + // This is a minimally-parsed line for facilitating binary search. type LocusLine = { contig: string; diff --git a/src/main/pileup.js b/src/main/pileup.js index 3b8d55b0..9e170b29 100644 --- a/src/main/pileup.js +++ b/src/main/pileup.js @@ -16,7 +16,6 @@ import ReferenceDataSource from './sources/ReferenceDataSource'; import BigBedDataSource from './sources/BigBedDataSource'; import VcfDataSource from './sources/VcfDataSource'; import VariantDataSource from './sources/VariantDataSource'; -import GenotypeDataSource from './sources/GenotypeDataSource'; import BamDataSource from './sources/BamDataSource'; import GA4GHDataSource from './sources/GA4GHDataSource'; import CoverageDataSource from './sources/CoverageDataSource'; @@ -132,7 +131,6 @@ var pileup = { ga4gh: GA4GHDataSource.create, vcf: VcfDataSource.create, variants: VariantDataSource.create, - genotypes: GenotypeDataSource.create, features: FeatureDataSource.create, twoBit: TwoBitDataSource.create, reference: ReferenceDataSource.create, diff --git a/src/main/sources/CoverageDataSource.js b/src/main/sources/CoverageDataSource.js index ae44c0b4..7d8151ad 100644 --- a/src/main/sources/CoverageDataSource.js +++ b/src/main/sources/CoverageDataSource.js @@ -77,7 +77,6 @@ function createFromCoverageUrl(remoteSource: RemoteRequest): CoverageDataSource // Cover the range immediately to prevent duplicate fetches. cache.coverRange(interval); - var numRequests = 1; o.trigger('networkprogress', newRanges.length); return Q.all(newRanges.map(range => remoteSource.getFeaturesInRange(range, endpointModifier).then(json => { diff --git a/src/main/sources/GenotypeDataSource.js b/src/main/sources/GenotypeDataSource.js deleted file mode 100644 index d9f85f1d..00000000 --- a/src/main/sources/GenotypeDataSource.js +++ /dev/null @@ -1,122 +0,0 @@ -/** - * The "glue" between TwoBit.js and GenomeTrack.js. - * - * GenomeTrack is pure view code -- it renders data which is already in-memory - * in the browser. - * - * TwoBit is purely for data parsing and fetching. It only knows how to return - * promises for various genome features. - * - * This code acts as a bridge between the two. It maintains a local version of - * the data, fetching remote data and informing the view when it becomes - * available. - * - * @flow - */ -'use strict'; - -import type {Genotype} from '../data/GenotypeEndpoint'; - -import Q from 'q'; -import _ from 'underscore'; -import {Events} from 'backbone'; - -import ContigInterval from '../ContigInterval'; -import {RemoteRequest} from '../RemoteRequest'; -import GenotypeEndpoint from '../data/GenotypeEndpoint'; - -export type GenotypeDataSource = { - rangeChanged: (newRange: GenomeRange) => void; - getFeaturesInRange: (range: ContigInterval) => Genotype[]; - on: (event: string, handler: Function) => void; - off: (event: string) => void; - trigger: (event: string, ...args:any) => void; -}; - - -// Requests for 2bit ranges are expanded to begin & end at multiples of this -// constant. Doing this means that panning typically won't require -// additional network requests. -var BASE_PAIRS_PER_FETCH = 1000; - -function expandRange(range: ContigInterval) { - var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; - var newStart = Math.max(1, roundDown(range.start())), - newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); - - return new ContigInterval(range.contig, newStart, newStop); -} - -function genotypeKey(v: Genotype): string { - return `${v.variant.contig}:${v.variant.position}`; -} - - -function createFromGenotypeUrl(remoteSource: GenotypeEndpoint): GenotypeDataSource { - var genotypes: {[key: string]: Genotype} = {}; - - // Ranges for which we have complete information -- no need to hit network. - var coveredRanges: ContigInterval[] = []; - - function addGenotype(v: Genotype) { - var key = genotypeKey(v); - if (!genotypes[key]) { - genotypes[key] = v; - } - } - - function fetch(range: GenomeRange) { - var interval = new ContigInterval(range.contig, range.start, range.stop); - - // Check if this interval is already in the cache. - if (interval.isCoveredBy(coveredRanges)) { - return Q.when(); - } - - interval = expandRange(interval); - - // "Cover" the range immediately to prevent duplicate fetches. - coveredRanges.push(interval); - coveredRanges = ContigInterval.coalesce(coveredRanges); - return remoteSource.getFeaturesInRange(interval).then(genotypes => { - if (genotypes !== null) - genotypes.forEach(genotype => addGenotype(genotype)); - o.trigger('newdata', interval); - }); - } - - function getFeaturesInRange(range: ContigInterval): Genotype[] { - if (!range) return []; // XXX why would this happen? - return _.filter(genotypes, v => range.chrContainsLocus(v.variant.contig, v.variant.position)); - } - - var o = { - rangeChanged: function(newRange: GenomeRange) { - fetch(newRange).done(); - }, - getFeaturesInRange, - - // These are here to make Flow happy. - on: () => {}, - off: () => {}, - trigger: () => {} - }; - _.extend(o, Events); // Make this an event emitter - - return o; -} - -function create(data: {url?:string}): GenotypeDataSource { - if (!data.url) { - throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); - } - var request = new RemoteRequest(data.url); - var endpoint = new GenotypeEndpoint(request); - return createFromGenotypeUrl(endpoint); -} - - -module.exports = { - create, - createFromGenotypeUrl -}; diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index 214ef16c..1850a900 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -15,7 +15,7 @@ */ 'use strict'; -import type {Variant} from '../data/vcf'; +import type {Variant, VariantContext} from '../data/vcf'; import Q from 'q'; import _ from 'underscore'; @@ -25,7 +25,6 @@ import {ResolutionCache} from '../ResolutionCache'; import ContigInterval from '../ContigInterval'; import type {VcfDataSource} from './VcfDataSource'; import {RemoteRequest} from '../RemoteRequest'; -import VariantEndpoint from '../data/VariantEndpoint'; var BASE_PAIRS_PER_FETCH = 10000; @@ -37,16 +36,18 @@ function expandRange(range: ContigInterval) { return new ContigInterval(range.contig, newStart, newStop); } -function keyFunction(v: Variant): string { - return `${v.contig}:${v.position}`; +function keyFunction(vc: VariantContext): string { + return `${vc.variant.contig}:${vc.variant.position}`; } -function filterFunction(range: ContigInterval, v: Variant): boolean { - return range.chrContainsLocus(v.contig, v.position); +function filterFunction(range: ContigInterval, vc: VariantContext): boolean { + return range.chrContainsLocus(vc.variant.contig, vc.variant.position); } -function createFromVariantUrl(remoteSource: RemoteRequest): VcfDataSource { - var cache: ResolutionCache = +function createFromVariantUrl(remoteSource: RemoteRequest, + samples?: string[]): VcfDataSource { + + var cache: ResolutionCache = new ResolutionCache(filterFunction, keyFunction); function fetch(range: GenomeRange) { @@ -73,26 +74,46 @@ function createFromVariantUrl(remoteSource: RemoteRequest): VcfDataSource { o.trigger('networkprogress', newRanges.length); return Q.all(newRanges.map(range => remoteSource.getFeaturesInRange(range, endpointModifier).then(e => { - var variants = e.response; - if (variants !== null) + var response = e.response; + if (response !== null) { + // parse VariantContexts + var variants = _.map(response, v => JSON.parse(v)); variants.forEach(v => cache.put(v, resolution)); + } o.trigger('networkdone'); o.trigger('newdata', interval); }))); } - function getFeaturesInRange(range: ContigInterval, resolution: ?number): Variant[] { + function getVariantsInRange(range: ContigInterval, resolution: ?number): Variant[] { if (!range) return []; // XXX why would this happen? var data = cache.get(range, resolution); - var sorted = data.sort((a, b) => a.position - b.position); + var sorted = data.sort((a, b) => a.variant.position - b.variant.position); + return _.map(sorted, s => s.variant); + } + + function getGenotypesInRange(range: ContigInterval, resolution: ?number): VariantContext[] { + if (!range || !samples) return []; // if no samples are specified + var data = cache.get(range, resolution); + var sorted = data.sort((a, b) => a.variant.position - b.variant.position); return sorted; } + function getSamples(): string[] { + if (!samples) { + throw new Error("No samples for genotypes"); + } else { + return samples; + } + } + var o = { rangeChanged: function(newRange: GenomeRange) { fetch(newRange).done(); }, - getFeaturesInRange, + getVariantsInRange, + getGenotypesInRange, + getSamples, // These are here to make Flow happy. on: () => {}, @@ -104,12 +125,15 @@ function createFromVariantUrl(remoteSource: RemoteRequest): VcfDataSource { return o; } -function create(data: {url?:string}): VcfDataSource { +function create(data: {url?:string, samples?:string[]}): VcfDataSource { if (!data.url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } + if (!data.samples) { + console.log("no genotype samples provided"); + } var endpoint = new RemoteRequest(data.url, BASE_PAIRS_PER_FETCH); - return createFromVariantUrl(endpoint); + return createFromVariantUrl(endpoint, data.samples); } diff --git a/src/main/sources/VcfDataSource.js b/src/main/sources/VcfDataSource.js index a8329361..39c10fc1 100644 --- a/src/main/sources/VcfDataSource.js +++ b/src/main/sources/VcfDataSource.js @@ -5,7 +5,7 @@ */ 'use strict'; -import type {Variant} from '../data/vcf'; +import type {Variant, VariantContext} from '../data/vcf'; import Events from 'backbone'; import _ from 'underscore'; @@ -18,7 +18,9 @@ import VcfFile from '../data/vcf'; export type VcfDataSource = { rangeChanged: (newRange: GenomeRange) => void; - getFeaturesInRange: (range: ContigInterval) => Variant[]; + getVariantsInRange: (range: ContigInterval) => Variant[]; + getGenotypesInRange: (range: ContigInterval) => VariantContext[]; + getSamples: () => string[]; on: (event: string, handler: Function) => void; off: (event: string) => void; trigger: (event: string, ...args:any) => void; @@ -71,16 +73,26 @@ function createFromVcfFile(remoteSource: VcfFile): VcfDataSource { }); } - function getFeaturesInRange(range: ContigInterval): Variant[] { + function getVariantsInRange(range: ContigInterval): Variant[] { if (!range) return []; // XXX why would this happen? return _.filter(variants, v => range.chrContainsLocus(v.contig, v.position)); } + function getGenotypesInRange(range: ContigInterval): VariantContext[] { + throw new Error(`Function getGenotypesInRange not implemented`); + } + + function getSamples(): string[] { + throw new Error(`Function getSamples not implemented`); + } + var o = { rangeChanged: function(newRange: GenomeRange) { fetch(newRange).done(); }, - getFeaturesInRange, + getVariantsInRange, + getGenotypesInRange, + getSamples, // These are here to make Flow happy. on: () => {}, diff --git a/src/main/style.js b/src/main/style.js index a2488dad..13f353ec 100644 --- a/src/main/style.js +++ b/src/main/style.js @@ -65,6 +65,7 @@ module.exports = { // Genotype Track GENOTYPE_SPACING: 1, - GENOTYPE_FILL: '#9494b8', GENOTYPE_HEIGHT: 10, + GENOTYPE_FILL: '#999999', + BACKGROUND_FILL: '#f2f2f2', }; diff --git a/src/main/viz/FeatureTrack.js b/src/main/viz/FeatureTrack.js index 1b46facf..f29d20c4 100644 --- a/src/main/viz/FeatureTrack.js +++ b/src/main/viz/FeatureTrack.js @@ -149,7 +149,7 @@ class FeatureTrack extends React.Component { componentDidUpdate(prevProps: any, prevState: any) { if (!shallowEquals(this.props, prevProps) || !shallowEquals(this.state, prevState)) { - this.tiles.update(this.props.height, this.props.options); + this.tiles.update(this.props.options); this.tiles.invalidateAll(); this.updateVisualization(); } diff --git a/src/main/viz/GenotypeTrack.js b/src/main/viz/GenotypeTrack.js index 310312ea..7fc3811a 100644 --- a/src/main/viz/GenotypeTrack.js +++ b/src/main/viz/GenotypeTrack.js @@ -4,132 +4,290 @@ */ 'use strict'; -import type {GenotypeDataSource} from '../sources/GenotypeDataSource'; -import type {Genotype} from '../data/GenotypeEndpoint'; +import type {VcfDataSource} from '../sources/VcfDataSource'; +import type {VariantContext} from '../data/vcf'; import type {DataCanvasRenderingContext2D} from 'data-canvas'; import type {VizProps} from '../VisualizationWrapper'; import type {Scale} from './d3utils'; import React from 'react'; -import ReactDOM from 'react-dom'; +import _ from 'underscore'; + import d3utils from './d3utils'; import shallowEquals from 'shallow-equals'; import ContigInterval from '../ContigInterval'; import canvasUtils from './canvas-utils'; +import TiledCanvas from './TiledCanvas'; import dataCanvas from 'data-canvas'; import style from '../style'; +import utils from '../utils'; +import type {State, NetworkStatus} from './pileuputils'; + +var MONSTER_REQUEST = 10000; +var LABEL_WIDTH = 100; + +class GenotypeTiledCanvas extends TiledCanvas { + options: Object; + source: VcfDataSource; + sampleIds: string[]; + + constructor(source: VcfDataSource, sampleIds: string[], options: Object) { + super(); + this.source = source; + this.options = options; + this.sampleIds = sampleIds; + } + + update(newOptions: Object) { + this.options = newOptions; + } + + heightForRef(ref: string): number { + return yForRow(this.sampleIds.length); + } + + render(ctx: DataCanvasRenderingContext2D, + scale: (x: number)=>number, + range: ContigInterval, + originalRange: ?ContigInterval, + resolution: ?number) { + var relaxedRange = + new ContigInterval(range.contig, range.start() - 1, range.stop() + 1); + + // relaxed range is just for this tile. make sure to get resolution for whole + // viewing area + var vGenotypes = this.source.getGenotypesInRange(relaxedRange, resolution); + renderGenotypes(ctx, scale, relaxedRange, vGenotypes, this.sampleIds); + } +} +// Draw genotypes +function renderGenotypes(ctx: DataCanvasRenderingContext2D, + scale: (num: number) => number, + range: ContigInterval, + genotypes: VariantContext[], + sampleIds) { + // draw genotypes + genotypes.forEach(genotype => { + var variant = genotype.variant; + var keys = genotype.sampleIds; + ctx.pushObject(variant); + ctx.fillStyle = style.GENOTYPE_FILL; + ctx.strokeStyle = style.GENOTYPE_FILL; + var x = Math.round(scale(variant.position)); + var width = Math.round(scale(variant.end)) - x; + keys.forEach(sampleId => { + var y = yForRow(sampleIds.indexOf(sampleId)); + ctx.fillRect(x - 0.2, y, width, style.GENOTYPE_HEIGHT); + ctx.strokeRect(x - 0.2, y, width, style.GENOTYPE_HEIGHT); + }); + ctx.popObject(); + }); +} function yForRow(row) { return row * (style.GENOTYPE_HEIGHT + style.GENOTYPE_SPACING); } class GenotypeTrack extends React.Component { - props: VizProps & {source: GenotypeDataSource}; - state: void; // no state + props: VizProps & {source: VcfDataSource}; + state: State; + tiles: GenotypeTiledCanvas; + sampleIds: string[]; constructor(props: Object) { super(props); + this.state = { + networkStatus: null + }; + this.sampleIds = props.source.getSamples(); } render(): any { - return ; + // These styles allow vertical scrolling to see the full pileup. + // Adding a vertical scrollbar shrinks the visible area, but we have to act + // as though it doesn't, since adjusting the scale would put it out of sync + // with other tracks. + var containerStyles = { + 'height': '100%' + }; + + var labelStyles = { + 'float': 'left', + 'overflow': 'hidden', + 'width:': `${ LABEL_WIDTH }px` + }; + + var canvasStyles = { + 'overflow': 'hidden' + }; + + var statusEl = null, + networkStatus = this.state.networkStatus; + if (networkStatus) { + statusEl = ( +
+
+ Loading Genotypes… +
+
+ ); + } + var rangeLength = this.props.range.stop - this.props.range.start; + // If range is too large, do not render 'canvas' + if (rangeLength >= MONSTER_REQUEST) { + return ( +
+
+ Zoom in to see genotypes +
+ +
+ ); + } else { + return ( +
+ {statusEl} +
+
+
+
+
+ ); + } } componentDidMount() { - this.updateVisualization(); + this.tiles = new GenotypeTiledCanvas(this.props.source, + this.sampleIds, this.props.options); - this.props.source.on('newdata', () => { - this.updateVisualization(); - }); + // Visualize new data as it comes in from the network. + this.props.source.on('newdata', (range) => { + this.tiles.invalidateRange(range); + this.updateVisualization(); + }); + this.props.source.on('networkprogress', e => { + this.setState({networkStatus: e}); + }); + this.props.source.on('networkdone', e => { + this.setState({networkStatus: null}); + }); + + this.updateVisualization(); } getScale(): Scale { - return d3utils.getTrackScale(this.props.range, this.props.width); + return d3utils.getTrackScale(this.props.range, this.props.width - LABEL_WIDTH); } componentDidUpdate(prevProps: any, prevState: any) { if (!shallowEquals(prevProps, this.props) || !shallowEquals(prevState, this.state)) { - this.updateVisualization(); + this.tiles.update(this.props.options); + this.tiles.invalidateAll(); + this.updateVisualization(); } } - updateVisualization() { - var canvas = ReactDOM.findDOMNode(this), + // draws genotype lines to visually separate genotype rows + drawLines(ctx: DataCanvasRenderingContext2D) { + var width = this.props.width; + + // draw background for each row + if (this.sampleIds !== null) { + ctx.font = "9px Arial"; + this.sampleIds.forEach(sampleId => { + ctx.pushObject(sampleId); + var y = yForRow(this.sampleIds.indexOf(sampleId)); + ctx.fillStyle = style.BACKGROUND_FILL; + ctx.fillRect(0, y, width, style.GENOTYPE_HEIGHT); + ctx.popObject(); + }); + } + } + + // draws sample names on side bar. This needs to be only rendered once. + drawLabels() { + // if already drawn, return + var labelCanvas = (this.refs.labelCanvas : HTMLCanvasElement), width = this.props.width; // Hold off until height & width are known. - if (width === 0) return; + if (width === 0 || typeof labelCanvas == 'undefined') return; - var ctx = canvasUtils.getContext(canvas); - var dtx = dataCanvas.getDataContext(ctx); - this.renderScene(dtx); - } + var height = yForRow(this.sampleIds.length); - renderScene(ctx: DataCanvasRenderingContext2D) { - var range = this.props.range, - interval = new ContigInterval(range.contig, range.start, range.stop), - genotypes = this.props.source.getFeaturesInRange(interval), - scale = this.getScale(), - sampleIds = []; - // add all samples to array of sample Ids - genotypes.forEach(genotype => { - var ids = genotype.sampleIds; - for (var i = 0; i < ids.length; i++) { - var id = ids[i]; - if (sampleIds.indexOf(id) < 0) { - sampleIds.push(id); - } + // only render once on load. + if (labelCanvas.clientHeight != height) { + var labelCtx = dataCanvas.getDataContext(canvasUtils.getContext(labelCanvas)); + d3utils.sizeCanvas(labelCanvas, LABEL_WIDTH, height); + + // draw label for each row + if (this.sampleIds !== null) { + labelCtx.font = "9px Arial"; + this.sampleIds.forEach(sampleId => { + labelCtx.pushObject(sampleId); + var y = yForRow(this.sampleIds.indexOf(sampleId)); + labelCtx.fillStyle = "black"; + labelCtx.fillText(sampleId, 0, y+style.GENOTYPE_HEIGHT); + labelCtx.popObject(); + }); } - }); - sampleIds = sampleIds.sort(); // sort sample ids + } + } - // Height can only be computed after the genotypes has been updated. - var newHeight = yForRow(sampleIds.length); - var canvas = ReactDOM.findDOMNode(this), + updateVisualization() { + var canvas = (this.refs.canvas : HTMLCanvasElement), width = this.props.width; - d3utils.sizeCanvas(canvas, width, newHeight); - // This is a hack to adjust parent div for resize - var el = d3utils.findParent(canvas, 'track-content'); - console.log("el", el); - // if (el) el.style.height = newHeight; + // Hold off until height & width are known. + if (width === 0 || typeof canvas == 'undefined') return; + + var height = yForRow(this.sampleIds.length); + d3utils.sizeCanvas(canvas, width - LABEL_WIDTH, height); + + var ctx = dataCanvas.getDataContext(canvasUtils.getContext(canvas)); + this.drawLabels(); + this.renderScene(ctx); + } + + renderScene(ctx: DataCanvasRenderingContext2D) { + var range = this.props.range, + interval = new ContigInterval(range.contig, range.start, range.stop), + scale = this.getScale(); - ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); ctx.reset(); - ctx.save(); + ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); - ctx.fillStyle = style.GENOTYPE_FILL; - genotypes.forEach(genotype => { - var variant = genotype.variant; - var keys = genotype.sampleIds; - ctx.pushObject(variant); - var x = Math.round(scale(variant.position)); - var width = Math.round(scale(variant.position + 1)) - 1 - x; - keys.forEach(sampleId => { - var y = yForRow(sampleIds.indexOf(sampleId)); - ctx.fillRect(x - 0.5, y - 0.5, width, style.GENOTYPE_HEIGHT); - }); - ctx.popObject(); - }); + // render lines after rectangle has been cleared + this.drawLines(ctx); + this.tiles.renderToScreen(ctx, interval, scale); ctx.restore(); } handleClick(reactEvent: any) { var ev = reactEvent.nativeEvent, - x = ev.offsetX, - y = ev.offsetY, - canvas = ReactDOM.findDOMNode(this), - ctx = canvasUtils.getContext(canvas), - trackingCtx = new dataCanvas.ClickTrackingContext(ctx, x, y); - this.renderScene(trackingCtx); - var genotype = trackingCtx.hit && trackingCtx.hit[0]; + x = ev.offsetX; + + var genomeRange = this.props.range, + // allow some buffering so click isn't so sensitive + range = new ContigInterval(genomeRange.contig, genomeRange.start-1, genomeRange.stop+1), + scale = this.getScale(), + // leave padding of 2px to reduce click specificity + clickStart = Math.floor(scale.invert(x)) - 2, + clickEnd = clickStart + 2, + // If click-tracking gets slow, this range could be narrowed to one + // closer to the click coordinate, rather than the whole visible range. + vGenotypes = this.props.source.getGenotypesInRange(range, 1); + + var genotype = _.find(vGenotypes, f => utils.tupleRangeOverlaps([[f.variant.position], [f.variant.end]], [[clickStart], [clickEnd]])); var alert = window.alert || console.log; if (genotype) { - alert(JSON.stringify(genotype)); + var variantString = `variant: ${JSON.stringify(genotype.variant)}`; + var samples = `samples with variant: ${JSON.stringify(genotype.sampleIds)}`; + alert(`${variantString}\n${samples}`); } } } diff --git a/src/main/viz/VariantTrack.js b/src/main/viz/VariantTrack.js index e46fde7f..a08d8dd4 100644 --- a/src/main/viz/VariantTrack.js +++ b/src/main/viz/VariantTrack.js @@ -11,11 +11,9 @@ import type {VizProps} from '../VisualizationWrapper'; import type {Scale} from './d3utils'; import React from 'react'; -import ReactDOM from 'react-dom'; import _ from 'underscore'; import d3utils from './d3utils'; -import RemoteRequest from '../RemoteRequest'; import shallowEquals from 'shallow-equals'; import ContigInterval from '../ContigInterval'; import canvasUtils from './canvas-utils'; @@ -56,7 +54,7 @@ class VariantTiledCanvas extends TiledCanvas { // relaxed range is just for this tile. make sure to get resolution for whole // viewing area - var vVariants = this.source.getFeaturesInRange(relaxedRange, resolution); + var vVariants = this.source.getVariantsInRange(relaxedRange, resolution); renderVariants(ctx, scale, relaxedRange, vVariants); } } @@ -133,7 +131,7 @@ class VariantTrack extends React.Component { componentDidMount() { this.tiles = new VariantTiledCanvas(this.props.source, this.props.options); - // Visualize ne data as it comes in from the network. + // Visualize new data as it comes in from the network. this.props.source.on('newdata', (range) => { this.tiles.invalidateRange(range); this.updateVisualization(); @@ -155,7 +153,7 @@ class VariantTrack extends React.Component { componentDidUpdate(prevProps: any, prevState: any) { if (!shallowEquals(prevProps, this.props) || !shallowEquals(prevState, this.state)) { - this.tiles.update(this.props.height, this.props.options); + this.tiles.update(this.props.options); this.tiles.invalidateAll(); this.updateVisualization(); } @@ -166,7 +164,7 @@ class VariantTrack extends React.Component { {width, height} = this.props; // Hold off until height & width are known. - if (width === 0) return; + if (width === 0|| typeof canvas == 'undefined') return; d3utils.sizeCanvas(canvas, width, height); var ctx = dataCanvas.getDataContext(canvasUtils.getContext(canvas)); @@ -177,8 +175,6 @@ class VariantTrack extends React.Component { var range = this.props.range, interval = new ContigInterval(range.contig, range.start, range.stop), scale = this.getScale(); - // height = this.props.height, - // y = height - style.VARIANT_HEIGHT - 1; ctx.reset(); ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height); @@ -199,7 +195,7 @@ class VariantTrack extends React.Component { clickEnd = clickStart + 2, // If click-tracking gets slow, this range could be narrowed to one // closer to the click coordinate, rather than the whole visible range. - vVariants = this.props.source.getFeaturesInRange(range); + vVariants = this.props.source.getVariantsInRange(range); var variant = _.find(vVariants, f => utils.tupleRangeOverlaps([[f.position], [f.end]], [[clickStart], [clickEnd]])); var alert = window.alert || console.log; diff --git a/src/test/sources/GenotypeDataSource-test.js b/src/test/sources/GenotypeDataSource-test.js deleted file mode 100644 index 2854f87c..00000000 --- a/src/test/sources/GenotypeDataSource-test.js +++ /dev/null @@ -1,77 +0,0 @@ -/* @flow */ -'use strict'; - - -import {expect} from 'chai'; - -import sinon from 'sinon'; - -import GenotypeDataSource from '../../main/sources/GenotypeDataSource'; -import ContigInterval from '../../main/ContigInterval'; -import RemoteFile from '../../main/RemoteFile'; - -describe('GenotypeDataSource', function() { - var server: any = null, response; - - before(function () { - return new RemoteFile('/test-data/genotypes-chrM-0-100.json').getAllString().then(data => { - response = data; - server = sinon.fakeServer.create(); - server.respondWith('GET', '/genotypes/chrM?start=1&end=1000',[200, { "Content-Type": "application/json" }, response]); - server.respondWith('GET', '/genotypes/chrM?start=1000&end=2000',[200, { "Content-Type": "application/json" }, response]); - }); - }); - - after(function () { - server.restore(); - }); - - function getTestSource() { - var source = GenotypeDataSource.create({ - url: '/genotypes' - }); - return source; - } - - it('should extract features in a range', function(done) { - var source = getTestSource(); - var range = new ContigInterval('chrM', 0, 25); - // No genotypes are cached yet. - var genotypes = source.getFeaturesInRange(range); - expect(genotypes).to.deep.equal([]); - - source.on('newdata', () => { - var genotypes = source.getFeaturesInRange(range); - expect(genotypes).to.have.length(2); - expect(genotypes[1].sampleIds).to.contain('sample1'); - expect(genotypes[1].variant.contig).to.equal('chrM'); - expect(genotypes[1].variant.position).to.equal(20); - expect(genotypes[1].variant.ref).to.equal('G'); - expect(genotypes[1].variant.alt).to.equal('T'); - done(); - }); - source.rangeChanged({ - contig: range.contig, - start: range.start(), - stop: range.stop() - }); - server.respond(); - }); - - it('should not fail when no genotypes are available', function(done) { - var source = getTestSource(); - var range = new ContigInterval('chrM', 1000, 1025); - - source.on('newdata', () => { - var genotypes = source.getFeaturesInRange(range); - expect(genotypes).to.have.length(0); - done(); - }); - source.rangeChanged({ - contig: range.contig, - start: range.start(), - stop: range.stop() - }); - server.respond(); - }); -}); diff --git a/src/test/sources/VariantDataSource-test.js b/src/test/sources/VariantDataSource-test.js index 9ee2a7ed..27a7b740 100644 --- a/src/test/sources/VariantDataSource-test.js +++ b/src/test/sources/VariantDataSource-test.js @@ -17,7 +17,7 @@ describe('VariantDataSource', function() { return new RemoteFile('/test-data/variants-chrM-0-100.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); - server.respondWith('GET', '/variants/chrM?start=1&end=1000',[200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/variants/chrM?start=1&end=10000&binning=1',[200, { "Content-Type": "application/json" }, response]); server.respondWith('GET', '/variants/chrM?start=1000&end=2000',[200, { "Content-Type": "application/json" }, '']); }); }); @@ -28,7 +28,8 @@ describe('VariantDataSource', function() { function getTestSource() { var source = VariantDataSource.create({ - url: '/variants' + url: '/variants', + samples: ["sample1", "sample2", "sample3"] }); return source; } @@ -36,11 +37,11 @@ describe('VariantDataSource', function() { var source = getTestSource(); var range = new ContigInterval('chrM', 0, 50); // No variants are cached yet. - var variants = source.getFeaturesInRange(range); + var variants = source.getVariantsInRange(range); expect(variants).to.deep.equal([]); source.on('newdata', () => { - var variants = source.getFeaturesInRange(range); + var variants = source.getVariantsInRange(range); expect(variants).to.have.length(3); expect(variants[1].contig).to.equal('chrM'); expect(variants[1].position).to.equal(20); @@ -61,7 +62,7 @@ describe('VariantDataSource', function() { var range = new ContigInterval('chrM', 1050, 1150); source.on('newdata', () => { - var variants = source.getFeaturesInRange(range); + var variants = source.getVariantsInRange(range); expect(variants).to.deep.equal([]); done(); }); diff --git a/src/test/sources/VcfDataSource-test.js b/src/test/sources/VcfDataSource-test.js index ea6b0559..2251e066 100644 --- a/src/test/sources/VcfDataSource-test.js +++ b/src/test/sources/VcfDataSource-test.js @@ -19,11 +19,11 @@ describe('VcfDataSource', function() { var range = new ContigInterval('20', 63799, 69094); // No variants are cached yet. - var variants = source.getFeaturesInRange(range); + var variants = source.getVariantsInRange(range); expect(variants).to.deep.equal([]); source.on('newdata', () => { - var variants = source.getFeaturesInRange(range); + var variants = source.getVariantsInRange(range); expect(variants).to.have.length(6); expect(variants[0].contig).to.equal('20'); expect(variants[0].position).to.equal(63799); diff --git a/src/test/viz/GenotypeTrack-test.js b/src/test/viz/GenotypeTrack-test.js index b43f934a..23db3768 100644 --- a/src/test/viz/GenotypeTrack-test.js +++ b/src/test/viz/GenotypeTrack-test.js @@ -59,7 +59,7 @@ describe('GenotypeTrack', function() { isReference: true }, { - data: pileup.formats.genotypes({ + data: pileup.formats.variants({ url: '/test-data/genotypes-17.json' }), viz: pileup.viz.genotypes(), @@ -74,8 +74,6 @@ describe('GenotypeTrack', function() { expect(genotypes).to.have.length(3); expect(genotypes.map(g => g.variant.position)).to.deep.equal( [10, 20, 30]); - expect(genotypes.map(g => g.sampleIds)).to.deep.equal( - [sampleIds, sampleIds, sampleIds]); p.destroy(); }); diff --git a/style/pileup.css b/style/pileup.css index 8e91c34c..64110d54 100644 --- a/style/pileup.css +++ b/style/pileup.css @@ -18,6 +18,10 @@ .pileup-root text, .track-label { font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; } +/* hack to hide track label for genotypes */ +.genotypes > .track-label { + display: none; +} .track-label { flex: 0 0 100px; /* fixed-width track labels */ text-align: right; @@ -177,7 +181,7 @@ } /* pileup track */ -.pileup-root > .pileup { +.pileup-root > .pileup, .pileup-root > .genotypes { flex: 1; /* stretch to fill remaining space */ } .pileup .alignment .match { diff --git a/test-data/variants-chrM-0-100.json b/test-data/variants-chrM-0-100.json index 44598dae..3293a56e 100644 --- a/test-data/variants-chrM-0-100.json +++ b/test-data/variants-chrM-0-100.json @@ -1,16 +1,23 @@ [{ - "contig": "chrM", - "position": 10, - "ref": "C", - "alt": "G" + "variant" : { + "contig": "chrM", + "position": 10, + "ref": "C", + "alt": "G" + }, "sampleIds": \["sample1", "sample2", "sample3"\] }, { - "contig": "chrM", - "position": 20, - "ref": "G", - "alt": "T" + "variant" : { + "contig": "chrM", + "position": 20, + "ref": "G", + "alt": "T" + }, "sampleIds": ["sample1", "sample3"] }, { - "contig": "chrM", - "position": 23, - "ref": "A", - "alt": "C" + "variant" : { + "contig": "chrM", + "position": 23, + "ref": "A", + "alt": "C" + }, "sampleIds": ["sample1"] }] +["{\"variant\":{\"contig\":\"chrM\",\"position\":10,\"end\":11,\"ref\":\"C\",\"alt\":\"G\"},\"sampleIds\":[\"s1\",\"s2\",\"s3\"]}","{\"variant\":{\"contig\":\"chrM\",\"position\":20,\"end\":21,\"ref\":\"G\",\"alt\":\"T\"},\"sampleIds\":[\"s1\",\"s3\"]}","{\"variant\":{\"contig\":\"chrM\",\"position\":23,\"end\":24,\"ref\":\"A\",\"alt\":\"C\"},\"sampleIds\":[\"s1\",\"s3\"]}"] From f1840853b2f7cdec71348e5128ac30658fe1f62c Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Fri, 27 Jan 2017 14:22:09 -0800 Subject: [PATCH 132/136] binning for features --- src/main/data/FeatureEndpoint.js | 35 --------------- src/main/sources/FeatureDataSource.js | 61 +++++++++++++++------------ src/main/sources/VariantDataSource.js | 1 - src/main/viz/FeatureTrack.js | 6 ++- 4 files changed, 39 insertions(+), 64 deletions(-) delete mode 100644 src/main/data/FeatureEndpoint.js diff --git a/src/main/data/FeatureEndpoint.js b/src/main/data/FeatureEndpoint.js deleted file mode 100644 index 230e8698..00000000 --- a/src/main/data/FeatureEndpoint.js +++ /dev/null @@ -1,35 +0,0 @@ -/** - * This module defines a parser for the 2bit file format. - * See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 - * @flow - */ -'use strict'; - -import Q from 'q'; -import ContigInterval from '../ContigInterval'; -import type {RemoteRequest} from '../RemoteRequest'; - -export type Feature = { - id: string; - featureType: string; - contig: string; - start: number; - stop: number; - score: number; -} - -class FeatureEndpoint { - remoteRequest: RemoteRequest; - - constructor(remoteRequest: RemoteRequest) { - this.remoteRequest = remoteRequest; - } - - getFeaturesInRange(range: ContigInterval): Q.Promise { - return this.remoteRequest.get(range).then(object => { - return object; - }); - } -} - -module.exports = FeatureEndpoint; diff --git a/src/main/sources/FeatureDataSource.js b/src/main/sources/FeatureDataSource.js index db0caa9c..9c96858a 100644 --- a/src/main/sources/FeatureDataSource.js +++ b/src/main/sources/FeatureDataSource.js @@ -18,11 +18,19 @@ import Q from 'q'; import _ from 'underscore'; import {Events} from 'backbone'; +import {ResolutionCache} from '../ResolutionCache'; import ContigInterval from '../ContigInterval'; import {RemoteRequest} from '../RemoteRequest'; -import FeatureEndpoint from '../data/FeatureEndpoint'; -import type {Feature} from '../data/FeatureEndpoint'; + +export type Feature = { + id: string; + featureType: string; + contig: string; + start: number; + stop: number; + score: number; +} // Flow type for export. export type FeatureDataSource = { @@ -47,54 +55,56 @@ function expandRange(range: ContigInterval): ContigInterval { return new ContigInterval(range.contig, newStart, newStop); } -function featureKey(f: Feature): string { +function keyFunction(f: Feature): string { return `${f.contig}:${f.start}`; } +function filterFunction(range: ContigInterval, f: Feature): boolean { + return range.chrIntersects(new ContigInterval(f.contig, f.start, f.stop)); +} -function createFromFeatureUrl(remoteSource: FeatureEndpoint): FeatureDataSource { - var features: {[key: string]: Feature} = {}; - - // Ranges for which we have complete information -- no need to hit network. - var coveredRanges: ContigInterval[] = []; - function addFeature(f: Feature) { - var key = featureKey(f); - if (!features[key]) { - features[key] = f; - } - } +function createFromFeatureUrl(remoteSource: RemoteRequest): FeatureDataSource { + var cache: ResolutionCache = + new ResolutionCache(filterFunction, keyFunction); function fetch(range: GenomeRange) { var interval = new ContigInterval(range.contig, range.start, range.stop); // Check if this interval is already in the cache. - if (interval.isCoveredBy(coveredRanges)) { + if (cache.coversRange(interval)) { return Q.when(); } + // modify endpoint to calculate coverage using binning + var resolution = ResolutionCache.getResolution(interval.interval); + var endpointModifier = `binning=${resolution}`; + interval = expandRange(interval); - var newRanges = interval.complementIntervals(coveredRanges); - coveredRanges.push(interval); - coveredRanges = ContigInterval.coalesce(coveredRanges); + var newRanges = cache.complementInterval(interval, resolution); + + // "Cover" the range immediately to prevent duplicate fetches. + // Because interval is expanded, make sure to use original resolution + cache.coverRange(interval, resolution); - o.trigger('networkprogress', 1); + o.trigger('networkprogress', newRanges.length); return Q.all(newRanges.map(range => - remoteSource.getFeaturesInRange(range) + remoteSource.getFeaturesInRange(range, endpointModifier) .then(e => { var features = e.response; if (features !== null) { - features.forEach(feature => addFeature(feature)); + features.forEach(feature => cache.put(feature, resolution)); } o.trigger('networkdone'); o.trigger('newdata', range); }))); } - function getFeaturesInRange(range: ContigInterval): Feature[] { + function getFeaturesInRange(range: ContigInterval, resolution: ?number): Feature[] { if (!range) return []; // XXX why would this happen? - var x = _.filter(features, f => range.chrContainsLocus(f.contig, f.start)); - return x; + var data = cache.get(range, resolution); + var sorted = data.sort((a, b) => a.start - b.start); + return sorted; } var o = { @@ -117,8 +127,7 @@ function create(data: {url?:string}): FeatureDataSource { if (!data.url) { throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); } - var request = new RemoteRequest(data.url); - var endpoint = new FeatureEndpoint(request); + var endpoint = new RemoteRequest(data.url); return createFromFeatureUrl(endpoint); } diff --git a/src/main/sources/VariantDataSource.js b/src/main/sources/VariantDataSource.js index 1850a900..45058770 100644 --- a/src/main/sources/VariantDataSource.js +++ b/src/main/sources/VariantDataSource.js @@ -62,7 +62,6 @@ function createFromVariantUrl(remoteSource: RemoteRequest, var resolution = ResolutionCache.getResolution(interval.interval); var endpointModifier = `binning=${resolution}`; - interval = expandRange(interval); // get all smaller intervals not yet covered in cache diff --git a/src/main/viz/FeatureTrack.js b/src/main/viz/FeatureTrack.js index f29d20c4..d3edd611 100644 --- a/src/main/viz/FeatureTrack.js +++ b/src/main/viz/FeatureTrack.js @@ -46,10 +46,12 @@ class FeatureTiledCanvas extends TiledCanvas { render(ctx: DataCanvasRenderingContext2D, scale: (x: number)=>number, - range: ContigInterval) { + range: ContigInterval, + originalRange: ?ContigInterval, + resolution: ?number) { var relaxedRange = new ContigInterval(range.contig, range.start() - 1, range.stop() + 1); - var vFeatures = this.source.getFeaturesInRange(relaxedRange); + var vFeatures = this.source.getFeaturesInRange(relaxedRange, resolution); renderFeatures(ctx, scale, relaxedRange, vFeatures); } } From 85c6ff1e0c313028c7e23babf18c7712a6aa1593 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Tue, 31 Jan 2017 10:22:41 -0800 Subject: [PATCH 133/136] Fixed error in coverage --- src/main/viz/CoverageTrack.js | 3 +-- src/main/viz/FeatureTrack.js | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/src/main/viz/CoverageTrack.js b/src/main/viz/CoverageTrack.js index f088b191..bff0518c 100644 --- a/src/main/viz/CoverageTrack.js +++ b/src/main/viz/CoverageTrack.js @@ -148,11 +148,10 @@ class CoverageTrack extends React.Component { var statusEl = null, networkStatus = this.state.networkStatus; if (networkStatus) { - var message = formatStatus(networkStatus); statusEl = (
- Loading coverage… ({message}) + Loading coverage…
); diff --git a/src/main/viz/FeatureTrack.js b/src/main/viz/FeatureTrack.js index d3edd611..3bee1588 100644 --- a/src/main/viz/FeatureTrack.js +++ b/src/main/viz/FeatureTrack.js @@ -4,8 +4,7 @@ */ 'use strict'; -import type {FeatureDataSource} from '../sources/FeatureDataSource'; -import type {Feature} from '../data/FeatureEndpoint'; +import type {Feature, FeatureDataSource} from '../sources/FeatureDataSource'; import type {DataCanvasRenderingContext2D} from 'data-canvas'; import type {VizProps} from '../VisualizationWrapper'; From 3172c3e99deb4ed8a7751e21b167f1d33f0437d4 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 22 Feb 2017 09:01:24 -0800 Subject: [PATCH 134/136] Removed unused imports, tests for FeatureDataSource and VariantDataSource now passing --- src/main/ResolutionCache.js | 1 + src/main/data/GeneEndpoint.js | 60 ------------- src/main/data/Sequence.js | 1 + src/main/sources/GeneDataSource.js | 99 ---------------------- src/main/viz/CoverageTrack.js | 1 - src/test/sources/FeatureDataSource-test.js | 8 +- src/test/sources/GeneDataSource-test.js | 55 ------------ src/test/viz/CoverageTrack-test.js | 3 - src/test/viz/GenotypeTrack-test.js | 1 - test-data/features-chrM-1000-1200.json | 4 +- test-data/variants-chrM-0-100.json | 22 ----- 11 files changed, 9 insertions(+), 246 deletions(-) delete mode 100644 src/main/data/GeneEndpoint.js delete mode 100644 src/main/sources/GeneDataSource.js delete mode 100644 src/test/sources/GeneDataSource-test.js diff --git a/src/main/ResolutionCache.js b/src/main/ResolutionCache.js index ae52da52..019bc22e 100644 --- a/src/main/ResolutionCache.js +++ b/src/main/ResolutionCache.js @@ -7,6 +7,7 @@ */ 'use strict'; +/* exported Interval, ContigInterval */ import _ from 'underscore'; import Interval from './Interval'; import ContigInterval from './ContigInterval'; diff --git a/src/main/data/GeneEndpoint.js b/src/main/data/GeneEndpoint.js deleted file mode 100644 index b1ab5f68..00000000 --- a/src/main/data/GeneEndpoint.js +++ /dev/null @@ -1,60 +0,0 @@ -/** - * This module defines a parser for the 2bit file format. - * See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 - * @flow - */ -'use strict'; - -import Q from 'q'; -import type {Gene} from '../sources/BigBedDataSource'; -import {RemoteRequest} from '../RemoteRequest'; -import Interval from '../Interval'; -import ContigInterval from '../../main/ContigInterval'; - -function extractGenes(genes: Object): Gene[] { - var mapped = genes.map(g => extractGene(g)); - return mapped; -} - -function extractGene(f: Object): Gene { - var pos = new ContigInterval(f.position.referenceName, Number(f.position.start), Number(f.position.end)); - // parse out exon intervals - var exons = f.exons - .map(ex => new Interval(ex.region.start, ex.region.end)); - - // parse strand to positive or negative boolean - var strand; - if (f.strand === false) { - strand = "-"; - } else { - strand = "+"; - } - return { - position: pos, - id: f.id, - strand: strand, // either + or - - codingRegion: new Interval(Number(f.codingRegion.start), Number(f.codingRegion.end)), - geneId: f.geneId, - name: f.name, - exons - }; -} - - -class GeneEndpoint { - remoteRequest: RemoteRequest; - - constructor(remoteRequest: RemoteRequest) { - this.remoteRequest = remoteRequest; - } - - getGenesInRange(range: ContigInterval): Q.Promise { - return this.remoteRequest.get(range).then(e => { - var genes = e.response; - var d = extractGenes(genes); - return d; - }); - } -} - -module.exports = GeneEndpoint; diff --git a/src/main/data/Sequence.js b/src/main/data/Sequence.js index 760cb329..c8fd5298 100644 --- a/src/main/data/Sequence.js +++ b/src/main/data/Sequence.js @@ -5,6 +5,7 @@ */ 'use strict'; +/* exported Q, ContigInterval, RemoteRequest */ import Q from 'q'; import ContigInterval from '../ContigInterval'; import {RemoteRequest} from '../RemoteRequest'; diff --git a/src/main/sources/GeneDataSource.js b/src/main/sources/GeneDataSource.js deleted file mode 100644 index f19149f1..00000000 --- a/src/main/sources/GeneDataSource.js +++ /dev/null @@ -1,99 +0,0 @@ -/* @flow */ -'use strict'; - -import type {Strand} from '../Alignment'; - -import _ from 'underscore'; -import Q from 'q'; -import {Events} from 'backbone'; - -import ContigInterval from '../ContigInterval'; -import Interval from '../Interval'; -import type { BigBedSource, Gene } from './BigBedDataSource'; -import {RemoteRequest} from '../RemoteRequest'; -import GeneEndpoint from '../data/GeneEndpoint'; - -var BASE_PAIRS_PER_FETCH = 5000; - -function expandRange(range: ContigInterval) { - var roundDown = x => x - x % BASE_PAIRS_PER_FETCH; - var newStart = Math.max(1, roundDown(range.start())), - newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1); - - return new ContigInterval(range.contig, newStart, newStop); -} - -function createFromGeneUrl(remoteSource: GeneEndpoint): BigBedSource { - // Collection of genes that have already been loaded. - var genes: {[key:string]: Gene} = {}; - - // Ranges for which we have complete information -- no need to hit network. - var coveredRanges: Array> = []; - - function addGene(newGene) { - if (!genes[newGene.id]) { - genes[newGene.id] = newGene; - } - } - - function getGenesInRange(range: ContigInterval): Gene[] { - if (!range) return []; - var results = []; - _.each(genes, gene => { - if (range.intersects(gene.position)) { - results.push(gene); - } - }); - return results; - } - - function fetch(range: GenomeRange) { - var interval = new ContigInterval(range.contig, range.start, range.stop); - - // Check if this interval is already in the cache. - if (interval.isCoveredBy(coveredRanges)) { - return Q.when(); - } - - interval = expandRange(interval); - - coveredRanges.push(interval); - coveredRanges = ContigInterval.coalesce(coveredRanges); - - return remoteSource.getGenesInRange(interval).then(genes => { - if (genes !== null) - genes.forEach(gene => addGene(gene)); - //we have new data from our internal block range - o.trigger('newdata', interval); - }); - } - - var o = { - rangeChanged: function(newRange: GenomeRange) { - fetch(newRange).done(); - }, - getGenesInRange, - - // These are here to make Flow happy. - on: () => {}, - off: () => {}, - trigger: () => {} - }; - _.extend(o, Events); // Make this an event emitter - - return o; -} - -function create(data: {url?:string}): BigBedSource { - if (!data.url) { - throw new Error(`Missing URL from track: ${JSON.stringify(data)}`); - } - var request = new RemoteRequest(data.url); - var endpoint = new GeneEndpoint(request); - return createFromGeneUrl(endpoint); -} - -module.exports = { - create, - createFromGeneUrl -}; diff --git a/src/main/viz/CoverageTrack.js b/src/main/viz/CoverageTrack.js index bff0518c..97f3883e 100644 --- a/src/main/viz/CoverageTrack.js +++ b/src/main/viz/CoverageTrack.js @@ -24,7 +24,6 @@ import style from '../style'; import ContigInterval from '../ContigInterval'; import TiledCanvas from './TiledCanvas'; import type {State, NetworkStatus} from './pileuputils'; -import {formatStatus} from './pileuputils'; class CoverageTiledCanvas extends TiledCanvas { diff --git a/src/test/sources/FeatureDataSource-test.js b/src/test/sources/FeatureDataSource-test.js index f6101de5..8021864b 100644 --- a/src/test/sources/FeatureDataSource-test.js +++ b/src/test/sources/FeatureDataSource-test.js @@ -16,7 +16,7 @@ describe('FeatureDataSource', function() { return new RemoteFile('/test-data/features-chrM-1000-1200.json').getAllString().then(data => { response = data; server = sinon.fakeServer.create(); - server.respondWith('GET', '/features/chrM?start=0&end=10000', [200, { "Content-Type": "application/json" }, response]); + server.respondWith('GET', '/features/chrM?start=1&end=10000&binning=1', [200, { "Content-Type": "application/json" }, response]); server.respondWith('GET', '/features/chrM?start=1&end=1000', [200, { "Content-Type": "application/json" }, '']); }); }); @@ -42,11 +42,13 @@ describe('FeatureDataSource', function() { // Fetching that one gene should cache its entire block. source.on('newdata', () => { - var features = source.getFeaturesInRange(range); + var features = source.getFeaturesInRange(range).sort((a, b) => { + return a.start - b.start; + }); expect(features).to.have.length(2); var feature = features[0]; - expect(feature.start).to.equal(1107); + expect(feature.start).to.equal(1011); expect(feature.contig).to.equal('chrM'); done(); }); diff --git a/src/test/sources/GeneDataSource-test.js b/src/test/sources/GeneDataSource-test.js deleted file mode 100644 index 5a11e478..00000000 --- a/src/test/sources/GeneDataSource-test.js +++ /dev/null @@ -1,55 +0,0 @@ -/* @flow */ -'use strict'; - -import {expect} from 'chai'; - -import sinon from 'sinon'; - -import ContigInterval from '../../main/ContigInterval'; -import RemoteFile from '../../main/RemoteFile'; -import GeneDataSource from '../../main/sources/GeneDataSource'; - -describe('GeneDataSource', function() { - var server: any = null, response; - - before(function () { - return new RemoteFile('/test-data/genes-chrM-0-30000.json').getAllString().then(data => { - response = data; - server = sinon.fakeServer.create(); - server.respondWith('GET', '/genes/chrM?start=1&end=100000', [200, { "Content-Type": "application/json" }, response]); - }); - }); - - after(function () { - server.restore(); - }); - - function getTestSource() { - var source = GeneDataSource.create({ - url: '/genes' - }); - return source; - } - - it('should extract genes in a range', function(done) { - var source = getTestSource(); - - // No genes fetched initially - var range = new ContigInterval('chrM', 0, 100000); - var emptyGenes = source.getGenesInRange(range); - expect(emptyGenes).to.deep.equal([]); - - // Fetching that one gene should cache its entire block. - source.on('newdata', () => { - var genes = source.getGenesInRange(range); - expect(genes).to.have.length(9); - done(); - }); - source.rangeChanged({ - contig: range.contig, - start: range.start(), - stop: range.stop() - }); - server.respond(); - }); -}); diff --git a/src/test/viz/CoverageTrack-test.js b/src/test/viz/CoverageTrack-test.js index 94b09f67..4c50aff8 100644 --- a/src/test/viz/CoverageTrack-test.js +++ b/src/test/viz/CoverageTrack-test.js @@ -12,9 +12,6 @@ import sinon from 'sinon'; import RemoteFile from '../../main/RemoteFile'; import pileup from '../../main/pileup'; -import TwoBit from '../../main/data/TwoBit'; -import TwoBitDataSource from '../../main/sources/TwoBitDataSource'; -import MappedRemoteFile from '../MappedRemoteFile'; import dataCanvas from 'data-canvas'; import {waitFor} from '../async'; diff --git a/src/test/viz/GenotypeTrack-test.js b/src/test/viz/GenotypeTrack-test.js index 23db3768..8ffb65b0 100644 --- a/src/test/viz/GenotypeTrack-test.js +++ b/src/test/viz/GenotypeTrack-test.js @@ -70,7 +70,6 @@ describe('GenotypeTrack', function() { return waitFor(ready, 2000) .then(() => { var genotypes = drawnObjects(testDiv, '.genotypes'); - var sampleIds = ["sample1", "sample2", "sample3"]; expect(genotypes).to.have.length(3); expect(genotypes.map(g => g.variant.position)).to.deep.equal( [10, 20, 30]); diff --git a/test-data/features-chrM-1000-1200.json b/test-data/features-chrM-1000-1200.json index a600170a..8cb7551c 100644 --- a/test-data/features-chrM-1000-1200.json +++ b/test-data/features-chrM-1000-1200.json @@ -3,13 +3,13 @@ "featureType": "peak", "contig": "chrM", "start": 1107, - "end": 1200, + "stop": 1200, "score": 1000 }, { "id": "e105ce29-a840-4fc6-819f-a9aac5166163", "featureType": "peak", "contig": "chrM", "start": 1011, - "end": 1012, + "stop": 1012, "score": 10 }] diff --git a/test-data/variants-chrM-0-100.json b/test-data/variants-chrM-0-100.json index 3293a56e..8b957e1f 100644 --- a/test-data/variants-chrM-0-100.json +++ b/test-data/variants-chrM-0-100.json @@ -1,23 +1 @@ -[{ - "variant" : { - "contig": "chrM", - "position": 10, - "ref": "C", - "alt": "G" - }, "sampleIds": \["sample1", "sample2", "sample3"\] -}, { - "variant" : { - "contig": "chrM", - "position": 20, - "ref": "G", - "alt": "T" - }, "sampleIds": ["sample1", "sample3"] -}, { - "variant" : { - "contig": "chrM", - "position": 23, - "ref": "A", - "alt": "C" - }, "sampleIds": ["sample1"] -}] ["{\"variant\":{\"contig\":\"chrM\",\"position\":10,\"end\":11,\"ref\":\"C\",\"alt\":\"G\"},\"sampleIds\":[\"s1\",\"s2\",\"s3\"]}","{\"variant\":{\"contig\":\"chrM\",\"position\":20,\"end\":21,\"ref\":\"G\",\"alt\":\"T\"},\"sampleIds\":[\"s1\",\"s3\"]}","{\"variant\":{\"contig\":\"chrM\",\"position\":23,\"end\":24,\"ref\":\"A\",\"alt\":\"C\"},\"sampleIds\":[\"s1\",\"s3\"]}"] From 87434a0f721d8797bf10399d480d3e05e5e75f87 Mon Sep 17 00:00:00 2001 From: Snaheth Date: Sun, 5 Mar 2017 19:39:14 -0800 Subject: [PATCH 135/136] Set transparency of feature based on score value --- src/main/viz/FeatureTrack.js | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/main/viz/FeatureTrack.js b/src/main/viz/FeatureTrack.js index 3bee1588..e3160c0a 100644 --- a/src/main/viz/FeatureTrack.js +++ b/src/main/viz/FeatureTrack.js @@ -69,7 +69,10 @@ function renderFeatures(ctx: DataCanvasRenderingContext2D, if (!position.chrIntersects(range)) return; ctx.pushObject(feature); ctx.lineWidth = 1; - ctx.fillStyle = 'black'; + + // Create transparency value based on score. Score of <= 200 is the same transparency. + var alphaScore = Math.max(feature.score / 1000.0, 0.2); + ctx.fillStyle = 'rgba(0, 0, 0, ' + alphaScore + ')'; var x = Math.round(scale(feature.start)); var width = Math.ceil(scale(feature.stop) - scale(feature.start)); From bad720106d25d1cf455ffd346e2637e18cbf8e85 Mon Sep 17 00:00:00 2001 From: Snaheth Date: Tue, 11 Apr 2017 14:56:14 -0700 Subject: [PATCH 136/136] Adjusting canvas height based GenotypeTrack height --- src/main/viz/GenotypeTrack.js | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/src/main/viz/GenotypeTrack.js b/src/main/viz/GenotypeTrack.js index 7fc3811a..b17ab0bc 100644 --- a/src/main/viz/GenotypeTrack.js +++ b/src/main/viz/GenotypeTrack.js @@ -173,6 +173,34 @@ class GenotypeTrack extends React.Component { this.setState({networkStatus: null}); }); + let height = yForRow(this.sampleIds.length); + + // This is very un-react-y, but we are doing this to avoid making prop changes on multiple classes. + var searchNode = this; + while (searchNode) { + + // Cycle the next parent node + searchNode = ReactDOM.findDOMNode(searchNode).parentNode; + + // If the current node has a class name with greater than or equal to 1 classes, it might be the GenotypeTrack + if (searchNode && searchNode.className && searchNode.className.split(' ') && searchNode.className.split(' ')[1]) { + + let name = searchNode.className.split(' ')[1]; + + // If the class name matches the GenotypeTrack, we can make changes + if (name == GenotypeTrack.displayName) { + let searchNodeHeight = $(searchNode).context.clientHeight; + + // If the height of the GenotypeTrack is less than the current height, we make the change + if (height < searchNodeHeight) { + $(searchNode).css('flex', '0 0 ' + height + 'px'); + } + + break; + } + } + } + this.updateVisualization(); }