Add track filetype guesser for BedGraph

plugins/alignments/src/CramAdapter/CramAdapter.test.ts

@@ -20,22 +20,26 @@ const getVolvoxSequenceSubAdapter: getSubAdapterType = async () => {
   }
 }
 
-test('adapter can fetch features from volvox-sorted.cram', async () => {
-  const adapter = new Adapter(
+function makeAdapter(arg: string) {
+  return new Adapter(
     configSchema.create({
       cramLocation: {
-        localPath: require.resolve('../../test_data/volvox-sorted.cram'),
+        localPath: require.resolve(arg),
         locationType: 'LocalPathLocation',
       },
       craiLocation: {
-        localPath: require.resolve('../../test_data/volvox-sorted.cram.crai'),
+        localPath: require.resolve(arg + '.crai'),
         locationType: 'LocalPathLocation',
       },
       sequenceAdapter: {},
     }),
     getVolvoxSequenceSubAdapter,
     pluginManager,
   )
+}
+
+test('adapter can fetch features from volvox-sorted.cram', async () => {
+  const adapter = makeAdapter('../../test_data/volvox-sorted.cram')
 
   const features = adapter.getFeatures({
     assemblyName: 'volvox',
@@ -57,22 +61,7 @@ test('adapter can fetch features from volvox-sorted.cram', async () => {
 })
 
 test('test usage of cramSlightlyLazyFeature toJSON (used in the widget)', async () => {
-  const adapter = new Adapter(
-    configSchema.create({
-      cramLocation: {
-        localPath: require.resolve('../../test_data/volvox-sorted.cram'),
-        locationType: 'LocalPathLocation',
-      },
-      craiLocation: {
-        localPath: require.resolve('../../test_data/volvox-sorted.cram.crai'),
-        locationType: 'LocalPathLocation',
-      },
-      sequenceAdapter: {},
-    }),
-    getVolvoxSequenceSubAdapter,
-    pluginManager,
-  )
-
+  const adapter = makeAdapter('../../test_data/volvox-sorted.cram')
   const features = adapter.getFeatures({
     assemblyName: 'volvox',
     refName: 'ctgA',

plugins/bed/src/BedGraphAdapter/BedGraphAdapter.test.ts

@@ -0,0 +1,32 @@
+import { firstValueFrom } from 'rxjs'
+import { toArray } from 'rxjs/operators'
+
+import BedGraphAdapter from './BedGraphAdapter'
+import configSchema from './configSchema'
+
+function makeAdapter() {
+  return new BedGraphAdapter(
+    configSchema.create({
+      bedGraphLocation: {
+        localPath: require.resolve('./test_data/test.bg'),
+        locationType: 'LocalPathLocation',
+      },
+    }),
+  )
+}
+test('basic', async () => {
+  const adapter = makeAdapter()
+
+  const features = await firstValueFrom(
+    adapter
+      .getFeatures({
+        assemblyName: 'volvox',
+        refName: 'chr1',
+        start: 0,
+        end: 10000,
+      })
+      .pipe(toArray()),
+  )
+
+  expect(features).toMatchSnapshot()
+})

plugins/bed/src/BedGraphAdapter/__snapshots__/BedGraphAdapter.test.ts.snap

@@ -0,0 +1,30 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`basic 1`] = `
+[
+  {
+    "end": 200,
+    "refName": "chr1",
+    "score": 4,
+    "source": "col0",
+    "start": 100,
+    "uniqueId": "test-chr1-0-0",
+  },
+  {
+    "end": 300,
+    "refName": "chr1",
+    "score": 5,
+    "source": "col0",
+    "start": 200,
+    "uniqueId": "test-chr1-1-0",
+  },
+  {
+    "end": 400,
+    "refName": "chr1",
+    "score": 6,
+    "source": "col0",
+    "start": 300,
+    "uniqueId": "test-chr1-2-0",
+  },
+]
+`;

plugins/bed/src/BedGraphAdapter/test_data/test.bg

@@ -0,0 +1,3 @@
+chr1	100	200	4
+chr1	200	300	5
+chr1	300	400	6

plugins/bed/src/BedGraphTabixAdapter/BedGraphTabixAdapter.test.ts

@@ -0,0 +1,38 @@
+import { firstValueFrom } from 'rxjs'
+import { toArray } from 'rxjs/operators'
+
+import BedGraphTabixAdapter from './BedGraphTabixAdapter'
+import configSchema from './configSchema'
+
+function makeAdapter() {
+  return new BedGraphTabixAdapter(
+    configSchema.create({
+      bedGraphGzLocation: {
+        localPath: require.resolve('./test_data/test.bg.gz'),
+        locationType: 'LocalPathLocation',
+      },
+      index: {
+        location: {
+          localPath: require.resolve('./test_data/test.bg.gz.tbi'),
+          locationType: 'LocalPathLocation',
+        },
+      },
+    }),
+  )
+}
+test('basic', async () => {
+  const adapter = makeAdapter()
+
+  const features = await firstValueFrom(
+    adapter
+      .getFeatures({
+        assemblyName: 'volvox',
+        refName: 'chr1',
+        start: 0,
+        end: 10000,
+      })
+      .pipe(toArray()),
+  )
+
+  expect(features).toMatchSnapshot()
+})

plugins/bed/src/BedGraphTabixAdapter/BedGraphTabixAdapter.ts

@@ -95,6 +95,12 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
             const start = +cols[colStart]!
             const end = +(same ? start + 1 : cols[colEnd]!)
             const rest = cols.slice(colEnd + 1)
+            if (Number.isNaN(start) || Number.isNaN(end)) {
+              throw new Error(
+                `start/end NaN on line "${line}", with colStart:${colStart} and colEnd:${colEnd}. run "tabix -p bed" to ensure bed preset`,
+              )
+            }
+
             for (let j = 0; j < rest.length; j++) {
               const uniqueId = `${this.id}-${fileOffset}-${j}`
               const score = Math.abs(+rest[j]!)

plugins/bed/src/BedGraphTabixAdapter/__snapshots__/BedGraphTabixAdapter.test.ts.snap

@@ -0,0 +1,30 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`basic 1`] = `
+[
+  {
+    "end": 200,
+    "refName": "chr1",
+    "score": 4,
+    "source": "col0",
+    "start": 100,
+    "uniqueId": "test-14548-0",
+  },
+  {
+    "end": 300,
+    "refName": "chr1",
+    "score": 5,
+    "source": "col0",
+    "start": 200,
+    "uniqueId": "test-14563-0",
+  },
+  {
+    "end": 400,
+    "refName": "chr1",
+    "score": 6,
+    "source": "col0",
+    "start": 300,
+    "uniqueId": "test-14578-0",
+  },
+]
+`;

plugins/bed/src/BedTabixAdapter/BedTabixAdapter.test.ts

@@ -4,22 +4,26 @@ import { toArray } from 'rxjs/operators'
 import BedTabixAdapter from './BedTabixAdapter'
 import MyConfigSchema from './configSchema'
 
-test('adapter can fetch features from volvox-bed12.bed.gz', async () => {
-  const adapter = new BedTabixAdapter(
+function makeAdapter(f: string, extra?: Record<string, unknown>) {
+  return new BedTabixAdapter(
     MyConfigSchema.create({
       bedGzLocation: {
-        localPath: require.resolve('./test_data/volvox-bed12.bed.gz'),
+        localPath: require.resolve(f),
         locationType: 'LocalPathLocation',
       },
       index: {
         location: {
-          localPath: require.resolve('./test_data/volvox-bed12.bed.gz.tbi'),
+          localPath: require.resolve(`${f}.tbi`),
           locationType: 'LocalPathLocation',
         },
       },
+      ...extra,
     }),
   )
+}
 
+test('adapter can fetch features from volvox-bed12.bed.gz', async () => {
+  const adapter = makeAdapter('./test_data/volvox-bed12.bed.gz')
   const features = adapter.getFeatures({
     refName: 'ctgA',
     start: 0,
@@ -35,21 +39,7 @@ test('adapter can fetch features from volvox-bed12.bed.gz', async () => {
 })
 
 test('adapter can fetch features from volvox.sort.bed.gz simple bed3', async () => {
-  const adapter = new BedTabixAdapter(
-    MyConfigSchema.create({
-      bedGzLocation: {
-        localPath: require.resolve('./test_data/volvox.sort.bed.gz'),
-        locationType: 'LocalPathLocation',
-      },
-      index: {
-        location: {
-          localPath: require.resolve('./test_data/volvox.sort.bed.gz.tbi'),
-          locationType: 'LocalPathLocation',
-        },
-      },
-    }),
-  )
-
+  const adapter = makeAdapter('./test_data/volvox.sort.bed.gz')
   const features = adapter.getFeatures({
     refName: 'contigA',
     start: 0,
@@ -65,19 +55,8 @@ test('adapter can fetch features from volvox.sort.bed.gz simple bed3', async ()
 })
 
 test('adapter can fetch features bed with autosql', async () => {
-  const adapter = new BedTabixAdapter(
-    MyConfigSchema.create({
-      bedGzLocation: {
-        localPath: require.resolve('./test_data/volvox-autosql.bed.gz'),
-        locationType: 'LocalPathLocation',
-      },
-      index: {
-        location: {
-          localPath: require.resolve('./test_data/volvox-autosql.bed.gz.tbi'),
-          locationType: 'LocalPathLocation',
-        },
-      },
-      autoSql: `table gdcCancer
+  const adapter = makeAdapter('./test_data/volvox-autosql.bed.gz', {
+    autoSql: `table gdcCancer
 "somatic variants converted from MAF files obtained through the NCI GDC"
     (
     string chrom;      "Chromosome (or contig, scaffold, etc.)"
@@ -118,8 +97,7 @@ test('adapter can fetch features bed with autosql', async () => {
     lstring Matched_Norm_Sample_Barcode;  "Matcheds normal sample barcode"
     lstring case_id;                "Case ID number"
 )`,
-    }),
-  )
+  })
   const features = adapter.getFeatures({
     refName: 'ctgA',
     start: 0,
@@ -135,25 +113,7 @@ test('adapter can fetch features bed with autosql', async () => {
 })
 
 test('adapter can fetch bed with header', async () => {
-  const adapter = new BedTabixAdapter(
-    MyConfigSchema.create({
-      bedGzLocation: {
-        localPath: require.resolve(
-          './test_data/volvox.sort.with.header.bed.gz',
-        ),
-        locationType: 'LocalPathLocation',
-      },
-      index: {
-        location: {
-          localPath: require.resolve(
-            './test_data/volvox.sort.with.header.bed.gz.tbi',
-          ),
-          locationType: 'LocalPathLocation',
-        },
-      },
-    }),
-  )
-
+  const adapter = makeAdapter('./test_data/volvox.sort.with.header.bed.gz')
   const features = adapter.getFeatures({
     refName: 'contigA',
     start: 0,
@@ -169,21 +129,7 @@ test('adapter can fetch bed with header', async () => {
 })
 
 test('adapter can use gwas header', async () => {
-  const adapter = new BedTabixAdapter(
-    MyConfigSchema.create({
-      bedGzLocation: {
-        localPath: require.resolve('./test_data/gwas.bed.gz'),
-        locationType: 'LocalPathLocation',
-      },
-      index: {
-        location: {
-          localPath: require.resolve('./test_data/gwas.bed.gz.tbi'),
-          locationType: 'LocalPathLocation',
-        },
-      },
-    }),
-  )
-
+  const adapter = makeAdapter('./test_data/gwas.bed.gz')
   const features = adapter.getFeatures({
     refName: '1',
     start: 0,