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Support for flow based sequencing (#7876)
Added Support for Ultima Genomics flow based sequencing data. The major new features are as follows:
- Added "FlowMode" argument to HaplotypeCaller which better supports flow based calling
- Added a new Haplotype Filtering step after assembly which removes suspicious haplotypes from the genoytper
- Added two new likelihoods models, FlowBasedHMM and the FlowBasedAlignmentLkelihoodEngine
- Added "FlowMode" to Mutect2 which better supports flow based calling
- Added support for uncertain read end-positions in MarkDuplicatesSpark
- Added a new tool FlowFeatureMapper for quick heuristic calling of bams for diagnostics
- Added a new tool GroundTruthReadsBuilder to generate ground truth files for Basecalling
- Added a new diagnostic tool HaplotypeBasedVariantRecaller for recalling VCF files using the HaplotypeCallerEngine
- Added a new tool breaking up CRAM files by their blocks, SplitCram
There are a number of code and technical changes as well
- Added a new read interface called `FlowBasedRead` that manages the new features for FlowBased data
- Added a number of flow-specific read filters
- Added a number of flow-specific variant annotations
- Added support for read annotation-clipping as part of clipreads and GATKRead
- Added a new PartialReadsWalker that supports terminating before traversal is finished
Co-authored-by: James <emeryj@broadinstitute.org>
Co-authored-by: Megan Shand <mshand@broadinstitute.org>
Co-authored-by: Dror Kessler <dror27.kessler@gmail.com>- Loading branch information
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Jul 26, 2022
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17 changes: 17 additions & 0 deletions
17
src/main/java/org/broadinstitute/hellbender/cmdline/programgroups/FlowBasedProgramGroup.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,17 @@ | ||
| package org.broadinstitute.hellbender.cmdline.programgroups; | ||
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| import org.broadinstitute.barclay.argparser.CommandLineProgramGroup; | ||
| import org.broadinstitute.hellbender.utils.help.HelpConstants; | ||
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| /** | ||
| * Tools that perform variant calling and genotyping for short variants (SNPs, SNVs and Indels) on | ||
| * flow-based sequencing platforms | ||
| */ | ||
| public class FlowBasedProgramGroup implements CommandLineProgramGroup { | ||
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| @Override | ||
| public String getName() { return HelpConstants.DOC_CAT_SHORT_FLOW_BASED; } | ||
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| @Override | ||
| public String getDescription() { return HelpConstants.DOC_CAT_SHORT_FLOW_BASED_SUMMARY; } | ||
| } |
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75 changes: 75 additions & 0 deletions
75
src/main/java/org/broadinstitute/hellbender/engine/PartialReadWalker.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,75 @@ | ||
| package org.broadinstitute.hellbender.engine; | ||
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| import org.broadinstitute.hellbender.engine.filters.CountingReadFilter; | ||
| import org.broadinstitute.hellbender.utils.SimpleInterval; | ||
| import org.broadinstitute.hellbender.utils.read.GATKRead; | ||
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| import java.util.Spliterator; | ||
| import java.util.concurrent.atomic.AtomicBoolean; | ||
| import java.util.function.BiConsumer; | ||
| import java.util.stream.Stream; | ||
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| /** | ||
| * A specialized read walker that may be gracefully stopped before the input stream ends | ||
| * | ||
| * A tool derived from this class should implement {@link PartialReadWalker#shouldExitEarly(GATKRead)} | ||
| * to indicate when to stop. This method is called before {@link ReadWalker#apply(GATKRead, ReferenceContext, FeatureContext)} | ||
| * | ||
| */ | ||
| abstract public class PartialReadWalker extends ReadWalker { | ||
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| /** | ||
| * traverse is overridden to consult the implementation class whether to stop | ||
| * | ||
| * The stoppage is implemented using a custom forEach method to compensate for the | ||
| * lack of .takeWhile() in Java 8 | ||
| */ | ||
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| @Override | ||
| public void traverse() { | ||
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| final CountingReadFilter countedFilter = makeReadFilter(); | ||
| breakableForEach(getTransformedReadStream(countedFilter), (read, breaker) -> { | ||
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| // check if we should stop | ||
| if ( shouldExitEarly(read) ) { | ||
| breaker.set(true); | ||
| } else { | ||
| // this is the body of the iteration | ||
| final SimpleInterval readInterval = getReadInterval(read); | ||
| apply(read, | ||
| new ReferenceContext(reference, readInterval), // Will create an empty ReferenceContext if reference or readInterval == null | ||
| new FeatureContext(features, readInterval)); // Will create an empty FeatureContext if features or readInterval == null | ||
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| progressMeter.update(readInterval); | ||
| } | ||
| }); | ||
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| logger.info(countedFilter.getSummaryLine()); | ||
| } | ||
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| /** | ||
| * Method to be overridden by the implementation class to determine when to stop the read stream traversal | ||
| * @param read - the read to be processed next (in case it is needed) | ||
| * @return boolean indicator: true means stop! | ||
| */ | ||
| protected abstract boolean shouldExitEarly(GATKRead read); | ||
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| /** | ||
| * Java 8 does not have a .takeWhile() on streams. The code below implements a custom forEach to allow | ||
| * breaking out of a stream prematurely. | ||
| * | ||
| * code adapted from: https://www.baeldung.com/java-break-stream-foreach | ||
| */ | ||
| private static <T> void breakableForEach(Stream<T> stream, BiConsumer<T, AtomicBoolean> consumer) { | ||
| Spliterator<T> spliterator = stream.spliterator(); | ||
| boolean hadNext = true; | ||
| AtomicBoolean breaker = new AtomicBoolean(); | ||
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| while (hadNext && !breaker.get()) { | ||
| hadNext = spliterator.tryAdvance(elem -> { | ||
| consumer.accept(elem, breaker); | ||
| }); | ||
| } | ||
| } | ||
| } |
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