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STEP 5: hookup of the inversion breakpoint linking to pipeline
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@SHuang-Broad
SHuang-Broad committed Jun 29, 2018
1 parent 1c67de5 commit 1992778
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Showing 2 changed files with 39 additions and 7 deletions.
7 changes: 4 additions & 3 deletions ...g/broadinstitute/hellbender/tools/spark/sv/StructuralVariationDiscoveryPipelineSpark.java
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Original file line number Diff line number Diff line change
Expand Up @@ -200,7 +200,7 @@ protected void runTool( final JavaSparkContext ctx ) {

// TODO: 1/14/18 this is the next version of precise variant calling
if ( expInterpret != null ) {
experimentalInterpretation(ctx, assembledEvidenceResults, svDiscoveryInputMetaData);
experimentalInterpretation(ctx, assembledEvidenceResults, svDiscoveryInputMetaData, evidenceAndAssemblyArgs.fastqDir);
}
}

Expand Down Expand Up @@ -277,7 +277,8 @@ private static List<VariantContext> processEvidenceTargetLinks(List<VariantConte

private static void experimentalInterpretation(final JavaSparkContext ctx,
final FindBreakpointEvidenceSpark.AssembledEvidenceResults assembledEvidenceResults,
final SvDiscoveryInputMetaData svDiscoveryInputMetaData) {
final SvDiscoveryInputMetaData svDiscoveryInputMetaData,
final String pathToFastq) {

final JavaRDD<GATKRead> assemblyRawAlignments = getContigRawAlignments(ctx, assembledEvidenceResults, svDiscoveryInputMetaData);

Expand All @@ -288,7 +289,7 @@ private static void experimentalInterpretation(final JavaSparkContext ctx,
= SvDiscoverFromLocalAssemblyContigAlignmentsSpark.preprocess(svDiscoveryInputMetaData, assemblyRawAlignments);

SvDiscoverFromLocalAssemblyContigAlignmentsSpark.dispatchJobs(ctx, contigsByPossibleRawTypes,
svDiscoveryInputMetaData, assemblyRawAlignments, true);
svDiscoveryInputMetaData, assemblyRawAlignments, pathToFastq, true);
}

private static JavaRDD<GATKRead> getContigRawAlignments(final JavaSparkContext ctx,
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39 changes: 35 additions & 4 deletions ...hellbender/tools/spark/sv/discovery/SvDiscoverFromLocalAssemblyContigAlignmentsSpark.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,17 +16,17 @@
import org.broadinstitute.barclay.help.DocumentedFeature;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.cmdline.programgroups.StructuralVariantDiscoveryProgramGroup;
import org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource;
import org.broadinstitute.hellbender.engine.filters.ReadFilter;
import org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary;
import org.broadinstitute.hellbender.engine.spark.GATKSparkTool;
import org.broadinstitute.hellbender.exceptions.GATKException;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryPipelineSpark;
import org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.*;
import org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantInterpreter;
import org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor;
import org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyInterpreter;
import org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.*;
import org.broadinstitute.hellbender.tools.spark.sv.utils.SVIntervalTree;
import org.broadinstitute.hellbender.tools.spark.sv.utils.SVLocalContext;
import org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils;
import org.broadinstitute.hellbender.tools.spark.sv.utils.SVVCFWriter;
import org.broadinstitute.hellbender.utils.Utils;
Expand Down Expand Up @@ -112,6 +112,9 @@ public final class SvDiscoverFromLocalAssemblyContigAlignmentsSpark extends GATK
fullName = "non-canonical-contig-names-file", optional = true)
private String nonCanonicalChromosomeNamesFile;

@Argument(doc = "path to dir for assembled fastqs", fullName = "fastq-dir", optional = true)
private String fastqDir;

@Argument(doc = "prefix for output files (including VCF files and if enabled, the signaling assembly contig's alignments); sample name will be appended after the provided argument",
shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME,
fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME)
Expand Down Expand Up @@ -155,7 +158,7 @@ protected void runTool(final JavaSparkContext ctx) {
final AssemblyContigsClassifiedByAlignmentSignatures contigsByPossibleRawTypes =
preprocess(svDiscoveryInputMetaData, assemblyRawAlignments);

dispatchJobs(ctx, contigsByPossibleRawTypes, svDiscoveryInputMetaData, assemblyRawAlignments, writeSAMFiles);
dispatchJobs(ctx, contigsByPossibleRawTypes, svDiscoveryInputMetaData, assemblyRawAlignments, fastqDir, writeSAMFiles);
}


Expand Down Expand Up @@ -282,6 +285,7 @@ public static void dispatchJobs(final JavaSparkContext ctx,
final AssemblyContigsClassifiedByAlignmentSignatures contigsByPossibleRawTypes,
final SvDiscoveryInputMetaData svDiscoveryInputMetaData,
final JavaRDD<GATKRead> assemblyRawAlignments,
final String pathToFastq,
final boolean writeSAMFiles) {

final String outputPrefixWithSampleName = svDiscoveryInputMetaData.getOutputPath();
Expand All @@ -307,6 +311,7 @@ public static void dispatchJobs(final JavaSparkContext ctx,
svDiscoveryInputMetaData.getSampleSpecificData().getHeaderBroadcast().getValue());
}

// reinterpret complex variants
final JavaRDD<VariantContext> complexVariantsRDD = ctx.parallelize(complexVariants);
final SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants reInterpretedSimple =
SegmentedCpxVariantSimpleVariantExtractor.extract(complexVariantsRDD, svDiscoveryInputMetaData, assemblyRawAlignments);
Expand All @@ -316,6 +321,32 @@ public static void dispatchJobs(final JavaSparkContext ctx,
final String derivedMultiSegmentSimpleVCF = outputPrefixWithSampleName + "cpx_reinterpreted_simple_multi_seg.vcf";
SVVCFWriter.writeVCF(reInterpretedSimple.getReInterpretZeroOrOneSegmentCalls(), derivedOneSegmentSimpleVCF, refSeqDict, toolLogger);
SVVCFWriter.writeVCF(reInterpretedSimple.getReInterpretMultiSegmentsCalls(), derivedMultiSegmentSimpleVCF, refSeqDict, toolLogger);

// linked inversion breakpoints
if (pathToFastq != null ){
final List<InversionBreakendPreFilter.OverlappingPair> preprocessingResult = InversionBreakendPreFilter
.preprocess(
simpleVariants.stream().filter(SVLocalContext::indicatesInversion)
.map(SVLocalContext.InvBreakEndContext::new).collect(Collectors.toList()),
complexVariants,
100_000, 30,
outputPrefixWithSampleName, refSeqDict, toolLogger);

if (preprocessingResult.isEmpty()) {
toolLogger.warn("No matched inversion breakpoint pairs found. This indicates something went wrong.");
return;
}

final ReferenceMultiSource reference = svDiscoveryInputMetaData.getReferenceData().getReferenceBroadcast().getValue();
final List<VariantContext> variantContexts = LinkedInversionBreakpointsInference
.makeInterpretation(preprocessingResult,
pathToFastq,
reference, toolLogger);

// TODO: 5/16/18 artifact that we currently don't have sample columns for discovery VCF (until genotyping code is in)
final String vcfName = outputPrefixWithSampleName + "inversions_from_bnds.vcf" ;
SVVCFWriter.writeVCF(variantContexts, vcfName, refSeqDict, toolLogger);
}
}

//==================================================================================================================
Expand Down

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