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fixed a merge conflict missed by github in recent PR #6159

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Sep 13, 2019
Merged

fixed a merge conflict missed by github in recent PR #6159

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26 changes: 13 additions & 13 deletions ...g/broadinstitute/hellbender/tools/walkers/realignmentfilter/FilterAlignmentArtifacts.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,6 @@
import com.google.common.collect.HashMultiset;
import com.google.common.collect.Multiset;
import com.google.common.collect.Multisets;
import htsjdk.samtools.Cigar;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.util.Locatable;
import htsjdk.variant.variantcontext.VariantContext;
Expand All @@ -17,15 +16,18 @@
import org.broadinstitute.barclay.argparser.ExperimentalFeature;
import org.broadinstitute.barclay.help.DocumentedFeature;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.engine.*;
import org.broadinstitute.hellbender.engine.AssemblyRegion;
import org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart;
import org.broadinstitute.hellbender.engine.ReadsContext;
import org.broadinstitute.hellbender.engine.ReferenceContext;
import org.broadinstitute.hellbender.engine.filters.CountingVariantFilter;
import org.broadinstitute.hellbender.engine.filters.ReadFilter;
import org.broadinstitute.hellbender.engine.filters.VariantFilterLibrary;
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.*;
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.*;
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex;
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection;
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils;
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet;
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine;
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler;
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph;
import org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection;
import org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine;
import org.broadinstitute.hellbender.utils.BaseUtils;
Expand All @@ -35,21 +37,18 @@
import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment;
import org.broadinstitute.hellbender.utils.downsampling.DownsamplingMethod;
import org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods;
import org.broadinstitute.hellbender.utils.genotyper.IndexedSampleList;
import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods;
import org.broadinstitute.hellbender.utils.genotyper.SampleList;
import org.broadinstitute.hellbender.utils.haplotype.EventMap;
import org.broadinstitute.hellbender.utils.haplotype.Haplotype;
import org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter;
import org.broadinstitute.hellbender.utils.io.IOUtils;
import org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState;
import org.broadinstitute.hellbender.utils.pileup.PileupElement;
import org.broadinstitute.hellbender.utils.pileup.ReadPileup;
import org.broadinstitute.hellbender.utils.read.CigarUtils;
import org.broadinstitute.hellbender.utils.read.GATKRead;
import org.broadinstitute.hellbender.utils.read.ReadUtils;
import org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner;
import org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanJavaAligner;
import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants;
import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines;
import picard.cmdline.programgroups.VariantFilteringProgramGroup;
Expand Down Expand Up @@ -216,9 +215,10 @@ public void apply(List<VariantContext> variantContexts, ReferenceContext referen

final Map<String,List<GATKRead>> reads = AssemblyBasedCallerUtils.splitReadsBySample(samplesList, bamHeader, regionForGenotyping.getReads());

final ReadLikelihoods<Haplotype> readLikelihoods = likelihoodCalculationEngine.computeReadLikelihoods(assemblyResult,samplesList,reads).copy(true);
final AlleleLikelihoods<GATKRead, Haplotype> readLikelihoods = likelihoodCalculationEngine.computeReadLikelihoods(assemblyResult,samplesList,reads);
readLikelihoods.switchToNaturalLog();
final Map<GATKRead,GATKRead> readRealignments = AssemblyBasedCallerUtils.realignReadsToTheirBestHaplotype(readLikelihoods, assemblyResult.getReferenceHaplotype(), assemblyResult.getPaddedReferenceLoc(), ALIGNER);
readLikelihoods.changeReads(readRealignments);
readLikelihoods.changeEvidence(readRealignments);
writeBamOutput(assemblyResult, readLikelihoods, new HashSet<>(readLikelihoods.alleles()), regionForGenotyping.getSpan());

final LocusIteratorByState libs = new LocusIteratorByState(regionForGenotyping.getReads().iterator(), DownsamplingMethod.NONE, false, samplesList.asListOfSamples(), bamHeader, true);
Expand Down Expand Up @@ -279,7 +279,7 @@ private AssemblyRegion makeAssemblyRegionFromVariantReads(final List<ReadsContex
return assemblyRegion;
}

private void writeBamOutput(final AssemblyResultSet assemblyResult, final ReadLikelihoods<Haplotype> readLikelihoods, final Set<Haplotype> haplotypes, Locatable callableRegion) {
private void writeBamOutput(final AssemblyResultSet assemblyResult, final AlleleLikelihoods<GATKRead, Haplotype> readLikelihoods, final Set<Haplotype> haplotypes, Locatable callableRegion) {
haplotypeBAMWriter.ifPresent(writer -> writer.writeReadsAlignedToHaplotypes(
assemblyResult.getHaplotypeList(),
assemblyResult.getPaddedReferenceLoc(),
Expand Down