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SW implementation is command line argument in FilterAlignmentArtifacts #7105

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merged 4 commits into from
Oct 26, 2021
Merged

SW implementation is command line argument in FilterAlignmentArtifacts #7105

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2d2a47b
SW implementation is command line argument in FilterAlignmentArtifacts
davidbenjamin Feb 25, 2021
2b3fa96
fastest available
davidbenjamin Oct 26, 2021
8e1d9df
which
davidbenjamin Oct 26, 2021
a68554f
whoops import
davidbenjamin Oct 26, 2021
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16 changes: 9 additions & 7 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 @@ -10,10 +10,7 @@
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderLine;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.ArgumentCollection;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.barclay.argparser.ExperimentalFeature;
import org.broadinstitute.barclay.argparser.*;
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I think we want to use explicit imports

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done

import org.broadinstitute.barclay.help.DocumentedFeature;
import org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
Expand Down Expand Up @@ -112,7 +109,6 @@ public class FilterAlignmentArtifacts extends MultiVariantWalkerGroupedOnStart {
public static final int DEFAULT_MAX_GROUPED_SPAN = 10_000;
private static final int MIN_UNITIG_LENGTH = 30;
private static final int ASSEMBLY_PADDING = 50;
private static final SmithWatermanAligner ALIGNER = SmithWatermanAligner.getAligner(SmithWatermanAligner.Implementation.FASTEST_AVAILABLE);

@Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME, shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME,
doc="The output filtered VCF file", optional=false)
Expand All @@ -136,10 +132,15 @@ public class FilterAlignmentArtifacts extends MultiVariantWalkerGroupedOnStart {
@Argument(fullName= AssemblyBasedCallerArgumentCollection.BAM_OUTPUT_LONG_NAME, shortName= AssemblyBasedCallerArgumentCollection.BAM_OUTPUT_SHORT_NAME, doc="File to which assembled haplotypes should be written", optional = true)
public String bamOutputPath = null;

@Advanced
@Argument(fullName = AssemblyBasedCallerArgumentCollection.SMITH_WATERMAN_LONG_NAME, doc = "Smith-Waterman implementation to use, generally FASTEST_AVAILABLE is the right choice", optional = true)
public SmithWatermanAligner.Implementation smithWatermanImplementation = SmithWatermanAligner.Implementation.FASTEST_AVAILABLE;


@ArgumentCollection
protected RealignmentArgumentCollection realignmentArgumentCollection = new RealignmentArgumentCollection();

private SmithWatermanAligner smithWatermanAligner;
private VariantContextWriter vcfWriter;
private RealignmentEngine realignmentEngine;
private SAMFileHeader bamHeader;
Expand Down Expand Up @@ -174,6 +175,7 @@ protected int defaultMaxGroupedSpan() {

@Override
public void onTraversalStart() {
smithWatermanAligner = SmithWatermanAligner.getAligner(smithWatermanImplementation);
realignmentEngine = new RealignmentEngine(realignmentArgumentCollection);
vcfWriter = createVCFWriter(outputVcf);

Expand Down Expand Up @@ -211,15 +213,15 @@ public void apply(List<VariantContext> variantContexts, ReferenceContext referen


// TODO: give this tool M2 Assembler args to allow override default M2ArgumentCollection?
final AssemblyResultSet assemblyResult = AssemblyBasedCallerUtils.assembleReads(assemblyRegion, Collections.emptyList(), MTAC, bamHeader, samplesList, logger, referenceReader, assemblyEngine, ALIGNER, false);
final AssemblyResultSet assemblyResult = AssemblyBasedCallerUtils.assembleReads(assemblyRegion, Collections.emptyList(), MTAC, bamHeader, samplesList, logger, referenceReader, assemblyEngine, smithWatermanAligner, false);
final AssemblyRegion regionForGenotyping = assemblyResult.getRegionForGenotyping();

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

final AlleleLikelihoods<GATKRead, Haplotype> readLikelihoods = likelihoodCalculationEngine.computeReadLikelihoods(assemblyResult,samplesList,reads);
readLikelihoods.switchToNaturalLog();
final SWParameters readToHaplotypeSWParameters = MTAC.getReadToHaplotypeSWParameters();
final Map<GATKRead,GATKRead> readRealignments = AssemblyBasedCallerUtils.realignReadsToTheirBestHaplotype(readLikelihoods, assemblyResult.getReferenceHaplotype(), assemblyResult.getPaddedReferenceLoc(), ALIGNER, readToHaplotypeSWParameters);
final Map<GATKRead,GATKRead> readRealignments = AssemblyBasedCallerUtils.realignReadsToTheirBestHaplotype(readLikelihoods, assemblyResult.getReferenceHaplotype(), assemblyResult.getPaddedReferenceLoc(), smithWatermanAligner, readToHaplotypeSWParameters);
readLikelihoods.changeEvidence(readRealignments);
writeBamOutput(assemblyResult, readLikelihoods, new HashSet<>(readLikelihoods.alleles()), regionForGenotyping.getSpan());

Expand Down