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output sample names in Mutect2 pon header #5733

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merged 1 commit into from
Mar 1, 2019
Merged

output sample names in Mutect2 pon header #5733

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19 changes: 10 additions & 9 deletions .../java/org/broadinstitute/hellbender/tools/walkers/mutect/CreateSomaticPanelOfNormals.java
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Original file line number Diff line number Diff line change
Expand Up @@ -5,10 +5,7 @@
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.VariantContextBuilder;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.vcf.VCFConstants;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import htsjdk.variant.vcf.*;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.BetaFeature;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
Expand All @@ -23,7 +20,9 @@
import picard.cmdline.programgroups.VariantFilteringProgramGroup;
import org.broadinstitute.hellbender.utils.SimpleInterval;

import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.function.DoubleUnaryOperator;
import java.util.stream.Collectors;

Expand Down Expand Up @@ -112,14 +111,16 @@ public class CreateSomaticPanelOfNormals extends VariantWalker {

@Override
public void onTraversalStart() {
final VCFHeader outputHeader = new VCFHeader();
getDefaultToolVCFHeaderLines().forEach(outputHeader::addMetaDataLine);
outputHeader.setSequenceDictionary(getHeaderForVariants().getSequenceDictionary());
final Set<VCFHeaderLine> headerInfo = new HashSet<>(getDefaultToolVCFHeaderLines());
headerInfo.add(new VCFInfoHeaderLine(FRACTION_INFO_FIELD, 1, VCFHeaderLineType.Float, "Fraction of samples exhibiting artifact"));
headerInfo.add(new VCFInfoHeaderLine(BETA_SHAPE_INFO_FIELD, 2, VCFHeaderLineType.Float, "Beta distribution parameters to fit artifact allele fractions"));

outputHeader.addMetaDataLine(new VCFInfoHeaderLine(FRACTION_INFO_FIELD, 1, VCFHeaderLineType.Float, "Fraction of samples exhibiting artifact"));
outputHeader.addMetaDataLine(new VCFInfoHeaderLine(BETA_SHAPE_INFO_FIELD, 2, VCFHeaderLineType.Float, "Beta distribution parameters to fit artifact allele fractions"));
getHeaderForVariants().getGenotypeSamples()
.forEach(sample -> headerInfo.add(new VCFHeaderLine(Mutect2Engine.NORMAL_SAMPLE_KEY_IN_VCF_HEADER, sample)));

vcfWriter = createVCFWriter(IOUtils.getPath(outputVcf));
final VCFHeader outputHeader = new VCFHeader(headerInfo);
outputHeader.setSequenceDictionary(getHeaderForVariants().getSequenceDictionary());
vcfWriter.writeHeader(outputHeader);

numSamples = getHeaderForVariants().getNGenotypeSamples();
Expand Down