Examples with VCFHeaderLine htsjdk.variant.vcf.VCFHeaderLine used on opensource projects

Example 16 with VCFHeaderLine

use of htsjdk.variant.vcf.VCFHeaderLine in project gatk by broadinstitute.

the class VcfUtilsUnitTest method createHeaderLines.

private Set<VCFHeaderLine> createHeaderLines() {
    Set<VCFHeaderLine> headerLines = new HashSet<>(2);
    headerLines.add(new VCFContigHeaderLine("##contig=<ID=1,length=249250621,assembly=b37>", vcfHeaderVersion, "", 0));
    headerLines.add(new VCFContigHeaderLine("##contig=<ID=2,length=249250622,assembly=b37>", vcfHeaderVersion, "", 0));
    return headerLines;
}

Example 17 with VCFHeaderLine

use of htsjdk.variant.vcf.VCFHeaderLine in project gatk-protected by broadinstitute.

the class ReferenceConfidenceModelUnitTest method testGetHeaderLines.

@Test
public void testGetHeaderLines() throws Exception {
    final Set<VCFHeaderLine> vcfHeaderLines = model.getVCFHeaderLines();
    Assert.assertEquals(vcfHeaderLines.size(), 1);
    Assert.assertEquals(vcfHeaderLines.iterator().next(), new VCFSimpleHeaderLine(GATKVCFConstants.SYMBOLIC_ALLELE_DEFINITION_HEADER_TAG, GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE_NAME, "Represents any possible alternative allele at this location"));
}

Example 18 with VCFHeaderLine

use of htsjdk.variant.vcf.VCFHeaderLine in project gatk by broadinstitute.

the class Concordance method onTraversalStart.

@Override
public void onTraversalStart() {
    Set<VCFHeaderLine> defaultToolHeaderLines = getDefaultToolVCFHeaderLines();
    for (final ConcordanceState state : ConcordanceState.values()) {
        snpCounts.put(state, new MutableLong(0));
        indelCounts.put(state, new MutableLong(0));
    }
    if (truePositivesAndFalseNegativesVcf != null) {
        truePositivesAndFalseNegativesVcfWriter = createVCFWriter(truePositivesAndFalseNegativesVcf);
        final VCFHeader truthHeader = getTruthHeader();
        truthHeader.addMetaDataLine(TRUTH_STATUS_HEADER_LINE);
        defaultToolHeaderLines.forEach(truthHeader::addMetaDataLine);
        truePositivesAndFalseNegativesVcfWriter.writeHeader(truthHeader);
    }
    if (truePositivesAndFalsePositivesVcf != null) {
        truePositivesAndFalsePositivesVcfWriter = createVCFWriter(truePositivesAndFalsePositivesVcf);
        final VCFHeader evalHeader = getEvalHeader();
        defaultToolHeaderLines.forEach(evalHeader::addMetaDataLine);
        evalHeader.addMetaDataLine(TRUTH_STATUS_HEADER_LINE);
        truePositivesAndFalsePositivesVcfWriter.writeHeader(evalHeader);
    }
    if (filteredTrueNegativesAndFalseNegativesVcf != null) {
        filteredTrueNegativesAndFalseNegativesVcfWriter = createVCFWriter(filteredTrueNegativesAndFalseNegativesVcf);
        final VCFHeader evalHeader = getEvalHeader();
        evalHeader.addMetaDataLine(TRUTH_STATUS_HEADER_LINE);
        defaultToolHeaderLines.forEach(evalHeader::addMetaDataLine);
        filteredTrueNegativesAndFalseNegativesVcfWriter.writeHeader(evalHeader);
    }
}

Example 19 with VCFHeaderLine

use of htsjdk.variant.vcf.VCFHeaderLine in project gatk by broadinstitute.

the class AnnotateVcfWithExpectedAlleleFraction method onTraversalStart.

@Override
public void onTraversalStart() {
    final VCFHeader inputHeader = getHeaderForVariants();
    final Set<VCFHeaderLine> headerLines = new HashSet<>(inputHeader.getMetaDataInSortedOrder());
    headerLines.add(new VCFInfoHeaderLine(EXPECTED_ALLELE_FRACTION_NAME, 1, VCFHeaderLineType.Float, "expected allele fraction in pooled bam"));
    final VCFHeader vcfHeader = new VCFHeader(headerLines, inputHeader.getGenotypeSamples());
    headerLines.addAll(getDefaultToolVCFHeaderLines());
    vcfWriter = createVCFWriter(outputVcf);
    vcfWriter.writeHeader(vcfHeader);
    final List<MixingFraction> mixingFractionsList = MixingFraction.readMixingFractions(inputMixingFractions);
    final Map<String, Double> mixingfractionsMap = mixingFractionsList.stream().collect(Collectors.toMap(MixingFraction::getSample, MixingFraction::getMixingFraction));
    mixingFractionsInSampleOrder = inputHeader.getSampleNamesInOrder().stream().mapToDouble(mixingfractionsMap::get).toArray();
}