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

Example 91 with VCFHeader

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

the class HaplotypeCallerEngine method writeHeader.

/**
     * Writes an appropriate VCF header, given our arguments, to the provided writer
     *
     * @param vcfWriter writer to which the header should be written
     */
public void writeHeader(final VariantContextWriter vcfWriter, final SAMSequenceDictionary sequenceDictionary, final Set<VCFHeaderLine> defaultToolHeaderLines) {
    Utils.nonNull(vcfWriter);
    final Set<VCFHeaderLine> headerInfo = new HashSet<>();
    headerInfo.addAll(defaultToolHeaderLines);
    headerInfo.addAll(genotypingEngine.getAppropriateVCFInfoHeaders());
    // all annotation fields from VariantAnnotatorEngine
    headerInfo.addAll(annotationEngine.getVCFAnnotationDescriptions());
    // all callers need to add these standard annotation header lines
    headerInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.DOWNSAMPLED_KEY));
    headerInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.MLE_ALLELE_COUNT_KEY));
    headerInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.MLE_ALLELE_FREQUENCY_KEY));
    // all callers need to add these standard FORMAT field header lines
    VCFStandardHeaderLines.addStandardFormatLines(headerInfo, true, VCFConstants.GENOTYPE_KEY, VCFConstants.GENOTYPE_QUALITY_KEY, VCFConstants.DEPTH_KEY, VCFConstants.GENOTYPE_PL_KEY);
    if (!hcArgs.doNotRunPhysicalPhasing) {
        headerInfo.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.HAPLOTYPE_CALLER_PHASING_ID_KEY));
        headerInfo.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.HAPLOTYPE_CALLER_PHASING_GT_KEY));
    }
    // FILTER fields are added unconditionally as it's not always 100% certain the circumstances
    // where the filters are used.  For example, in emitting all sites the lowQual field is used
    headerInfo.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.LOW_QUAL_FILTER_NAME));
    if (emitReferenceConfidence()) {
        headerInfo.addAll(referenceConfidenceModel.getVCFHeaderLines());
    }
    final VCFHeader vcfHeader = new VCFHeader(headerInfo, sampleSet);
    vcfHeader.setSequenceDictionary(sequenceDictionary);
    vcfWriter.writeHeader(vcfHeader);
}

Example 92 with VCFHeader

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

the class CreateSomaticPanelOfNormals method doWork.

public Object doWork() {
    final List<File> inputVcfs = new ArrayList<>(vcfs);
    final Collection<CloseableIterator<VariantContext>> iterators = new ArrayList<>(inputVcfs.size());
    final Collection<VCFHeader> headers = new HashSet<>(inputVcfs.size());
    final VCFHeader headerOfFirstVcf = new VCFFileReader(inputVcfs.get(0), false).getFileHeader();
    final SAMSequenceDictionary sequenceDictionary = headerOfFirstVcf.getSequenceDictionary();
    final VariantContextComparator comparator = headerOfFirstVcf.getVCFRecordComparator();
    for (final File vcf : inputVcfs) {
        final VCFFileReader reader = new VCFFileReader(vcf, false);
        iterators.add(reader.iterator());
        final VCFHeader header = reader.getFileHeader();
        Utils.validateArg(comparator.isCompatible(header.getContigLines()), () -> vcf.getAbsolutePath() + " has incompatible contigs.");
        headers.add(header);
    }
    final VariantContextWriter writer = GATKVariantContextUtils.createVCFWriter(outputVcf, sequenceDictionary, false, Options.INDEX_ON_THE_FLY);
    writer.writeHeader(new VCFHeader(VCFUtils.smartMergeHeaders(headers, false)));
    final MergingIterator<VariantContext> mergingIterator = new MergingIterator<>(comparator, iterators);
    SimpleInterval currentPosition = new SimpleInterval("FAKE", 1, 1);
    final List<VariantContext> variantsAtThisPosition = new ArrayList<>(20);
    while (mergingIterator.hasNext()) {
        final VariantContext vc = mergingIterator.next();
        if (!currentPosition.overlaps(vc)) {
            processVariantsAtSamePosition(variantsAtThisPosition, writer);
            variantsAtThisPosition.clear();
            currentPosition = new SimpleInterval(vc.getContig(), vc.getStart(), vc.getStart());
        }
        variantsAtThisPosition.add(vc);
    }
    mergingIterator.close();
    writer.close();
    return "SUCCESS";
}

Example 93 with VCFHeader

use of htsjdk.variant.vcf.VCFHeader in project gatk-protected 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();
}

Example 94 with VCFHeader

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

the class FilterMutectCalls method onTraversalStart.

@Override
public void onTraversalStart() {
    final VCFHeader inputHeader = getHeaderForVariants();
    final Set<VCFHeaderLine> headerLines = new HashSet<>(inputHeader.getMetaDataInSortedOrder());
    Mutect2FilteringEngine.M_2_FILTER_NAMES.stream().map(GATKVCFHeaderLines::getFilterLine).forEach(headerLines::add);
    headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.ARTIFACT_IN_NORMAL_FILTER_NAME, "artifact_in_normal"));
    headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.MEDIAN_BASE_QUALITY_DIFFERENCE_FILTER_NAME, "ref - alt median base quality"));
    headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.MEDIAN_MAPPING_QUALITY_DIFFERENCE_FILTER_NAME, "ref - alt median mapping quality"));
    headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.MEDIAN_CLIPPING_DIFFERENCE_FILTER_NAME, "ref - alt median clipping"));
    headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.MEDIAN_FRAGMENT_LENGTH_DIFFERENCE_FILTER_NAME, "abs(ref - alt) median fragment length"));
    headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.READ_POSITION_FILTER_NAME, "median distance of alt variants from end of reads"));
    headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.CONTAMINATION_FILTER_NAME, "contamination"));
    headerLines.addAll(getDefaultToolVCFHeaderLines());
    final VCFHeader vcfHeader = new VCFHeader(headerLines, inputHeader.getGenotypeSamples());
    vcfWriter = createVCFWriter(new File(outputVcf));
    vcfWriter.writeHeader(vcfHeader);
}

Example 95 with VCFHeader

use of htsjdk.variant.vcf.VCFHeader 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);
    }
}