Java Code Examples for htsjdk.variant.vcf.VCFHeader#getMetaDataInSortedOrder()

The following examples show how to use htsjdk.variant.vcf.VCFHeader#getMetaDataInSortedOrder() . You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.
Example 1
Source File: AnnotateVcfWithExpectedAlleleFraction.java    From gatk-protected with BSD 3-Clause "New" or "Revised" License 6 votes vote down vote up 
@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 2
Source File: FilterMutectCalls.java    From gatk-protected with BSD 3-Clause "New" or "Revised" License 6 votes vote down vote up 
@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 3
Source File: AnnotateVcfWithExpectedAlleleFraction.java    From gatk with BSD 3-Clause "New" or "Revised" License 6 votes vote down vote up 
@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 4
Source File: FilterAlignmentArtifacts.java    From gatk with BSD 3-Clause "New" or "Revised" License 6 votes vote down vote up 
@Override
public void onTraversalStart() {
    realignmentEngine = new RealignmentEngine(realignmentArgumentCollection);
    vcfWriter = createVCFWriter(new File(outputVcf));

    final VCFHeader inputHeader = getHeaderForVariants();
    final Set<VCFHeaderLine> headerLines = new HashSet<>(inputHeader.getMetaDataInSortedOrder());
    headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.ALIGNMENT_ARTIFACT_FILTER_NAME));
    headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.UNITIG_SIZES_KEY));
    headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.ALIGNMENT_SCORE_DIFFERENCE_KEY));
    headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.JOINT_ALIGNMENT_COUNT_KEY));
    headerLines.addAll(getDefaultToolVCFHeaderLines());
    final VCFHeader vcfHeader = new VCFHeader(headerLines, inputHeader.getGenotypeSamples());
    vcfWriter.writeHeader(vcfHeader);
    bamHeader = getHeaderForReads();
    samplesList = new IndexedSampleList(new ArrayList<>(ReadUtils.getSamplesFromHeader(bamHeader)));
    referenceReader = AssemblyBasedCallerUtils.createReferenceReader(Utils.nonNull(referenceArguments.getReferenceSpecifier()));
    assemblyEngine = MTAC.createReadThreadingAssembler();
    likelihoodCalculationEngine = AssemblyBasedCallerUtils.createLikelihoodCalculationEngine(MTAC.likelihoodArgs);
    haplotypeBAMWriter = bamOutputPath == null ? Optional.empty() :
            Optional.of(new HaplotypeBAMWriter(HaplotypeBAMWriter.WriterType.ALL_POSSIBLE_HAPLOTYPES, IOUtils.getPath(bamOutputPath), true, false, getHeaderForSAMWriter()));
}
Example 5
Source File: RemoveNearbyIndels.java    From gatk-protected with BSD 3-Clause "New" or "Revised" License 5 votes vote down vote up 
@Override
public void onTraversalStart() {
    final VCFHeader inputHeader = getHeaderForVariants();
    final VCFHeader vcfHeader = new VCFHeader(inputHeader.getMetaDataInSortedOrder(), inputHeader.getGenotypeSamples());
    getDefaultToolVCFHeaderLines().forEach(vcfHeader::addMetaDataLine);
    vcfWriter = createVCFWriter(new File(outputVcf));
    vcfWriter.writeHeader(vcfHeader);
}
Example 6
Source File: RemoveNearbyIndels.java    From gatk with BSD 3-Clause "New" or "Revised" License 5 votes vote down vote up 
@Override
public void onTraversalStart() {
    final VCFHeader inputHeader = getHeaderForVariants();
    final VCFHeader vcfHeader = new VCFHeader(inputHeader.getMetaDataInSortedOrder(), inputHeader.getGenotypeSamples());
    getDefaultToolVCFHeaderLines().forEach(vcfHeader::addMetaDataLine);
    vcfWriter = createVCFWriter(new File(outputVcf));
    vcfWriter.writeHeader(vcfHeader);
}
Example 7
Source File: CNNScoreVariants.java    From gatk with BSD 3-Clause "New" or "Revised" License 5 votes vote down vote up 
private void writeVCFHeader(VariantContextWriter vcfWriter) {
    // setup the header fields
    final VCFHeader inputHeader = getHeaderForVariants();
    final Set<VCFHeaderLine> inputHeaders = inputHeader.getMetaDataInSortedOrder();
    final Set<VCFHeaderLine> hInfo = new HashSet<>(inputHeaders);
    hInfo.add(GATKVCFHeaderLines.getInfoLine(scoreKey));
    final TreeSet<String> samples = new TreeSet<>();
    samples.addAll(inputHeader.getGenotypeSamples());
    hInfo.addAll(getDefaultToolVCFHeaderLines());
    final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
    vcfWriter.writeHeader(vcfHeader);
}