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

Example 6 with VCFHeader

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

the class FeatureDataSource method getSequenceDictionary.

/**
     * Returns the sequence dictionary for this source of Features.
     * Uses the dictionary from the VCF header (if present) for variant inputs,
     * otherwise attempts to create a sequence dictionary from the index file (if present).
     * Returns null if no dictionary could be created from either the header or the index.
     */
public SAMSequenceDictionary getSequenceDictionary() {
    SAMSequenceDictionary dict = null;
    final Object header = getHeader();
    if (header instanceof VCFHeader) {
        dict = ((VCFHeader) header).getSequenceDictionary();
    }
    if (dict != null && !dict.isEmpty()) {
        return dict;
    }
    if (hasIndex) {
        return IndexUtils.createSequenceDictionaryFromFeatureIndex(new File(featureInput.getFeaturePath()));
    }
    return null;
}

Example 7 with VCFHeader

use of htsjdk.variant.vcf.VCFHeader in project gatk 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 8 with VCFHeader

use of htsjdk.variant.vcf.VCFHeader in project gatk 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 9 with VCFHeader

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

the class FeatureContextUnitTest method testGetHeader.

@Test
public void testGetHeader() {
    final ArtificialFeatureContainingCommandLineProgram toolInstance = new ArtificialFeatureContainingCommandLineProgram();
    try (final FeatureManager featureManager = new FeatureManager(toolInstance)) {
        final FeatureContext featureContext = new FeatureContext(featureManager, new SimpleInterval("1", 1, 1));
        final Object header = featureContext.getHeader(toolInstance.featureArgument);
        Assert.assertTrue(header instanceof VCFHeader, "Header for " + toolInstance.featureArgument.getFeaturePath() + " not a VCFHeader");
    }
}

Example 10 with VCFHeader

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

the class GATKToolUnitTest method writeHeaderAndBadVariant.

private void writeHeaderAndBadVariant(final VariantContextWriter writer) {
    final VariantContextBuilder vcBuilder = new VariantContextBuilder("chr1", "1", 1, 1, Arrays.asList(Allele.create("A", true)));
    vcBuilder.attribute("fake", new Object());
    final VariantContext vc = vcBuilder.make();
    final VCFHeader vcfHeader = new VCFHeader();
    writer.writeHeader(vcfHeader);
    writer.add(vc);
}