Examples with VariantContextWriter htsjdk.variant.variantcontext.writer.VariantContextWriter used on opensource projects

Example 6 with VariantContextWriter

use of htsjdk.variant.variantcontext.writer.VariantContextWriter in project gatk by broadinstitute.

the class RenameSampleInVcf method doWork.

@Override
protected Object doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsWritable(OUTPUT);
    try (final VCFFileReader in = new VCFFileReader(INPUT)) {
        final VCFHeader header = in.getFileHeader();
        Utils.validateArg(header.getGenotypeSamples().size() == 1, "Input VCF must be single-sample.");
        Utils.validateArg(OLD_SAMPLE_NAME == null || OLD_SAMPLE_NAME.equals(header.getGenotypeSamples().get(0)), () -> "Input VCF did not contain expected sample. Contained: " + header.getGenotypeSamples().get(0));
        final EnumSet<Options> options = EnumSet.copyOf(VariantContextWriterBuilder.DEFAULT_OPTIONS);
        if (CREATE_INDEX)
            options.add(Options.INDEX_ON_THE_FLY);
        else
            options.remove(Options.INDEX_ON_THE_FLY);
        final VCFHeader outHeader = new VCFHeader(header.getMetaDataInInputOrder(), CollectionUtil.makeList(NEW_SAMPLE_NAME));
        try (final VariantContextWriter out = new VariantContextWriterBuilder().setOutputFile(OUTPUT).setReferenceDictionary(outHeader.getSequenceDictionary()).setOptions(options).build()) {
            out.writeHeader(outHeader);
            for (final VariantContext ctx : in) {
                out.add(ctx);
            }
        }
    }
    return null;
}

Example 7 with VariantContextWriter

use of htsjdk.variant.variantcontext.writer.VariantContextWriter in project gatk by broadinstitute.

the class SortVcf method writeSortedOutput.

private void writeSortedOutput(final VCFHeader outputHeader, final SortingCollection<VariantContext> sortedOutput) {
    final ProgressLogger writeProgress = new ProgressLogger(logger, 25000, "wrote", "records");
    final EnumSet<Options> options = CREATE_INDEX ? EnumSet.of(Options.INDEX_ON_THE_FLY) : EnumSet.noneOf(Options.class);
    final VariantContextWriter out = new VariantContextWriterBuilder().setReferenceDictionary(outputHeader.getSequenceDictionary()).setOptions(options).setOutputFile(OUTPUT).build();
    out.writeHeader(outputHeader);
    for (final VariantContext variantContext : sortedOutput) {
        out.add(variantContext);
        writeProgress.record(variantContext.getContig(), variantContext.getStart());
    }
    out.close();
}

Example 8 with VariantContextWriter

use of htsjdk.variant.variantcontext.writer.VariantContextWriter 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 9 with VariantContextWriter

use of htsjdk.variant.variantcontext.writer.VariantContextWriter in project gatk by broadinstitute.

the class GATKVariantContextUtilsUnitTest method testCreateVariantContextWriterNoReference.

@Test(expectedExceptions = IllegalArgumentException.class)
public void testCreateVariantContextWriterNoReference() {
    // should throw due to lack of reference
    final File outFile = createTempFile("testVCFWriter", ".vcf");
    final VariantContextWriter vcw = GATKVariantContextUtils.createVCFWriter(outFile, null, true, Options.INDEX_ON_THE_FLY);
    vcw.close();
}

Example 10 with VariantContextWriter

use of htsjdk.variant.variantcontext.writer.VariantContextWriter in project gatk-protected by broadinstitute.

the class HaplotypeCallerSpark method writeVariants.

/**
     * WriteVariants, this is currently going to be horribly slow and explosive on a full size file since it performs a collect.
     *
     * This will be replaced by a parallel writer similar to what's done with {@link org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink}
     */
private void writeVariants(JavaRDD<VariantContext> variants) {
    final List<VariantContext> collectedVariants = variants.collect();
    final SAMSequenceDictionary referenceDictionary = getReferenceSequenceDictionary();
    final List<VariantContext> sortedVariants = collectedVariants.stream().sorted((o1, o2) -> IntervalUtils.compareLocatables(o1, o2, referenceDictionary)).collect(Collectors.toList());
    final HaplotypeCallerEngine hcEngine = new HaplotypeCallerEngine(hcArgs, getHeaderForReads(), new ReferenceMultiSourceAdapter(getReference(), getAuthHolder()));
    try (final VariantContextWriter writer = hcEngine.makeVCFWriter(output, getBestAvailableSequenceDictionary())) {
        hcEngine.writeHeader(writer, getHeaderForReads().getSequenceDictionary(), Collections.emptySet());
        sortedVariants.forEach(writer::add);
    }
}