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

Example 1 with VCFCodec

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

the class GenomicsDBImport method getReaderFromVCFUri.

/**
     * Creates a feature reader object from a given VCF URI (can also be
     * a local file path) and returns it
     * @param variantPath  URI or file path
     * @return  Feature reader
     */
private AbstractFeatureReader<VariantContext, LineIterator> getReaderFromVCFUri(final String variantPath) {
    final String variantURI = IOUtils.getPath(variantPath).toAbsolutePath().toUri().toString();
    final Function<SeekableByteChannel, SeekableByteChannel> cloudWrapper = (cloudPrefetchBuffer > 0 ? is -> SeekableByteChannelPrefetcher.addPrefetcher(cloudPrefetchBuffer, is) : Function.identity());
    final Function<SeekableByteChannel, SeekableByteChannel> cloudIndexWrapper = (cloudIndexPrefetchBuffer > 0 ? is -> SeekableByteChannelPrefetcher.addPrefetcher(cloudIndexPrefetchBuffer, is) : Function.identity());
    return AbstractFeatureReader.getFeatureReader(variantURI, null, new VCFCodec(), true, cloudWrapper, cloudIndexWrapper);
}

Example 2 with VCFCodec

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

the class GatherVcfs method getReaderFromVCFUri.

private static FeatureReader<VariantContext> getReaderFromVCFUri(final Path variantPath, final int cloudPrefetchBuffer) {
    final String variantURI = variantPath.toUri().toString();
    final Function<SeekableByteChannel, SeekableByteChannel> cloudWrapper = (cloudPrefetchBuffer > 0 ? is -> SeekableByteChannelPrefetcher.addPrefetcher(cloudPrefetchBuffer, is) : Function.identity());
    return AbstractFeatureReader.getFeatureReader(variantURI, null, new VCFCodec(), false, cloudWrapper, Function.identity());
}

Example 3 with VCFCodec

use of htsjdk.variant.vcf.VCFCodec in project hmftools by hartwigmedical.

the class SvVCFAnnotator method readFromVcf.

private List<VariantContext> readFromVcf(String vcfFilename) {
    List<VariantContext> variants = Lists.newArrayList();
    final StructuralVariantFactory factory = new StructuralVariantFactory(false);
    try (final AbstractFeatureReader<VariantContext, LineIterator> reader = AbstractFeatureReader.getFeatureReader(vcfFilename, new VCFCodec(), false)) {
        while (reader.iterator().hasNext()) variants.add(reader.iterator().next());
    } catch (Exception e) {
    }
    return variants;
}

Example 4 with VCFCodec

use of htsjdk.variant.vcf.VCFCodec in project hmftools by hartwigmedical.

the class BachelorApplication method processSV.

private static Collection<EligibilityReport> processSV(final String patient, final File vcf, final BachelorEligibility eligibility) {
    LOGGER.info("processing sv: {}", vcf.getPath());
    final StructuralVariantFactory factory = new StructuralVariantFactory(true);
    try {
        try (final AbstractFeatureReader<VariantContext, LineIterator> reader = AbstractFeatureReader.getFeatureReader(vcf.getPath(), new VCFCodec(), false)) {
            reader.iterator().forEach(factory::addVariantContext);
        }
    } catch (IOException e) {
        LOGGER.error("error with SV file {}: {}", vcf.getPath(), e.getMessage());
        return Collections.emptyList();
    }
    return eligibility.processStructuralVariants(patient, factory.results());
}

Example 5 with VCFCodec

use of htsjdk.variant.vcf.VCFCodec in project ASCIIGenome by dariober.

the class IntervalFeatureTest method canFormatVCFLine.

@Test
public void canFormatVCFLine() throws InvalidGenomicCoordsException, InvalidColourException, IOException, InvalidConfigException {
    List<Double> rulerMap = new ArrayList<Double>();
    for (int i = 1; i < 100; i++) {
        rulerMap.add((double) i);
    }
    // Prepare header
    VCFFileReader reader = new VCFFileReader(new File("test_data/CHD.exon.2010_03.sites.vcf.gz"));
    VCFHeader vcfHeader = reader.getFileHeader();
    reader.close();
    VCFCodec vcfCodec = new VCFCodec();
    vcfCodec.setVCFHeader(vcfHeader, Utils.getVCFHeaderVersion(vcfHeader));
    String vcfLine = "1 10 . C G 23 PASS AA=.;AC=.;AN=.DP=.".replaceAll(" ", "\t");
    IntervalFeature ift = new IntervalFeature(vcfLine, TrackFormat.VCF, vcfCodec);
    ift.mapToScreen(rulerMap);
    assertEquals(1, ift.getIdeogram(true, true).size());
    assertEquals('G', ift.getIdeogram(true, true).get(0).getText());
    // Just check there is a formatting char
    assertTrue(ift.getIdeogram(true, true).get(0).format(false).contains("["));
    // Deletion
    vcfLine = "1 10 . CTTG C 23 PASS AA=.;AC=.;AN=.DP=.".replaceAll(" ", "\t");
    ift = new IntervalFeature(vcfLine, TrackFormat.VCF, vcfCodec);
    ift.mapToScreen(rulerMap);
    assertEquals('D', ift.getIdeogram(true, true).get(0).getText());
    assertEquals(3, ift.getIdeogram(true, true).size());
    // Insertion
    vcfLine = "1 10 . C CTTG 23 PASS AA=.;AC=.;AN=.DP=.".replaceAll(" ", "\t");
    ift = new IntervalFeature(vcfLine, TrackFormat.VCF, vcfCodec);
    ift.mapToScreen(rulerMap);
    assertEquals("I", ift.getIdeogram(true, true).get(0).format(true));
    assertEquals(3, ift.getIdeogram(true, true).size());
    // Multiple alleles
    vcfLine = "1 10 . C CTTG,A 23 PASS AA=.;AC=.;AN=.DP=.".replaceAll(" ", "\t");
    ift = new IntervalFeature(vcfLine, TrackFormat.VCF, vcfCodec);
    ift.mapToScreen(rulerMap);
    assertEquals("|", ift.getIdeogram(true, true).get(0).format(true));
}