Package htsjdk.tribble

Examples of htsjdk.tribble.FeatureCodecHeader

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     * @throws IOException
     */
    public final static <SOURCE> Pair<VCFHeader, VCIterable<SOURCE>> readAllVCs( final File file, final FeatureCodec<VariantContext, SOURCE> codec) throws IOException {
        // read in the features
        SOURCE source = codec.makeSourceFromStream(new FileInputStream(file));
        FeatureCodecHeader header = codec.readHeader(source);
        final VCFHeader vcfHeader = (VCFHeader)header.getHeaderValue();
        return new Pair<>(vcfHeader, new VCIterable<>(source, codec, vcfHeader));
    }
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    @Override
    public FeatureCodecHeader readHeader(final LineIterator lineIterator) throws IOException {
        final String header = (String) readActualHeader(lineIterator);
        // TODO: This approach may cause issues with files formatted with \r\n-style line-endings.
        return new FeatureCodecHeader(header, header.length() + 1);
    }
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Related Classes of htsjdk.tribble.FeatureCodecHeader

  • org.broadinstitute.gatk.utils.codecs.hapmap.RawHapMapCodec
  • org.broadinstitute.gatk.utils.variant.GATKVCFUtils
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