Package htsjdk.variant.bcf2

Examples of htsjdk.variant.bcf2.BCF2Codec

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    //@Test
    public void rawTestFile() throws Exception {
        String path = "/path/to/myfile.bcf";
        PositionalBufferedStream ps = new PositionalBufferedStream(new FileInputStream(path));

        BCF2Codec codec = new BCF2Codec();
        codec.readHeader(ps);

    }
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        if (fn.endsWith(".vcf4")) {
            return new VCFWrapperCodec(new VCFCodec(), genome);
        } else if (fn.endsWith(".vcf")) {
            return new VCFWrapperCodec(getVCFCodec(locator), genome);
        } else if (fn.endsWith(".bcf")) {
            return new BCF2WrapperCodec(new BCF2Codec(), genome);
        } else if (fn.endsWith(".bed")) {
            final IGVBEDCodec codec = new IGVBEDCodec(genome);
            if (fn.endsWith("junctions.bed")) {
                codec.setSpliceJunctions(true);
            }
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            case BLOCK_COMPRESSED_VCF:
                // getFeatureReader will handle both block-compressed and plain text VCFs
                reader = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), new VCFCodec(), false);
                break;
            case BCF:
                reader = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), new BCF2Codec(), false);
                break;
        }
        return reader;
    }
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        }
    }

    public static void assertVCFandBCFFilesAreTheSame(final File vcfFile, final File bcfFile) throws IOException {
        final Pair<VCFHeader, GATKVCFUtils.VCIterable<LineIterator>> vcfData = GATKVCFUtils.readAllVCs(vcfFile, new VCFCodec());
        final Pair<VCFHeader, GATKVCFUtils.VCIterable<PositionalBufferedStream>> bcfData = GATKVCFUtils.readAllVCs(bcfFile, new BCF2Codec());
        assertVCFHeadersAreEqual(bcfData.getFirst(), vcfData.getFirst());
        assertVariantContextStreamsAreEqual(bcfData.getSecond(), vcfData.getSecond());
    }
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Related Classes of htsjdk.variant.bcf2.BCF2Codec

  • org.broad.igv.feature.tribble.CodecFactory
  • org.broad.igv.variant.vcf.BCFReaderTest
  • org.broadinstitute.gatk.tools.CatVariants
  • org.broadinstitute.gatk.utils.BaseTest
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