Package htsjdk.variant.vcf

Examples of htsjdk.variant.vcf.VCF3Codec

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    }

    @Test
    public void testIntervalIndex33() throws Exception {
        String testFile = TestUtils.LARGE_DATA_DIR + "CEU.SRP000032.2010_03_v3.3.genotypes.head.vcf";
        FeatureCodec codec = new VCF3Codec();
        tstIntervalIndex(testFile, codec);
    }
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        String path = locator.getPath();
        String fn = locator.getTypeString().toLowerCase();

        if (fn.endsWith(".vcf3")) {
            return new VCFWrapperCodec(new VCF3Codec(), genome);
        }
        if (fn.endsWith(".vcf4")) {
            return new VCFWrapperCodec(new VCFCodec(), genome);
        } else if (fn.endsWith(".vcf")) {
            return new VCFWrapperCodec(getVCFCodec(locator), genome);
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                        formatLine.toLowerCase().startsWith("##format")) {
                    String[] tmp = formatLine.split("=");
                    if (tmp.length > 1) {
                        String version = tmp[1].toLowerCase();
                        if (version.startsWith("vcfv3")) {
                            return new VCF3Codec();
                        } else {
                            return new VCFCodec();
                        }
                    }
                }
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Related Classes of htsjdk.variant.vcf.VCF3Codec

  • org.broad.igv.feature.tribble.CodecFactory
  • org.broad.igv.tools.IGVToolsTest
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