String version = tmp[1].toLowerCase(); if (version.startsWith("vcfv3")) { return new VCF3Codec(); } else { return new VCFCodec();
@Test public void testGetTabixFormat() { Assert.assertEquals(new VCFCodec().getTabixFormat(), TabixFormat.VCF); Assert.assertEquals(new VCF3Codec().getTabixFormat(), TabixFormat.VCF); }
return new VCFWrapperCodec(new VCF3Codec(), genome);
@Test @Ignore("Requires largedata bundle") 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); }
@Test public void simpleTest() throws Exception { final VCF3Codec codec = new VCF3Codec(); final FeatureReader<VariantContext> reader = AbstractFeatureReader.getFeatureReader(SMALL_VCF.getAbsolutePath(), codec, false); final VCFHeader headerFromFile = (VCFHeader)reader.getHeader(); final File vcf = File.createTempFile("TabixOnTheFlyIndexCreationTest.", IOUtil.COMPRESSED_VCF_FILE_EXTENSION); final File tabix = new File(vcf.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION); vcf.deleteOnExit(); tabix.deleteOnExit(); final VariantContextWriter vcfWriter = new VariantContextWriterBuilder() .setOutputFile(vcf) .setReferenceDictionary(headerFromFile.getSequenceDictionary()) .setOptions(EnumSet.of(Options.INDEX_ON_THE_FLY, Options.ALLOW_MISSING_FIELDS_IN_HEADER)) .build(); vcfWriter.writeHeader(headerFromFile); final CloseableTribbleIterator<VariantContext> it = reader.iterator(); while (it.hasNext()) { vcfWriter.add(it.next()); } it.close(); vcfWriter.close(); // Hard to validate, so just confirm that index can be read. new TabixIndex(tabix); } }