@Override public int compareTo(Object other) { return toString().compareTo(other.toString()); }
@Override public int compareTo(Object other) { return toString().compareTo(other.toString()); }
public int compareTo(Object other) { return toString().compareTo(other.toString()); }
writer.write(line.toString()); writer.write("\n");
writer.write(line.toString()); writer.write("\n");
writer.write(line.toString()); writer.write("\n");
@Override public VcfHeader convert(VCFHeader header) { VcfHeader avroVcfHeader = new VcfHeader(); LinkedHashMap<String, List<Object>> meta = new LinkedHashMap<>(); avroVcfHeader.setMeta(meta); for (VCFHeaderLine line : header.getMetaDataInInputOrder()) { if (line.getKey().equalsIgnoreCase("fileFormat")) { avroVcfHeader.setFileFormat(line.getValue()); continue; } Object value; if (line.getValue().isEmpty()) { value = VCFHeaderLineTranslator.parseLine(VCFHeaderVersion.VCF4_2, line.toString(), null); } else { value = line.getValue(); } if (!meta.containsKey(line.getKey())) { meta.put(line.getKey(), new LinkedList<>()); } meta.get(line.getKey()).add(value); } return avroVcfHeader; }
@Test(enabled = true) public void testMultipleGATKVersionsInVCF() throws Exception { WalkerTestSpec spec = new WalkerTestSpec("-T TestPrintVariantsWalker -R " + b37KGReference + " -V " + privateTestDir + "gatkCommandLineInHeader.vcf" + " -o %s", 1, Arrays.asList("")); spec.disableShadowBCF(); final File vcf = executeTest("testMultipleGATKVersionsInVCF", spec).first.get(0); final VCFCodec codec = new VCFCodec(); final VCFHeader header = (VCFHeader) codec.readActualHeader(codec.makeSourceFromStream(new FileInputStream(vcf))); boolean foundHC = false; boolean foundPV = false; for ( final VCFHeaderLine line : header.getMetaDataInInputOrder() ) { if ( line.getKey().startsWith(GATKVCFUtils.GATK_COMMAND_LINE_KEY) ) { if ( line.toString().contains("HaplotypeCaller") ) { Assert.assertFalse(foundHC); foundHC = true; } if ( line.toString().contains("TestPrintVariantsWalker") ) { Assert.assertFalse(foundPV); foundPV = true; } } } Assert.assertTrue(foundHC, "Didn't find HaplotypeCaller command line header field"); Assert.assertTrue(foundPV, "Didn't find TestPrintVariantsWalker command line header field"); }
@Test public void testAskingGCContent() throws IOException{ WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000 -A GCContent", 1, Arrays.asList("fcc42d7e0351efa7c3db0a114cbc17ed")); final File outputVCF = executeTest("test file has annotations, adding GCContent annotation", spec).getFirst().get(0); final VCFCodec codec = new VCFCodec(); final VCFHeader header = (VCFHeader) codec.readActualHeader(codec.makeSourceFromStream(new FileInputStream(outputVCF))); final VCFHeaderLine infoLineGC = header.getInfoHeaderLine(GATKVCFConstants.GC_CONTENT_KEY); // GC content must be a Float type Assert.assertTrue(infoLineGC.toString().contains("Type=Float")); }
@Test(enabled = true) public void testGATKVersionInVCF() throws Exception { WalkerTestSpec spec = new WalkerTestSpec("-T TestPrintVariantsWalker -R " + b37KGReference + " -V " + privateTestDir + "NA12878.WGS.b37.chr20.firstMB.vcf" + " -o %s -L 20:61098", 1, Arrays.asList("")); spec.disableShadowBCF(); final File vcf = executeTest("testGATKVersionInVCF", spec).first.get(0); final VCFCodec codec = new VCFCodec(); final VCFHeader header = (VCFHeader) codec.readActualHeader(codec.makeSourceFromStream(new FileInputStream(vcf))); // go through the metadata headers and look for ones that start with the GATK_COMMAND_LINE_KEY VCFHeaderLine versionLine = null; for ( final VCFHeaderLine headerLine : header.getMetaDataInInputOrder()) { if(headerLine.getKey().startsWith(GATKVCFUtils.GATK_COMMAND_LINE_KEY)) { versionLine = headerLine; break; } } Assert.assertNotNull(versionLine); Assert.assertTrue(versionLine.toString().contains("TestPrintVariantsWalker")); }
Map<String, String> map = VCFHeaderLineTranslator.parseLine(VCFHeaderVersion.VCF4_2, line.toString(), null); VariantFileHeaderComplexLine.Builder builder = VariantFileHeaderComplexLine.newBuilder(); setValue(map, "ID", builder::setId);