@Override public List<VCFFormatHeaderLine> getDescriptions() { return Collections.singletonList(VCFStandardHeaderLines.getFormatLine(VCFConstants.DEPTH_KEY)); } }
public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(VCFStandardHeaderLines.getFormatLine(getKeyNames().get(0))); } }
private static VariantContextWriter getVariantContextWriter(final File outputFile, final File referenceSequenceFileName, final String sample, final String source, final ReferenceSequenceFile ref) { final VariantContextWriter variantContextWriter = new VariantContextWriterBuilder() .setReferenceDictionary(ref.getSequenceDictionary()) .setOutputFile(outputFile).build(); final Set<VCFHeaderLine> lines = new LinkedHashSet<>(); lines.add(new VCFHeaderLine("reference", referenceSequenceFileName.getAbsolutePath())); lines.add(new VCFHeaderLine("source", source)); lines.add(new VCFHeaderLine("fileDate", new Date().toString())); lines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_PL_KEY)); lines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_ALLELE_DEPTHS)); lines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.DEPTH_KEY)); final VCFHeader header = new VCFHeader(lines, Collections.singletonList(sample)); header.setSequenceDictionary(ref.getSequenceDictionary()); variantContextWriter.writeHeader(header); return variantContextWriter; }
private static VariantContextWriter getVariantContextWriter(final File outputFile, final File referenceSequenceFileName, final String sample, final String source, final ReferenceSequenceFile ref) { final VariantContextWriter variantContextWriter = new VariantContextWriterBuilder() .setReferenceDictionary(ref.getSequenceDictionary()) .setOutputFile(outputFile).build(); final Set<VCFHeaderLine> lines = new LinkedHashSet<>(); lines.add(new VCFHeaderLine("reference", referenceSequenceFileName.getAbsolutePath())); lines.add(new VCFHeaderLine("source", source)); lines.add(new VCFHeaderLine("fileDate", new Date().toString())); lines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_PL_KEY)); lines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_ALLELE_DEPTHS)); lines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.DEPTH_KEY)); final VCFHeader header = new VCFHeader(lines, Collections.singletonList(sample)); header.setSequenceDictionary(ref.getSequenceDictionary()); variantContextWriter.writeHeader(header); return variantContextWriter; }
/** * Gets the header lines for the VCF writer * * @return A set of VCF header lines */ private static Set<VCFHeaderLine> getHeaderInfo() { Set<VCFHeaderLine> headerLines = new HashSet<>(); // INFO fields for overall data headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY)); headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AVG_INTERVAL_DP_KEY)); headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.INTERVAL_GC_CONTENT_KEY)); headerLines.add(new VCFInfoHeaderLine("Diagnose Targets", 0, VCFHeaderLineType.Flag, "DiagnoseTargets mode")); // FORMAT fields for each genotype headerLines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_FILTER_KEY)); headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.AVG_INTERVAL_DP_BY_SAMPLE_KEY)); headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.LOW_COVERAGE_LOCI)); headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.ZERO_COVERAGE_LOCI)); // FILTER fields for (CallableStatus stat : CallableStatus.values()) headerLines.add(new VCFFilterHeaderLine(stat.name(), stat.description)); return headerLines; }
hInfo.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_KEY));
@Test(dataProvider = "getStandardLines") public void getStandardLines(final String key, final String type, final boolean expectedToBeStandard) { VCFCompoundHeaderLine line = null; if ( type.equals("info") ) line = VCFStandardHeaderLines.getInfoLine(key, false); else if ( type.equals("format") ) line = VCFStandardHeaderLines.getFormatLine(key, false); else throw new IllegalArgumentException("Unexpected type in getStandardLines " + type); if ( expectedToBeStandard ) { Assert.assertNotNull(line); Assert.assertEquals(line.getID(), key); Assert.assertTrue(deeperTest(line)); } else { Assert.assertNull(line); } }
hInfo.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_FILTER_KEY));
public static void addFormatHeaders(VCFHeader header) { header.addMetaDataLine(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_KEY)); for (VcfFormatAttributes attr : VcfFormatAttributes.values()) { if (attr.formatHeader() != null) { header.addMetaDataLine(attr.formatHeader()); } } } }
hInfo.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.PHASE_QUALITY_KEY, true)); hInfo.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.RBP_HAPLOTYPE_KEY)); hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.RBP_INCONSISTENT_KEY));
@DataProvider(name = "RepairHeaderTest") public Object[][] makeRepairHeaderTest() { final VCFInfoHeaderLine standardAC = VCFStandardHeaderLines.getInfoLine("AC"); final VCFInfoHeaderLine goodAC = new VCFInfoHeaderLine("AC", VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "x"); final VCFFormatHeaderLine standardGT = VCFStandardHeaderLines.getFormatLine("GT"); final VCFFormatHeaderLine goodGT = new VCFFormatHeaderLine("GT", 1, VCFHeaderLineType.String, "x"); List<Object[]> tests = new ArrayList<Object[]>(); tests.add(new Object[]{new RepairHeaderTest( standardGT, standardGT)}); tests.add(new Object[]{new RepairHeaderTest( goodGT, goodGT )}); tests.add(new Object[]{new RepairHeaderTest( new VCFFormatHeaderLine("GT", 2, VCFHeaderLineType.String, "x"), standardGT)}); tests.add(new Object[]{new RepairHeaderTest( new VCFFormatHeaderLine("GT", 1, VCFHeaderLineType.Integer, "x"), standardGT)}); tests.add(new Object[]{new RepairHeaderTest( new VCFFormatHeaderLine("GT", 1, VCFHeaderLineType.Float, "x"), standardGT)}); tests.add(new Object[]{new RepairHeaderTest( new VCFFormatHeaderLine("GT", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Float, "x"), standardGT)}); tests.add(new Object[]{new RepairHeaderTest( new VCFFormatHeaderLine("GT", VCFHeaderLineCount.G, VCFHeaderLineType.String, "x"), standardGT)}); tests.add(new Object[]{new RepairHeaderTest( new VCFFormatHeaderLine("GT", VCFHeaderLineCount.A, VCFHeaderLineType.String, "x"), standardGT)}); tests.add(new Object[]{new RepairHeaderTest( standardAC, standardAC)}); tests.add(new Object[]{new RepairHeaderTest( goodAC, goodAC )}); tests.add(new Object[]{new RepairHeaderTest( new VCFInfoHeaderLine("AC", 1, VCFHeaderLineType.Integer, "x"), standardAC)}); tests.add(new Object[]{new RepairHeaderTest( new VCFInfoHeaderLine("AC", VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "x"), standardAC)}); tests.add(new Object[]{new RepairHeaderTest( new VCFInfoHeaderLine("AC", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x"), standardAC)}); tests.add(new Object[]{new RepairHeaderTest( new VCFInfoHeaderLine("AC", 1, VCFHeaderLineType.Float, "x"), standardAC)}); tests.add(new Object[]{new RepairHeaderTest( new VCFInfoHeaderLine("AC", 1, VCFHeaderLineType.String, "x"), standardAC)}); tests.add(new Object[]{new RepairHeaderTest( new VCFInfoHeaderLine("AC", 0, VCFHeaderLineType.Flag, "x"), standardAC)}); tests.add(new Object[]{new RepairHeaderTest( new VCFInfoHeaderLine("AC", 0, VCFHeaderLineType.Flag, "x", "source", "v1.2.3"), standardAC)}); tests.add(new Object[]{new RepairHeaderTest( new VCFInfoHeaderLine("NON_STANDARD_INFO", 1, VCFHeaderLineType.String, "x"))}); tests.add(new Object[]{new RepairHeaderTest( new VCFFormatHeaderLine("NON_STANDARD_FORMAT", 1, VCFHeaderLineType.String, "x"))}); return tests.toArray(new Object[][]{}); }