/** * Returns the standard info line for {@code ID}. * If none exists throw a {@link TribbleException}. */ public static VCFInfoHeaderLine getInfoLine(final String ID) { return getInfoLine(ID, true); }
/** * Returns the standard info line for {@code ID}. * If none exists throw a {@link TribbleException}. */ public static VCFInfoHeaderLine getInfoLine(final String ID) { return getInfoLine(ID, true); }
/** * Returns the standard info line for ID. If none exists throw an exception * * @param ID * @return */ public static VCFInfoHeaderLine getInfoLine(final String ID) { return getInfoLine(ID, true); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(VCFStandardHeaderLines.getInfoLine(getKeyNames().get(0))); } }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(VCFStandardHeaderLines.getInfoLine(getKeyNames().get(0))); } }
public Set<VCFHeaderLine> getVCFAnnotationDescriptions() { final Set<VCFHeaderLine> descriptions = new HashSet<>(); for ( final InfoFieldAnnotation annotation : requestedInfoAnnotations ) descriptions.addAll(annotation.getDescriptions()); for ( final GenotypeAnnotation annotation : requestedGenotypeAnnotations ) descriptions.addAll(annotation.getDescriptions()); for ( final String db : variantOverlapAnnotator.getOverlapNames() ) { if ( VCFStandardHeaderLines.getInfoLine(db, false) != null ) descriptions.add(VCFStandardHeaderLines.getInfoLine(db)); else descriptions.add(new VCFInfoHeaderLine(db, 0, VCFHeaderLineType.Flag, db + " Membership")); } return descriptions; }
public static void addVQSRStandardHeaderLines(final Set<VCFHeaderLine> hInfo) { hInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY)); hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.VQS_LOD_KEY)); hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.CULPRIT_KEY)); hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.POSITIVE_LABEL_KEY)); hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.NEGATIVE_LABEL_KEY)); }
@Override //this needs an override because MQ is a VCF standard so it's headerline is in a different place public List<VCFInfoHeaderLine> getDescriptions() { final List<VCFInfoHeaderLine> headerLines = new ArrayList<>(); //only HC in GVCF mode should get the raw header line if ((callingWalker instanceof HaplotypeCaller && ((HaplotypeCaller) callingWalker).emitReferenceConfidence()) || callingWalker instanceof CombineGVCFs) headerLines.add(GATKVCFHeaderLines.getInfoLine(getRawKeyName())); headerLines.add(VCFStandardHeaderLines.getInfoLine(getKeyNames().get(0))); return headerLines; }
/** * 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.getInfoLine(VCFConstants.ALLELE_COUNT_KEY)); hInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY)); hInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_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); } }
headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY)); headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY)); headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY)); headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.ORIGINAL_DP_KEY)); headerLines.addAll(Arrays.asList(ChromosomeCountConstants.descriptions)); headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.DEPTH_KEY));
/** * Write the VCF header * * Adds standard GVCF fields to the header * * @param header a non-null header */ @Override public void writeHeader(VCFHeader header) { if ( header == null ) throw new IllegalArgumentException("header cannot be null"); header.addMetaDataLine(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY)); header.addMetaDataLine(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.MIN_DP_FORMAT_KEY)); for ( final HomRefBlock partition : GQPartitions ) { header.addMetaDataLine(partition.toVCFHeaderLine()); } underlyingWriter.writeHeader(header); }
public void initialize() { // take care of the VCF headers final Map<String, VCFHeader> vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit()); final Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true); headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.DEPTH_KEY)); // needed for gVCFs without DP tags final Set<String> samples = SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE); final VCFHeader vcfHeader = new VCFHeader(headerLines, samples); vcfWriter.writeHeader(vcfHeader); // collect the actual rod bindings into a list for use later for ( final RodBindingCollection<VariantContext> variantCollection : variantCollections ) variants.addAll(variantCollection.getRodBindings()); genomeLocParser = getToolkit().getGenomeLocParser(); // create the annotation engine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationGroupsToUse), annotationsToUse, Collections.<String>emptyList(), this, getToolkit()); //now that we have all the VCF headers, initialize the annotations (this is particularly important to turn off RankSumTest dithering in integration tests) annotationEngine.invokeAnnotationInitializationMethods(headerLines); // optimization to prevent mods when we always just want to break bands if ( multipleAtWhichToBreakBands == 1 ) USE_BP_RESOLUTION = true; }
@Override public void initialize() { vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit()); final Set<String> samples = SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE); final Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true); headerLines.addAll(Arrays.asList(ChromosomeCountConstants.descriptions)); headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.DEPTH_KEY)); final VCFHeader vcfHeader = new VCFHeader(headerLines, samples); vcfWriter.writeHeader(vcfHeader); }
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.MLE_ALLELE_FREQUENCY_KEY)); headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.REFERENCE_GENOTYPE_QUALITY)); headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.DEPTH_KEY)); // needed for gVCFs without DP tags
@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[][]{}); }
header.addMetaDataLine(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY)); header.addMetaDataLine(VcfStructuralVariantHeaderLines.CONFIDENCE_INTERVAL_END_POSITION); header.addMetaDataLine(new VCFSimpleHeaderLine("ALT", "INV", "Inversion"));