/** * @see #addStandardFormatLines(java.util.Set, boolean, java.util.Collection) */ public static Set<String> addStandardFormatLines(final Set<VCFHeaderLine> headerLines, final boolean throwErrorForMissing, final String ... IDs) { return addStandardFormatLines(headerLines, throwErrorForMissing, Arrays.asList(IDs)); }
/** * @see #addStandardFormatLines(java.util.Set, boolean, java.util.Collection) * * @param headerLines * @param throwErrorForMissing * @param IDs * @return */ public static Set<String> addStandardFormatLines(final Set<VCFHeaderLine> headerLines, final boolean throwErrorForMissing, final String ... IDs) { return addStandardFormatLines(headerLines, throwErrorForMissing, Arrays.asList(IDs)); }
/** * @see #addStandardFormatLines(java.util.Set, boolean, java.util.Collection) */ public static Set<String> addStandardFormatLines(final Set<VCFHeaderLine> headerLines, final boolean throwErrorForMissing, final String ... IDs) { return addStandardFormatLines(headerLines, throwErrorForMissing, Arrays.asList(IDs)); }
private VariantAnnotatorEngine initializeVCFOutput() { // initialize the output VCF header if (MTAC.ENABLE_CLUSTERED_READ_POSITION_FILTER) { annotationsToUse.add("ClusteredReadPosition"); } final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit()); final Set<VCFHeaderLine> headerInfo = new HashSet<>(); // all annotation fields from VariantAnnotatorEngine headerInfo.addAll(annotationEngine.getVCFAnnotationDescriptions()); // all callers need to add these standard FORMAT field header lines VCFStandardHeaderLines.addStandardFormatLines(headerInfo, true, VCFConstants.GENOTYPE_KEY, VCFConstants.GENOTYPE_ALLELE_DEPTHS, VCFConstants.GENOTYPE_QUALITY_KEY, VCFConstants.DEPTH_KEY, VCFConstants.GENOTYPE_PL_KEY); headerInfo.addAll(getM2HeaderLines()); headerInfo.addAll(getSampleHeaderLines()); // if printTCGAsampleHeader, we already checked for exactly 1 tumor and 1 normal in printTCGAsampleHeader assignment in initialize() final List<String> outputSampleNames = printTCGAsampleHeader ? Arrays.asList("TUMOR", "NORMAL") : SampleListUtils.asList(samplesList); vcfWriter.writeHeader(new VCFHeader(headerInfo, outputSampleNames)); return annotationEngine; }
VCFStandardHeaderLines.addStandardFormatLines(headerInfo, true, VCFConstants.GENOTYPE_KEY, VCFConstants.GENOTYPE_QUALITY_KEY,
VCFStandardHeaderLines.addStandardFormatLines(headerLines, false, Genotype.PRIMARY_KEYS); // This is very frustrating to have to add headerLines.addAll(filterHeaderLines.values()); headerLines.addAll(infoHeaderLines.values());
VCFStandardHeaderLines.addStandardFormatLines(headerLines, false, Genotype.PRIMARY_KEYS); // This is very frustrating to have to add headerLines.addAll(filterHeaderLines.values()); headerLines.addAll(infoHeaderLines.values());
headerInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.MLE_ALLELE_FREQUENCY_KEY)); VCFStandardHeaderLines.addStandardFormatLines(headerInfo, true, VCFConstants.GENOTYPE_KEY, VCFConstants.GENOTYPE_QUALITY_KEY,