if ( ! this.header.hasInfoLine(field.getKey())) fieldIsMissingFromHeaderError(context, field.getKey(), "INFO");
if (!this.header.hasInfoLine(field.getKey())) fieldIsMissingFromHeaderError(context, field.getKey(), "INFO");
if (!this.header.hasInfoLine(field.getKey())) fieldIsMissingFromHeaderError(context, field.getKey(), "INFO");
if ( header.hasInfoLine(GATKVCFConstants.MLE_ALLELE_COUNT_KEY) ) { final VCFInfoHeaderLine mleLine = header.getInfoHeaderLine(GATKVCFConstants.MLE_ALLELE_COUNT_KEY); if ( mleLine.getCountType() != VCFHeaderLineCount.A ) {
Assert.assertTrue(liftReader.getFileHeader().hasInfoLine(LiftoverUtils.SWAPPED_ALLELES)); for (final VariantContext vc : liftReader) { Assert.assertFalse(vc.hasAttribute(LiftoverVcf.ORIGINAL_CONTIG));
.stream() .map(VCFInfoHeaderLine::getID) .filter(id -> !existingHeader.hasInfoLine(id)) .forEach(id -> log.info("INFO line found in HEADER will be added to OUTPUT: " + id)); outHeader.getFormatHeaderLines() .stream() .map(VCFFormatHeaderLine::getID) .filter(id -> !existingHeader.hasInfoLine(id)) .forEach(id -> log.info("FORMAT line found in HEADER will be added to OUTPUT: " + id)); if (!existingHeader.hasInfoLine(id) && !infoHeaderLines.containsKey(id)) { log.info("Will add an INFO line with id: " + id); infoHeaderLines.put(id, new VCFInfoHeaderLine(id, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Missing description: this INFO line was added by Picard's FixVCFHeader"));
.stream() .map(VCFInfoHeaderLine::getID) .filter(id -> !existingHeader.hasInfoLine(id)) .forEach(id -> log.info("INFO line found in HEADER will be added to OUTPUT: " + id)); outHeader.getFormatHeaderLines() .stream() .map(VCFFormatHeaderLine::getID) .filter(id -> !existingHeader.hasInfoLine(id)) .forEach(id -> log.info("FORMAT line found in HEADER will be added to OUTPUT: " + id)); if (!existingHeader.hasInfoLine(id) && !infoHeaderLines.containsKey(id)) { log.info("Will add an INFO line with id: " + id); infoHeaderLines.put(id, new VCFInfoHeaderLine(id, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Missing description: this INFO line was added by Picard's FixVCFHeader"));
/** * Add header line describing the INFO field. * * @param vcfHeader */ public void extendHeader(VCFHeader vcfHeader) { if (!vcfHeader.hasInfoLine(options.getInfoField())) { if (options.getColNo() < 0) { vcfHeader.addMetaDataLine(new VCFInfoHeaderLine(options.getInfoField(), 0, VCFHeaderLineType.Flag, options.getDescription())); } else { vcfHeader.addMetaDataLine(new VCFInfoHeaderLine(options.getInfoField(), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, options.getDescription() + "; column " + options.getColNo())); } } }