private String getFilterString(final VariantContext vc) { if (vc.isFiltered()) { for (final String filter : vc.getFilters()) { if (!this.header.hasFilterLine(filter)) fieldIsMissingFromHeaderError(vc, filter, "FILTER"); } return ParsingUtils.join(";", ParsingUtils.sortList(vc.getFilters())); } else if (vc.filtersWereApplied()) return VCFConstants.PASSES_FILTERS_v4; else return VCFConstants.UNFILTERED; }
private String getFilterString(final VariantContext vc) { if (vc.isFiltered()) { for (final String filter : vc.getFilters()) { if (!this.header.hasFilterLine(filter)) fieldIsMissingFromHeaderError(vc, filter, "FILTER"); } return ParsingUtils.join(";", ParsingUtils.sortList(vc.getFilters())); } else if (vc.filtersWereApplied()) return VCFConstants.PASSES_FILTERS_v4; else return VCFConstants.UNFILTERED; }
private String getFilterString(final VariantContext vc) { if (vc.isFiltered()) { for (final String filter : vc.getFilters()) { if ( ! this.header.hasFilterLine(filter)) fieldIsMissingFromHeaderError(vc, filter, "FILTER"); } return ParsingUtils.join(";", ParsingUtils.sortList(vc.getFilters())); } else if (vc.filtersWereApplied()) return VCFConstants.PASSES_FILTERS_v4; else return VCFConstants.UNFILTERED; }
.stream() .map(VCFFilterHeaderLine::getID) .filter(id -> !existingHeader.hasFilterLine(id)) .forEach(id -> log.info("FILTER line found in HEADER will be added to OUTPUT: " + id)); outHeader.getInfoHeaderLines() if (!existingHeader.hasFilterLine(filter) && !filterHeaderLines.containsKey(filter)) { log.info("Will add an FILTER line with id: " + filter); filterHeaderLines.put(filter, new VCFFilterHeaderLine(filter, "Missing description: this FILTER line was added by Picard's FixVCFHeader"));
.stream() .map(VCFFilterHeaderLine::getID) .filter(id -> !existingHeader.hasFilterLine(id)) .forEach(id -> log.info("FILTER line found in HEADER will be added to OUTPUT: " + id)); outHeader.getInfoHeaderLines() if (!existingHeader.hasFilterLine(filter) && !filterHeaderLines.containsKey(filter)) { log.info("Will add an FILTER line with id: " + filter); filterHeaderLines.put(filter, new VCFFilterHeaderLine(filter, "Missing description: this FILTER line was added by Picard's FixVCFHeader"));