/** * Provides the next record from the underlying iterator after applying filter strings generated * by the set of filters in use by the iterator. */ @Override public VariantContext next() { final VariantContext ctx = this.iterator.next(); final Set<String> filterStrings = new HashSet<String>(); // Collect variant level filters for (final VariantFilter filter : this.filters) { final String val = filter.filter(ctx); if (val != null) filterStrings.add(val); } // Collect genotype level filters in a Map of Sample -> List<filter string> final ListMap<String, String> gtFilterStrings = new ListMap<String, String>(); final Set<String> variantSamples = new HashSet<String>(); for (final Genotype gt : ctx.getGenotypes()) { if (gt.isCalled() && !gt.isHomRef()) variantSamples.add(gt.getSampleName()); for (final GenotypeFilter filter : gtFilters) { final String filterString = filter.filter(ctx, gt); if (filterString != null) gtFilterStrings.add(gt.getSampleName(), filterString); } } // If all genotypes are filtered apply a site level filter if (gtFilterStrings.keySet().containsAll(variantSamples)) { filterStrings.add(ALL_GTS_FILTERED); } // Make a builder and set the site level filter appropriately final VariantContextBuilder builder = new VariantContextBuilder(ctx); if (filterStrings.isEmpty()) { builder.passFilters(); } else { builder.filters(filterStrings); } // Apply filters to the necessary genotypes builder.noGenotypes(); final List<Genotype> newGenotypes = new ArrayList<Genotype>(ctx.getNSamples()); for (final Genotype gt : ctx.getGenotypes()) { final GenotypeBuilder gtBuilder = new GenotypeBuilder(gt); final List<String> filtersLocal = gtFilterStrings.get(gt.getSampleName()); if (filtersLocal == null || filtersLocal.isEmpty()) { gtBuilder.filter(PASS_FILTER); } else { gtBuilder.filters(filtersLocal); } newGenotypes.add(gtBuilder.make()); } builder.genotypes(newGenotypes); return builder.make(); }
/** * Takes the interval, finds it in the stash, prints it to the VCF * * @param stats The statistics of the interval * @param refAllele the reference allele */ private void outputStatsToVCF(final IntervalStratification stats, final Allele refAllele) { GenomeLoc interval = stats.getInterval(); final List<Allele> alleles = new ArrayList<>(); final Map<String, Object> attributes = new HashMap<>(); final ArrayList<Genotype> genotypes = new ArrayList<>(); for (String sample : samples) { final GenotypeBuilder gb = new GenotypeBuilder(sample); SampleStratification sampleStat = stats.getSampleStatistics(sample); gb.attribute( GATKVCFConstants.AVG_INTERVAL_DP_BY_SAMPLE_KEY, sampleStat.averageCoverage(interval.size())); gb.attribute(GATKVCFConstants.LOW_COVERAGE_LOCI, sampleStat.getNLowCoveredLoci()); gb.attribute(GATKVCFConstants.ZERO_COVERAGE_LOCI, sampleStat.getNUncoveredLoci()); gb.filters(statusToStrings(stats.getSampleStatistics(sample).callableStatuses(), false)); genotypes.add(gb.make()); } alleles.add(refAllele); alleles.add(SYMBOLIC_ALLELE); VariantContextBuilder vcb = new VariantContextBuilder( "DiagnoseTargets", interval.getContig(), interval.getStart(), interval.getStop(), alleles); vcb = vcb.log10PError(VariantContext.NO_LOG10_PERROR); vcb.filters(new LinkedHashSet<>(statusToStrings(stats.callableStatuses(), true))); attributes.put(VCFConstants.END_KEY, interval.getStop()); attributes.put(GATKVCFConstants.AVG_INTERVAL_DP_KEY, stats.averageCoverage(interval.size())); attributes.put(GATKVCFConstants.INTERVAL_GC_CONTENT_KEY, stats.gcContent()); vcb = vcb.attributes(attributes); vcb = vcb.genotypes(genotypes); vcfWriter.add(vcb.make()); }