b16a048adccf0a257be66ffc01579021fd561bb6,public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java,BeagleOutputToVCF,map,#RefMetaDataTracker#ReferenceContext#AlignmentContext#,158

Before Change


        if ( ! ( beagleVarCounts > 0 || DONT_FILTER_MONOMORPHIC_SITES ) ) {
            Set<String> removedFilters = vc_input.filtersWereApplied() ? new HashSet<String>(vc_input.getFilters()) : new HashSet<String>(1);
            removedFilters.add(String.format("BGL_RM_WAS_%s",vc_input.getAlternateAllele(0)));
            builder.alleles(new HashSet<Allele>(Arrays.asList(vc_input.getReference()))).filters(removedFilters);
        }

        // re-compute chromosome counts

After Change


        final VariantContextBuilder builder = new VariantContextBuilder(vc_input).source("outputvcf").genotypes(genotypes);
        if ( ! ( beagleVarCounts > 0 || DONT_FILTER_MONOMORPHIC_SITES ) ) {
            builder.attribute(ORIGINAL_ALT_ALLELE_INFO_KEY, vc_input.getAlternateAllele(0));
            builder.alleles(Collections.singleton(vc_input.getReference())).filter(BEAGLE_MONO_FILTER_STRING);
        }

        // re-compute chromosome counts