Package htsjdk.variant.variantcontext

Examples of htsjdk.variant.variantcontext.VariantContextBuilder.filters()

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                final String filterString = generateFilterString(lod);

                if( filterString.equals(VCFConstants.PASSES_FILTERS_v4) ) {
                    builder.passFilters();
                } else {
                    builder.filters(filterString);
                }

                final VariantContext outputVC = builder.make();
                if( !EXCLUDE_FILTERED || outputVC.isNotFiltered() ) {
                    vcfWriter.add( outputVC );
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        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());
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