Examples of filtersWereApplied()

Examples of htsjdk.variant.variantcontext.VariantContext.filtersWereApplied()

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                vcRoot.add("POS", vc.getStart());
                vcRoot.add("ID", vc.getID());
                vcRoot.add("REF", vc.getReference());
                vcRoot.add("ALT", vc.getAlternateAlleles());
                vcRoot.add("QUAL", vc.hasLog10PError() ? vc.getLog10PError() * -10 : VCFConstants.MISSING_VALUE_v4);
                vcRoot.add("FILTER", ! vc.filtersWereApplied() // needs null to differentiate between PASS and .
                        ? VCFConstants.MISSING_VALUE_v4
                        : ( vc.getFilters().isEmpty() ? VCFConstants.PASSES_FILTERS_v4 : vc.getFilters()) );

                // add info fields
                for (Map.Entry<String, Object> attribute : vc.getAttributes().entrySet()) {
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