public void update2( VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { if (eval == null || (getWalker().ignoreAC0Sites() && eval.isMonomorphicInSamples())) return; final Type type = getType(eval); if (type == null) return; TypeSampleMap titvTable = null; // update DP, if possible if (eval.hasAttribute(VCFConstants.DEPTH_KEY)) depthPerSample.inc(type, ALL); // update counts allVariantCounts.inc(type, ALL); // type specific calculations if (type == Type.SNP && eval.isBiallelic()) { titvTable = VariantContextUtils.isTransition(eval) ? transitionsPerSample : transversionsPerSample; titvTable.inc(type, ALL); } // novelty calculation if (comp != null || (type == Type.CNV && overlapsKnownCNV(eval))) knownVariantCounts.inc(type, ALL); // per sample metrics for (final Genotype g : eval.getGenotypes()) { if (!g.isNoCall() && !g.isHomRef()) { countsPerSample.inc(type, g.getSampleName()); // update transition / transversion ratio if (titvTable != null) titvTable.inc(type, g.getSampleName()); if (g.hasDP()) depthPerSample.inc(type, g.getSampleName()); } } }