public void finalizeEvaluation() {
nProcessedLoci = getWalker().getnProcessedLoci();
nSNPs = allVariantCounts.all(Type.SNP);
nIndels = allVariantCounts.all(Type.INDEL);
nSVs = allVariantCounts.all(Type.CNV);
TiTvRatio = transitionsPerSample.ratioValue(Type.SNP, transversionsPerSample, true);
TiTvRatioPerSample = transitionsPerSample.ratioValue(Type.SNP, transversionsPerSample, false);
nSNPsPerSample = countsPerSample.meanValue(Type.SNP);
nIndelsPerSample = countsPerSample.meanValue(Type.INDEL);
nSVsPerSample = countsPerSample.meanValue(Type.CNV);
SNPNoveltyRate = noveltyRate(Type.SNP);
IndelNoveltyRate = noveltyRate(Type.INDEL);
SVNoveltyRate = noveltyRate(Type.CNV);
SNPDPPerSample = depthPerSample.meanValue(Type.SNP);
IndelDPPerSample = depthPerSample.meanValue(Type.INDEL);
}
