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);
}
public final double ratioValue(Type type, TypeSampleMap denoms, boolean allP) {
double sum = 0;
int n = 0;
for (final String sample : get(type).keySet()) {
if ((allP && sample == ALL) || (!allP && sample != ALL)) { // truly must be string ==
final long num = get(type).get(sample);
final long denom = denoms.get(type).get(sample);
sum += ratio(num, denom);
n++;
}
}
return n > 0 ? sum / (1.0 * n) : 0.0;
}
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());
}
}
}
private String noveltyRate(Type type) {
final int all = allVariantCounts.all(type);
final int known = knownVariantCounts.all(type);
return Utils.formattedNoveltyRate(known, all);
}