// Overload function in GenotypeLikelihoodsCalculationModel so that, for an indel case, we
// consider a deletion as part of the pileup,
// so that per-sample DP will include deletions covering the event.
protected int getFilteredDepth(ReadBackedPileup pileup) {
int count = 0;
for (PileupElement p : pileup) {
if (p.isDeletion() || BaseUtils.isRegularBase(p.getBase())) count++;
}
return count;
}
private Map<String, Object> annotateSNP(AlignmentContext stratifiedContext, VariantContext vc) {
if (!stratifiedContext.hasBasePileup()) return null;
HashMap<Byte, Integer> alleleCounts = new HashMap<Byte, Integer>();
for (Allele allele : vc.getAlternateAlleles()) alleleCounts.put(allele.getBases()[0], 0);
ReadBackedPileup pileup = stratifiedContext.getBasePileup();
int totalDepth = pileup.size();
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), totalDepth); // put total depth in right away
if (totalDepth == 0) return map; // done, can not compute FA at 0 coverage!!
int mq0 = 0; // number of "ref" reads that are acually mq0
for (PileupElement p : pileup) {
if (p.getMappingQual() == 0) {
mq0++;
continue;
}
if (alleleCounts.containsKey(p.getBase())) // non-mq0 read and it's an alt
alleleCounts.put(p.getBase(), alleleCounts.get(p.getBase()) + 1);
}
if (mq0 == totalDepth) return map; // if all reads are mq0, there is nothing left to do
// we need to add counts in the correct order
String[] fracs = new String[alleleCounts.size()];
for (int i = 0; i < vc.getAlternateAlleles().size(); i++) {
fracs[i] =
String.format(
"%.3f",
((float) alleleCounts.get(vc.getAlternateAllele(i).getBases()[0]))
/ (totalDepth - mq0));
}
map.put(getKeyNames().get(1), fracs);
return map;
}