public Map<String, Object> annotate(
final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,
final ReferenceContext ref,
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc,
final Map<String, PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
int depth = 0;
if (stratifiedContexts != null) {
if (stratifiedContexts.size() == 0) return null;
for (Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet())
depth += sample.getValue().getBasePileup().depthOfCoverage();
} else if (perReadAlleleLikelihoodMap != null) {
if (perReadAlleleLikelihoodMap.size() == 0) return null;
for (PerReadAlleleLikelihoodMap maps : perReadAlleleLikelihoodMap.values()) {
depth += maps.getLikelihoodReadMap().size();
}
} else return null;
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%d", depth));
return map;
}
/**
* Loop over all of the reads in this likelihood map and realign them to its most likely haplotype
*
* @param haplotypes the collection of haplotypes
* @param paddedReferenceLoc the active region
*/
public void realignReadsToMostLikelyHaplotype(
final Collection<Haplotype> haplotypes, final GenomeLoc paddedReferenceLoc) {
// we need to remap the Alleles back to the Haplotypes; inefficient but unfortunately this is a
// requirement currently
final Map<Allele, Haplotype> alleleToHaplotypeMap = new HashMap<>(haplotypes.size());
Haplotype refHaplotype = null;
for (final Haplotype haplotype : haplotypes) {
alleleToHaplotypeMap.put(Allele.create(haplotype.getBases()), haplotype);
if (refHaplotype == null && haplotype.isReference()) refHaplotype = haplotype;
}
final Map<GATKSAMRecord, Map<Allele, Double>> newLikelihoodReadMap =
new LinkedHashMap<>(likelihoodReadMap.size());
for (final Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : likelihoodReadMap.entrySet()) {
final MostLikelyAllele bestAllele =
PerReadAlleleLikelihoodMap.getMostLikelyAllele(entry.getValue());
final GATKSAMRecord alignedToRef =
AlignmentUtils.createReadAlignedToRef(
entry.getKey(),
alleleToHaplotypeMap.get(bestAllele.getMostLikelyAllele()),
refHaplotype,
paddedReferenceLoc.getStart(),
bestAllele.isInformative());
newLikelihoodReadMap.put(alignedToRef, entry.getValue());
}
likelihoodReadMap.clear();
likelihoodReadMap.putAll(newLikelihoodReadMap);
}