/**
* 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);
}
/**
* Convert the @likelihoodReadMap to a map of alleles to reads, where each read is mapped uniquely
* to the allele for which it has the greatest associated likelihood
*
* @return a map from each allele to a list of reads that 'support' the allele
*/
protected Map<Allele, List<GATKSAMRecord>> getAlleleStratifiedReadMap() {
final Map<Allele, List<GATKSAMRecord>> alleleReadMap = new HashMap<>(alleles.size());
for (final Allele allele : alleles) alleleReadMap.put(allele, new ArrayList<GATKSAMRecord>());
for (final Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : likelihoodReadMap.entrySet()) {
final MostLikelyAllele bestAllele = getMostLikelyAllele(entry.getValue());
if (bestAllele.isInformative())
alleleReadMap.get(bestAllele.getMostLikelyAllele()).add(entry.getKey());
}
return alleleReadMap;
}