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Bug fix when running nondiploid mode in UG with EMIT_ALL_SITES: if site was reference-only, QUAL is produced OK but genotypes were being set to no-call because of unnecessary likelihood normalization. May change integration test md5 which I'll fix later today

This commit is contained in:
Guillermo del Angel 2012-10-12 12:45:55 -04:00
parent 81532a0529
commit 5971006678
1 changed files with 4 additions and 1 deletions
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5
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculation.java
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@ -627,7 +627,10 @@ public class GeneralPloidyExactAFCalculation extends ExactAFCalculation {
// create the new likelihoods array from the alleles we are allowed to use // create the new likelihoods array from the alleles we are allowed to use
final double[] originalLikelihoods = g.getLikelihoods().getAsVector(); final double[] originalLikelihoods = g.getLikelihoods().getAsVector();
double[] newLikelihoods; double[] newLikelihoods;
if ( numOriginalAltAlleles == numNewAltAlleles) {
// Optimization: if # of new alt alleles = 0 (pure ref call), keep original likelihoods so we skip normalization
// and subsetting
if ( numOriginalAltAlleles == numNewAltAlleles || numNewAltAlleles == 0) {
newLikelihoods = originalLikelihoods; newLikelihoods = originalLikelihoods;
} else { } else {
newLikelihoods = GeneralPloidyGenotypeLikelihoods.subsetToAlleles(originalLikelihoods, ploidy, vc.getAlleles(), allelesToUse); newLikelihoods = GeneralPloidyGenotypeLikelihoods.subsetToAlleles(originalLikelihoods, ploidy, vc.getAlleles(), allelesToUse);