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keep working on loglessHMM in UG

This commit is contained in:
Ami Levy-Moonshine 2012-12-21 11:06:12 -05:00
parent 6590039bc3
commit 3ca3fd4b3e
1 changed files with 3 additions and 1 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -335,6 +335,7 @@ public class PairHMMIndelErrorModel {
getContextHomopolymerLength(readBases,hrunProfile);
fillGapProbabilities(hrunProfile, contextLogGapOpenProbabilities, contextLogGapContinuationProbabilities);
boolean firstHap = true;
for (Allele a: haplotypeMap.keySet()) {
Haplotype haplotype = haplotypeMap.get(a);
@ -374,7 +375,7 @@ public class PairHMMIndelErrorModel {
readLikelihood = pairHMM.computeReadLikelihoodGivenHaplotypeLog10(haplotypeBases, readBases, readQuals,
(read.hasBaseIndelQualities() ? read.getBaseInsertionQualities() : contextLogGapOpenProbabilities),
(read.hasBaseIndelQualities() ? read.getBaseDeletionQualities() : contextLogGapOpenProbabilities),
contextLogGapContinuationProbabilities, startIndexInHaplotype, previousHaplotypeSeen == null);
contextLogGapContinuationProbabilities, startIndexInHaplotype, firstHap);
if (DEBUG) {
@ -386,6 +387,7 @@ public class PairHMMIndelErrorModel {
perReadAlleleLikelihoodMap.add(p, a, readLikelihood);
readLikelihoods[readIdx][j++] = readLikelihood;
firstHap = false;
}
}
}