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Small bug fix in simple indel genotyper: Likelihood of case where best haplotype pair was (REF,REF) was not computed correctly. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4314 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2010-09-20 17:04:39 +00:00
parent f5a30d0248
commit a10cfe213b
1 changed files with 3 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimpleIndelGenotyperWalker.java
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@ -227,7 +227,7 @@ public class SimpleIndelGenotyperWalker extends RefWalker<Integer,Integer> {
} }
int bestIndexI =-1, bestIndexJ=-1; int bestIndexI =-1, bestIndexJ=-1;
double callConfidence = 0.0; double callConfidence = bestLikelihood;
if (pileup.getReads().size() > 0) { if (pileup.getReads().size() > 0) {
@ -270,8 +270,8 @@ public class SimpleIndelGenotyperWalker extends RefWalker<Integer,Integer> {
if (haplotypeLikehoodMatrix[i][j] < bestLikelihood) { if (haplotypeLikehoodMatrix[i][j] < bestLikelihood) {
bestIndexI = i; bestIndexI = i;
bestIndexJ = j; bestIndexJ = j;
if (i > 0 || j > 0)
callConfidence = bestLikelihood - haplotypeLikehoodMatrix[i][j]; callConfidence = bestLikelihood - haplotypeLikehoodMatrix[i][j];
bestLikelihood = haplotypeLikehoodMatrix[i][j]; bestLikelihood = haplotypeLikehoodMatrix[i][j];
} }
} }