zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimpleIndelGenotyperWalker.java
View File

@ -227,7 +227,7 @@ public class SimpleIndelGenotyperWalker extends RefWalker<Integer,Integer> {
}
int bestIndexI =-1, bestIndexJ=-1;
double callConfidence = 0.0;
double callConfidence = bestLikelihood;
if (pileup.getReads().size() > 0) {
@ -270,8 +270,8 @@ public class SimpleIndelGenotyperWalker extends RefWalker<Integer,Integer> {
if (haplotypeLikehoodMatrix[i][j] < bestLikelihood) {
bestIndexI = i;
bestIndexJ = j;
if (i > 0 || j > 0)
callConfidence = bestLikelihood - haplotypeLikehoodMatrix[i][j];
callConfidence = bestLikelihood - haplotypeLikehoodMatrix[i][j];
bestLikelihood = haplotypeLikehoodMatrix[i][j];
}
}