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

Fixed indel genotyper which broke yet again because we can't just call context.getBasePileup() without checking again for its existence in the first place. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4553 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2010-10-22 15:17:11 +00:00
parent c0b4317311
commit e24f7fec47
1 changed files with 12 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

13
java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -371,7 +371,18 @@ public class UnifiedGenotyperEngine {
if ( ignoreCoveredSamples && isCovered )
continue;
int depth = isCovered ? contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup().size() : 0;
int depth = 0;
if (isCovered) {
AlignmentContext context = contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE);
if (context.hasBasePileup())
depth = context.getBasePileup().size();
else if (context.hasExtendedEventPileup())
depth = context.getExtendedEventPileup().size();
}
P_of_ref *= 1.0 - (theta / 2.0) * MathUtils.binomialProbability(0, depth, 0.5);
}