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If the annotation engine has not been supplied, don't try to annotate anything. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3081 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2010-03-26 20:52:21 +00:00
parent 8048b709a0
commit 391e5843e4
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -223,9 +223,10 @@ public class UnifiedGenotyperEngine {
call = gcm.get().callLocus(tracker, ref, rawContext.getLocation(), stratifiedContexts, priors); call = gcm.get().callLocus(tracker, ref, rawContext.getLocation(), stratifiedContexts, priors);
// annotate the call, if possible // annotate the call, if possible
if ( call != null && call.vc != null ) { if ( call != null && call.vc != null && annotationEngine != null ) {
// first off, we want to use the *unfiltered* context for the annotations // first off, we want to use the *unfiltered* context for the annotations
stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(rawContext.getBasePileup()); stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(rawContext.getBasePileup());
call.vc = annotationEngine.annotateContext(tracker, refContext, stratifiedContexts, call.vc); call.vc = annotationEngine.annotateContext(tracker, refContext, stratifiedContexts, call.vc);
} }
} }