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Now that extended events work for reference traversals, turn it off in the genotyper for non-indel models (thereby fixing busted integration tests). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2974 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-03-10 03:14:06 +00:00
parent 7ddd45d059
commit 5c35be39ef
1 changed files with 1 additions and 4 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -66,8 +66,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
public boolean includeReadsWithDeletionAtLoci() { return true; } public boolean includeReadsWithDeletionAtLoci() { return true; }
// enable extended events for indels // enable extended events for indels
public boolean generateExtendedEvents() { return true; } public boolean generateExtendedEvents() { return UAC.genotypeModel == GenotypeCalculationModel.Model.INDELS; }
//public boolean generateExtendedEvents() { return UAC.genotypeModel == GenotypeCalculationModel.Model.INDELS; }
/** /**
* Inner class for collecting output statistics from the UG * Inner class for collecting output statistics from the UG
@ -174,8 +173,6 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
* @return the VariantCallContext object * @return the VariantCallContext object
*/ */
public VariantCallContext map(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) { public VariantCallContext map(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
if ( rawContext.hasExtendedEventPileup() )
System.out.println("Saw extended event at location " + rawContext.getLocation());
return UG_engine.runGenotyper(tracker, refContext, rawContext); return UG_engine.runGenotyper(tracker, refContext, rawContext);
} }