From 5c35be39ef1e81e5adc290263aa479557f1ef1d9 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 10 Mar 2010 03:14:06 +0000
Subject: [PATCH] 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
---
 .../sting/gatk/walkers/genotyper/UnifiedGenotyper.java       | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 6ec9ed068..e55892fee 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -66,8 +66,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
     public boolean includeReadsWithDeletionAtLoci() { return true; }
 
     // 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
@@ -174,8 +173,6 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
      * @return the VariantCallContext object
      */
     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);
     }