From 7fa1ab1bae051d1d4973f8c5e244a28b3c093e72 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Tue, 13 Dec 2011 17:19:40 -0500
Subject: [PATCH] Fix to allow haplotype caller to call indels after UG engine
 entry points were unified. Adding Haplotype Caller integration test

---
 .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 21aaeffba..2308e1759 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -371,8 +371,11 @@ public class UnifiedGenotyperEngine {
         builder.log10PError(phredScaledConfidence/-10.0);
         if ( ! passesCallThreshold(phredScaledConfidence) )
             builder.filters(filter);
-        if ( !limitedContext )
+        if ( limitedContext ) {
+            builder.referenceBaseForIndel(vc.getReferenceBaseForIndel());
+        } else {
             builder.referenceBaseForIndel(refContext.getBase());
+        }
 
         // create the genotypes
         GenotypesContext genotypes = assignGenotypes(vc, altAllelesToUse);