From 4437456bb50075829600802ef939239533cd2277 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 20 Apr 2010 17:41:13 +0000
Subject: [PATCH] Pass array of ref bases to callExtendedLocus()

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3213 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index f602a8d93..b64da9d65 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -189,7 +189,7 @@ public class UnifiedGenotyperEngine {
             if ( stratifiedContexts == null )
                 return null;
 
-            call = gcm.get().callExtendedLocus(tracker, ref, rawContext.getLocation(), stratifiedContexts);
+            call = gcm.get().callExtendedLocus(tracker, refContext.getBasesAtLocus(-1), rawContext.getLocation(), stratifiedContexts);
 
         } else {