From 0d6ce91614425970e3e9d2e8e000feddc9e10a5f Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 10 Jun 2011 14:35:48 +0000
Subject: [PATCH] When running CombineVariants with -mergeInfoWithMaxAC the set
 field will be added appropriately

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5974 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/contexts/variantcontext/VariantContextUtils.java    | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
index 60c17d17c..fbfcd91f3 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
@@ -586,7 +586,10 @@ public class VariantContextUtils {
                 setValue = Utils.join("-", s);
             }
 
-            if ( setKey != null ) attributes.put(setKey, setValue);
+            if ( setKey != null ) {
+                attributes.put(setKey, setValue);
+                if( mergeInfoWithMaxAC ) { maxACAttributes.put(setKey, setValue); }
+            }
         }
 
         if ( depth > 0 )