From 7a5f297083851d972d6846926d1939ecab15dd04 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 27 Aug 2010 19:03:21 +0000
Subject: [PATCH] actually modify the vcf when a sample has been down-sampled

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4150 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 4e60cf5ff..fa702a5c9 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -202,7 +202,7 @@ public class UnifiedGenotyperEngine {
             if ( rawContext.hasPileupBeenDownsampled() ) {
                 Map<String, Object> attrs = new HashMap<String, Object>(call.vc.getAttributes());
                 attrs.put(VCFConstants.DOWNSAMPLED_KEY, true);
-                VariantContextUtils.modifyAttributes(call.vc, attrs);
+                call.vc = VariantContextUtils.modifyAttributes(call.vc, attrs);
             }
         }
         return call;