From 9eb83a0771ac4f4697b276117a8a7cc30814e5a7 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 31 May 2012 11:21:08 -0400
Subject: [PATCH] Enable adding contigs to VariantContextWriters on output

---
 .../sting/gatk/io/stubs/VariantContextWriterStub.java           | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
index 0c24258de..3cbffe577 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
@@ -215,7 +215,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
                     vcfHeader.addMetaDataLine(commandLineArgHeaderLine);
             }
 
-            //vcfHeader = VCFUtils.withUpdatedContigs(vcfHeader, engine);
+            vcfHeader = VCFUtils.withUpdatedContigs(vcfHeader, engine);
         }
 
         outputTracker.getStorage(this).writeHeader(vcfHeader);