From c39675d2c1ba9e52b3adb252b28ac5fec5c2ecdf Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 18 Dec 2009 21:33:53 +0000
Subject: [PATCH] VCFTool.java got left off of the last commit

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2407 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/playground/tools/vcf/VCFTool.java | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFTool.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFTool.java
index 9fff99a30..e676b4171 100644
--- a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFTool.java
+++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFTool.java
@@ -232,7 +232,8 @@ class FixRefFields extends CommandLineProgram
 			PrintStream output;
 			try
 			{
-				VCFWriter writer = new VCFWriter(header, new File(output_filename));
+				VCFWriter writer = new VCFWriter(new File(output_filename));
+                writer.writeHeader(header);
 				writer.close();
 				output = new PrintStream(new FileOutputStream(output_filename, true));
 			}