From b62bddee42155ef3f66d3ef19461d4529b15f0da Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 14 May 2009 17:18:51 +0000
Subject: [PATCH] The header was never being set. Added this hack for now and
 will alert the authorities ASAP...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@708 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/traversals/TraversalEngine.java   | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
index 4971b2efd..e87f99fd2 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
@@ -179,6 +179,8 @@ public abstract class TraversalEngine {
      * @return the header if it's stored, null if not
      */
     public SAMFileHeader getSAMHeader() {
+        if ( myHeader == null )
+            myHeader = samReader.getFileHeader();
         return myHeader;
     }