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

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;
     }