All headers are now converted to VCF4 by default.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3741 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java

@@ -138,6 +138,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
                         logger.warn(String.format("Ignoring header line already in map: this header line = " + line + " already present header = " + other));
                     }
                 } else {
+                    line.setVersion(VCFHeaderVersion.VCF4_0);
                     map.put(key, line);
                     //System.out.printf("Adding header line %s%n", line);
                 }