Fixed an issue with VCF combine in sites like the following:

Broad: Filtered     BC: No call

These were being treated the same as

Broad: Call         BC: No call

Added some verbosity to separate them.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3686 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/vcf/VCFCombine.java

@@ -204,6 +204,8 @@ public class VCFCombine extends RodWalker<VCFRecord, VCFWriter> {
                         set = priority2 + "-filteredInOther";
                         call = vcf2;
                     }
+                } else {
+                    set = priority1 + "-filteredAndNoCall";
                 }
             } else { // good call
                 if ( vcf2 != null ) {