Some minor changes to in-process functions that nobody else uses. CGL now properly ignores no-calls for external VCFs.

public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala

@@ -44,6 +44,7 @@ class VCFExtractIntervals(inVCF: File, outList: File, useFilterSites: Boolean) e
         }
       }
     }
+    out.printf("%s%n",cur)
 
     out.close
   }