From 52a474b27d200100826d70fee6dcc65a9f4b433c Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 30 Jun 2010 16:49:31 +0000
Subject: [PATCH] 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
---
 .../org/broadinstitute/sting/gatk/walkers/vcf/VCFCombine.java   | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/vcf/VCFCombine.java b/java/src/org/broadinstitute/sting/gatk/walkers/vcf/VCFCombine.java
index 3d32ef27d..7db48b5fb 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/vcf/VCFCombine.java
+++ b/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 ) {