From 49af5269e55170f6d650c18dee034868e815009e Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 14 Oct 2009 17:08:57 +0000
Subject: [PATCH] Jared: feel free to change or revert, but until we move over
 to UG version... Only print out positions with at least one non-ref call

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1830 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/playground/gatk/walkers/MultiSampleCaller.java        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller.java
index 80e451396..0bda08a6f 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller.java
@@ -290,7 +290,7 @@ public class MultiSampleCaller extends LocusWalker<MultiSampleCaller.MultiSample
 
     public String reduce(MultiSampleCallResult record, String sum) 
 	{
-		if (record != null)
+		if (record != null && record.n_ref != record.EM_N)
 		{
 			discovery_output_file.printf(record.toString() + "\n");
 		}