From dbf2cc037c3b8d2dcde4e169e6ecd303a5c799be Mon Sep 17 00:00:00 2001
From: jmaguire <jmaguire@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 12 Jun 2009 13:59:16 +0000
Subject: [PATCH] don't have a null-pointer hissy fit when the reference is N.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@997 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/playground/gatk/walkers/SingleSampleGenotyper.java     | 1 +
 1 file changed, 1 insertion(+)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
index d1661f28e..d6b31d0c7 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
@@ -208,6 +208,7 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
 
     public String reduce(AlleleFrequencyEstimate alleleFreq, String sum) 
 	{
+		if (alleleFreq == null) { return ""; }
         if ( alleleFreq.lodVsRef >= lodThreshold ) {
             String line = GeliOutputFormat ? alleleFreq.asGeliString() : alleleFreq.asTabularString();
 		    calls_file.println(line);