From 5992d884090151b3d81ad6d224484fa7f6f8df60 Mon Sep 17 00:00:00 2001
From: jmaguire <jmaguire@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 17 Jun 2009 23:22:35 +0000
Subject: [PATCH] skip N's in the reference (rather than crash. doh!)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1039 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/playground/gatk/walkers/MultiSampleCaller.java         | 1 +
 1 file changed, 1 insertion(+)

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 9115ce440..2838f361a 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller.java
@@ -80,6 +80,7 @@ public class MultiSampleCaller extends LocusWalker<String,String>
 
     public String map(RefMetaDataTracker tracker, char ref, LocusContext context) 
 	{
+		if (ref == 'N') { return null; }
 		this.ref = ref;
 		if (tracker.lookup("DBSNP", null) != null) { in_dbsnp = "known"; } else { in_dbsnp = "novel"; }
 		this.MultiSampleCall(context, sample_names);