From 54c0b6c4306f1987d4501c09925884f329e59ee7 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 1 Sep 2009 12:43:18 +0000
Subject: [PATCH] Allow this ROD to consist of just the positions

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1497 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/refdata/CleanedOutSNPROD.java  | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/CleanedOutSNPROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/CleanedOutSNPROD.java
index 608b93748..4b66e81e8 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/CleanedOutSNPROD.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/CleanedOutSNPROD.java
@@ -17,5 +17,8 @@ public class CleanedOutSNPROD extends TabularROD {
         return GenomeLocParser.parseGenomeLoc(this.get("0"));
     }
 
-    public boolean isRealSNP() { return this.get("1").equals(REAL_SNP_STRING); }
+    public boolean isRealSNP() {
+        String s = this.get("1");
+        return s != null && s.equals(REAL_SNP_STRING);
+    }
  }
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