From 5b0b9e79ba2610cdf5a94f308b8b2991c3ed2b40 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 9 Aug 2010 19:21:39 +0000
Subject: [PATCH] protect against nulls

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3987 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/utils/interval/IntervalUtils.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java b/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
index e8ffcae62..40f8337dd 100644
--- a/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
@@ -79,7 +79,7 @@ public class IntervalUtils {
      */
     public static List<GenomeLoc> mergeListsBySetOperator(List<GenomeLoc> setOne, List<GenomeLoc> setTwo, IntervalSetRule rule) {
         // shortcut, if either set is zero, return the other set
-        if (setOne.size() == 0 || setTwo.size() == 0) return (setOne.size() == 0) ? setTwo : setOne;
+        if (setOne == null || setOne.size() == 0 || setTwo == null || setTwo.size() == 0) return (setOne == null || setOne.size() == 0) ? setTwo : setOne;
 
         // if we're set to UNION, just add them all
         if (rule == IntervalSetRule.UNION) {