From 7b627fd622a00e267ee78af757844885e65aeb2d Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 21 Sep 2009 04:34:26 +0000
Subject: [PATCH] Check for empty interval lists to merge

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1664 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/IntervalMergerWalker.java         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
index f8915b078..cf1a1f2d2 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
@@ -57,7 +57,7 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
     @Override
     public void initialize() {
         intervals = parseIntervals(intervalsSource);
-        currentInterval = intervals.removeFirst();
+        currentInterval = (intervals.size() > 0 ? intervals.removeFirst() : null);
     }
 
     @Override