diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java
index ca1d385a2..394220106 100755
--- a/public/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java
+++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java
@@ -149,7 +149,7 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
         previousOverlapSearchIndex = Collections.binarySearch(mArray, loc);
 
         // if it matches an interval exactly, we are done
-        if ( previousOverlapSearchIndex > 0 )
+        if ( previousOverlapSearchIndex >= 0 )
             return true;
 
         // check whether it overlaps the interval before or after the insertion point