diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java b/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java
index 03b410878..22aeeae65 100755
--- a/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java
@@ -174,10 +174,10 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
                     GenomeLoc before = GenomeLocParser.createGenomeLoc(g.getContigIndex(), g.getStart(), e.getStart() - 1);
                     GenomeLoc after = GenomeLocParser.createGenomeLoc(g.getContigIndex(), e.getStop() + 1, g.getStop());
                     int index = mArray.indexOf(g);
-                    if (after.getStop() - after.getStart() > 0) {
+                    if (after.getStop() - after.getStart() >= 0) {
                         mArray.add(index, after);
                     }
-                    if (before.getStop() - before.getStart() > 0) {
+                    if (before.getStop() - before.getStart() >= 0) {
                         mArray.add(index, before);
                     }
                     mArray.remove(mArray.indexOf(g));
diff --git a/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetTest.java b/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetTest.java
index 111265045..528a153c8 100755
--- a/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetTest.java
+++ b/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetTest.java
@@ -142,6 +142,30 @@ public class GenomeLocSortedSetTest extends BaseTest {
         assertTrue(loc.getContigIndex() == 1);
     }
 
+    @Test
+    public void deleteAllButTwoEndBases() {
+        GenomeLoc e = GenomeLocParser.createGenomeLoc(1, 1, 50);
+        mSortedSet.add(e);
+
+        // now delete the region
+        GenomeLoc d = GenomeLocParser.createGenomeLoc(1, 2, 49);
+        mSortedSet.removeRegion(d);
+        Iterator<GenomeLoc> iter = mSortedSet.iterator();
+
+        // we expect to find the two end bases only, this was added because we were
+        // dropping intervals that were of size one.
+        GenomeLoc loc = iter.next();
+        assertTrue(loc.getStart() == 1);
+        assertTrue(loc.getStop() == 1);
+        assertTrue(loc.getContigIndex() == 1);
+
+        loc = iter.next();
+        assertTrue(loc.getStart() == 50);
+        assertTrue(loc.getStop() == 50);
+        assertTrue(loc.getContigIndex() == 1);
+    }
+
+
     @Test
     public void deleteAllByRegion() {
         GenomeLoc e = GenomeLocParser.createGenomeLoc(1, 1, 100);