diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java
index 54e964bc4..ec3c6c45b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java
@@ -573,10 +573,11 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
             String qualStr = read.getBaseQualityString();
 
             for (int j=0; j < readStr.length(); j++, refIdx++ ) {
-                //                if ( refIdx < 0 || refIdx >= reference.length() ) {
-                //                    System.out.println( "Read: "+read.getRead().getReadName() + "; length = " + readStr.length() );
-                //                    System.out.println( "Ref left: "+ leftmostIndex +"; ref length=" + reference.length() + "; read alignment start: "+read.getOriginalAlignmentStart() ); 
-                //                }
+                if ( refIdx < 0 || refIdx >= reference.length() ) {
+                    //System.out.println( "Read: "+read.getRead().getReadName() + "; length = " + readStr.length() );
+                    //System.out.println( "Ref left: "+ leftmostIndex +"; ref length=" + reference.length() + "; read alignment start: "+read.getOriginalAlignmentStart() );
+                    break;
+                }
                 totalBases[refIdx] += (int)qualStr.charAt(j) - 33;
                 if ( Character.toUpperCase(readStr.charAt(j)) != Character.toUpperCase(reference.charAt(refIdx)) )
                     originalMismatchBases[refIdx] += (int)qualStr.charAt(j) - 33;
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalsTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalsTest.java
new file mode 100755
index 000000000..5283bd2e3
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalsTest.java
@@ -0,0 +1,31 @@
+package org.broadinstitute.sting.gatk.walkers.indels;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.junit.Test;
+
+import java.util.Arrays;
+
+public class IntervalsTest extends WalkerTest {
+    @Test
+    public void testIntervals() {
+
+        WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
+                "-T IndelIntervals -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-11,000,000 -o %s",
+                 1,
+                 Arrays.asList("a4a795755b18f4ecdbc50975612bd819"));
+        executeTest("testIndelIntervals", spec1);
+
+        WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
+                "-T MismatchIntervals -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-11,000,000 -o %s",
+                 1,
+                 Arrays.asList("31e8b5d4c42f2c63c08b8f6b8e10ac99"));
+        executeTest("testMismatchIntervals", spec2);
+
+        WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
+                "-T IntervalMerger -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-11,000,000 -intervals /humgen/gsa-scr1/GATK_Data/Validation_Data/indelIntervals.test -intervals /humgen/gsa-scr1/GATK_Data/Validation_Data/mismatchIntervals.test -o %s",
+                 1,
+                 Arrays.asList("bf1f23667ef0065bbcb9754f50c2d664"));
+        executeTest("testMergeIntervals", spec3);
+
+    }
+}