diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
index 8c1061494..c3684034c 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
@@ -168,7 +168,14 @@ public class ReadClipper {
             try {
                 GATKSAMRecord clippedRead = (GATKSAMRecord) read.clone();
                 for (ClippingOp op : getOps()) {
-                    clippedRead = op.apply(algorithm, clippedRead);
+                    //check if the clipped read can still be clipped in the range requested
+                    if (op.start < clippedRead.getReadLength()) {
+                        ClippingOp fixedOperation = op;
+                        if (op.stop > clippedRead.getReadLength())
+                            fixedOperation = new ClippingOp(op.start, clippedRead.getReadLength() - 1);
+
+                        clippedRead = fixedOperation.apply(algorithm, clippedRead);
+                    }
                 }
                 wasClipped = true;
                 ops.clear();
diff --git a/public/java/test/org/broadinstitute/sting/utils/clipreads/ClipReadsTestUtils.java b/public/java/test/org/broadinstitute/sting/utils/clipreads/ClipReadsTestUtils.java
index a5524e6f1..4a5b9107b 100644
--- a/public/java/test/org/broadinstitute/sting/utils/clipreads/ClipReadsTestUtils.java
+++ b/public/java/test/org/broadinstitute/sting/utils/clipreads/ClipReadsTestUtils.java
@@ -48,7 +48,7 @@ public class ClipReadsTestUtils {
             Assert.assertTrue(read.isEmpty());
     }
 
-    private static byte[] subtractToArray(byte[] array, int n) {
+    public static byte[] subtractToArray(byte[] array, int n) {
         if (array == null)
             return null;
 
diff --git a/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
index ff33e3184..264b73663 100644
--- a/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
@@ -231,7 +231,7 @@ public class ReadClipperUnitTest extends BaseTest {
     @Test(enabled = true)
     public void testHardClipLowQualEnds() {
         // Needs a thorough redesign
-        logger.warn("Executing testHardClipByReferenceCoordinates");
+        logger.warn("Executing testHardClipLowQualEnds");
 
         //Clip whole read
         Assert.assertEquals(readClipper.hardClipLowQualEnds((byte) 64), new GATKSAMRecord(readClipper.read.getHeader()));