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 00405a98c..85063ad14 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
@@ -50,7 +50,7 @@ public class ReadClipper {
 
     public SAMRecord hardClipByReferenceCoordinates(int refStart, int refStop) {
         int start = (refStart < 0) ? 0 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart);
-        int stop = (refStop < 0) ? read.getReadLength()-1 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop);
+        int stop =  (refStop  < 0) ? read.getReadLength() - 1 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop);
 
         System.out.println("DEBUG -- clipping start/stop: " + start + "/" + stop);
         this.addOp(new ClippingOp(start, stop));
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
index 5d39a01a5..ef89a8820 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -655,16 +655,16 @@ public class ReadUtils {
     public static int getReadCoordinateForReferenceCoordinate(SAMRecord read, int refCoord) {
         int readBases = 0;
         int refBases = 0;
-        int goal = refCoord - read.getAlignmentStart();  // read coords are 0-based!
+        int goal = refCoord - read.getAlignmentStart();  // The goal is to move this many reference bases
         boolean goalReached = refBases == goal;
 
         Iterator<CigarElement> cigarElementIterator = read.getCigar().getCigarElements().iterator();
         while (!goalReached && cigarElementIterator.hasNext()) {
             CigarElement cigarElement = cigarElementIterator.next();
             int shift = 0;
-            if (refBases == 0 && readBases == 0 && cigarElement.getOperator() == CigarOperator.HARD_CLIP) {
-                goal -= cigarElement.getLength();
-            }
+            //if (refBases == 0 && readBases == 0 && cigarElement.getOperator() == CigarOperator.HARD_CLIP) {
+            //    goal -= cigarElement.getLength();
+            //}
 
             if (cigarElement.getOperator().consumesReferenceBases()) {
                 if (refBases + cigarElement.getLength() < goal) {