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 62b25ddf3..6248849f9 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
@@ -76,8 +76,8 @@ public class ReadClipper {
         int rightClipIndex = read.getReadLength() - 1;
 
         // check how far we can clip both sides
-        while (quals[rightClipIndex] <= lowQual) rightClipIndex--;
-        while (quals[leftClipIndex] <= lowQual) leftClipIndex++;
+        while (rightClipIndex >= 0 && quals[rightClipIndex] <= lowQual) rightClipIndex--;
+        while (leftClipIndex < read.getReadLength() && quals[leftClipIndex] <= lowQual) leftClipIndex++;
 
         // if the entire read should be clipped, then return an empty read. (--todo: maybe null is better? testing this for now)
         if (leftClipIndex > rightClipIndex)
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 ef89a8820..79967f49f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -630,26 +630,51 @@ public class ReadUtils {
      * @return the overlap type as described by ReadAndIntervalOverlap enum (see above)
      */
     public static ReadAndIntervalOverlap getReadAndIntervalOverlapType(SAMRecord read, GenomeLoc interval) {
+
+        int start = getSoftUnclippedStart(read);
+        int stop = getSoftUnclippedStop(read);
+
         if ( (!read.getReferenceName().equals(interval.getContig())) ||
-             (read.getUnclippedEnd() < interval.getStart()) ||
-             (read.getUnclippedStart() > interval.getStop()) )
+             (stop < interval.getStart()) ||
+             (start > interval.getStop()) )
             return ReadAndIntervalOverlap.NO_OVERLAP;
 
-        else if ( (read.getUnclippedStart() >= interval.getStart()) &&
-                  (read.getUnclippedEnd() <= interval.getStop()) )
+        else if ( (start >= interval.getStart()) &&
+                  (stop <= interval.getStop()) )
             return ReadAndIntervalOverlap.CONTAINED;
 
-        else if ( (read.getUnclippedStart() < interval.getStart()) &&
-                  (read.getUnclippedEnd() > interval.getStop()) )
+        else if ( (start < interval.getStart()) &&
+                  (stop > interval.getStop()) )
             return ReadAndIntervalOverlap.FULL_OVERLAP;
 
-        else if ( (read.getAlignmentStart() < interval.getStart()) )
+        else if ( (start < interval.getStart()) )
             return ReadAndIntervalOverlap.LEFT_OVERLAP;
 
         else
             return ReadAndIntervalOverlap.RIGHT_OVERLAP;
     }
 
+    public static int getSoftUnclippedStart(SAMRecord read) {
+        int start = read.getUnclippedStart();
+        for (CigarElement cigarElement : read.getCigar().getCigarElements()) {
+            if (cigarElement.getOperator() == CigarOperator.HARD_CLIP)
+                start += cigarElement.getLength();
+            else
+                break;
+        }
+        return start;
+    }
+
+    public static int getSoftUnclippedStop(SAMRecord read) {
+        int stop = getSoftUnclippedStart(read);
+        for (CigarElement cigarElement : read.getCigar().getCigarElements())
+            if (cigarElement.getOperator().consumesReadBases())
+                stop += cigarElement.getLength();
+        return stop;
+    }
+
+
+
     @Requires({"refCoord >= read.getAlignmentStart()", "refCoord <= read.getAlignmentEnd()"})
     @Ensures({"result >= 0", "result < read.getReadLength()"})
     public static int getReadCoordinateForReferenceCoordinate(SAMRecord read, int refCoord) {