Fixed memory leak and bug with deletions in clipping

The ClippingOp clip cigar function would run into a endless loop if the parameter were out of the reads range, I stopped the bug.
* There is no check to make sure the read coordinate are covered by the read though
When Hard clipping to interval, I added a check for deletions.
NOTE: method works for NA12878 WEx but needs to be more thoroughly tested/optimized

public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java

@@ -324,6 +324,8 @@ public class ClippingOp {
 
                 if (index <= stop && cigarElementIterator.hasNext())
                     cigarElement = cigarElementIterator.next();
+                else
+                    break;
             }
 
             // add the remaining cigar elements
@@ -363,6 +365,8 @@ public class ClippingOp {
                 index += shift;
                 if (index < start && cigarElementIterator.hasNext())
                     cigarElement = cigarElementIterator.next();
+                else
+                    break;
             }
 
             // check if we are hard clipping indels

public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java

@@ -1,6 +1,8 @@
 package org.broadinstitute.sting.utils.clipreads;
 
 import com.google.java.contract.Requires;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
@@ -56,17 +58,34 @@ public class ReadClipper {
         return hardClipByReferenceCoordinates(refStart, -1);
     }
 
+    private int numDeletions(SAMRecord read) {
+        int result = 0;
+        for (CigarElement e: read.getCigar().getCigarElements()) {
+            if ( e.getOperator() == CigarOperator.DELETION || e.getOperator() == CigarOperator.D )
+                result =+ e.getLength();
+        }
+        return result;
+    }
+
     private 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);
 
-        if (start < 0 || stop > read.getReadLength() - 1)
+        if (start < 0 || stop > read.getReadLength() - 1 + numDeletions(read))
             throw new ReviewedStingException("Trying to clip before the start or after the end of a read");
 
-        // TODO add requires statement/check in the Hardclip function
+        // TODO add check in the Hardclip function
         if ( start > stop )
             stop = ReadUtils.getReadCoordinateForReferenceCoordinate(read, ReadUtils.getRefCoordSoftUnclippedEnd(read));
 
+
+        //This tries to fix the bug where the deletion is counted a read base and as a result, the hardCLipper runs into
+        //an endless loop when hard clipping the cigar string because the read coordinates are not covered by the read
+        stop -= numDeletions(read);
+        if ( start > stop )
+            start -= numDeletions(read);
+
+
         //System.out.println("Clipping start/stop: " + start + "/" + stop);
         this.addOp(new ClippingOp(start, stop));
         SAMRecord clippedRead = clipRead(ClippingRepresentation.HARDCLIP_BASES);