Several bug fixes

* When hard clipping a read that had insertions in it, the insertion was being added to the cigar string's hard clip element. This way, the old UnclippedStart() was being modified and so was the calculation of the new AlignmentStart(). Fixed it by subtracting the number of insertions clipped from the total number of hard clipped bases.
* Walker was sending read instead of filtered read when deleting a read that contains only Q2 bases
* Sliding the window was causing reads that started on the new start position to be entirely clipped.

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

@@ -262,7 +262,9 @@ public class ClippingOp {
         int copyStart = (start == 0) ? stop + 1 : 0;
 
         System.arraycopy(read.getReadBases(), copyStart, newBases, 0, newLength);
-        System.arraycopy(read.getBaseQualities(), copyStart, newQuals, 0, newLength);        Cigar newCigar = hardClipCigar(read.getCigar(), start, stop);
+        System.arraycopy(read.getBaseQualities(), copyStart, newQuals, 0, newLength);
+
+        Cigar newCigar = hardClipCigar(read.getCigar(), start, stop);
 
         SAMRecord hardClippedRead;
         try {
@@ -286,6 +288,7 @@ public class ClippingOp {
         Cigar newCigar = new Cigar();
         int index = 0;
         int totalHardClipCount = stop - start + 1;
+        int alignmentShift = 0; // caused by hard clipping insertions or deletions
 
         // hard clip the beginning of the cigar string
         if (start == 0) {
@@ -307,15 +310,19 @@ public class ClippingOp {
 
                 // we're still clipping or just finished perfectly
                 if (index + shift == stop + 1) {
-                    newCigar.add(new CigarElement(totalHardClipCount, CigarOperator.HARD_CLIP));
+                    alignmentShift += calculateHardClippingAlignmentShift(cigarElement, cigarElement.getLength());
+                    newCigar.add(new CigarElement(totalHardClipCount + alignmentShift, CigarOperator.HARD_CLIP));
                 }
                 // element goes beyond what we need to clip
                 else if (index + shift > stop + 1) {
                     int elementLengthAfterChopping = cigarElement.getLength() - (stop - index + 1);
-                    newCigar.add(new CigarElement(totalHardClipCount, CigarOperator.HARD_CLIP));
+                    alignmentShift += calculateHardClippingAlignmentShift(cigarElement, stop-index+1);
+                    newCigar.add(new CigarElement(totalHardClipCount + alignmentShift, CigarOperator.HARD_CLIP));
                     newCigar.add(new CigarElement(elementLengthAfterChopping, cigarElement.getOperator()));
                 }
                 index += shift;
+                alignmentShift += calculateHardClippingAlignmentShift(cigarElement, shift);
+
                 if (index <= stop && cigarElementIterator.hasNext())
                     cigarElement = cigarElementIterator.next();
             }
@@ -345,6 +352,8 @@ public class ClippingOp {
                 // element goes beyond our clip starting position
                 else {
                     int elementLengthAfterChopping = start - index;
+                    alignmentShift += calculateHardClippingAlignmentShift(cigarElement, cigarElement.getLength() - (start - index));
+
                     // if this last element is a HARD CLIP operator, just merge it with our hard clip operator to be added later
                     if (cigarElement.getOperator() == CigarOperator.HARD_CLIP)
                         totalHardClipCount += elementLengthAfterChopping;
@@ -356,7 +365,13 @@ public class ClippingOp {
                 if (index < start && cigarElementIterator.hasNext())
                     cigarElement = cigarElementIterator.next();
             }
-            newCigar.add(new CigarElement(totalHardClipCount, CigarOperator.HARD_CLIP));
+
+            // check if we are hard clipping indels
+            while(cigarElementIterator.hasNext()) {
+                cigarElement = cigarElementIterator.next();
+                alignmentShift += calculateHardClippingAlignmentShift(cigarElement, cigarElement.getLength());
+            }
+            newCigar.add(new CigarElement(totalHardClipCount + alignmentShift, CigarOperator.HARD_CLIP));
         }
         return newCigar;
     }
@@ -379,6 +394,24 @@ public class ClippingOp {
             else
                 break;
         }
+
+
         return shift;
     }
+
+
+    private int calculateHardClippingAlignmentShift(CigarElement cigarElement, int clippedLength) {
+        if (cigarElement.getOperator() == CigarOperator.INSERTION) {
+            int cigarElementLength = cigarElement.getLength();
+            if (clippedLength >= cigarElementLength)
+                return -cigarElement.getLength();
+            else
+                return -clippedLength;
+        }
+
+        if (cigarElement.getOperator() == CigarOperator.DELETION)
+            return cigarElement.getLength();
+
+        return 0;
+    }
 }

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

@@ -51,7 +51,15 @@ public class ReadClipper {
         return read;
     }
 
-    public SAMRecord hardClipByReferenceCoordinates(int refStart, int refStop) {
+    public SAMRecord hardClipByReferenceCoordinatesLeftTail(int refStop) {
+        return hardClipByReferenceCoordinates(-1, refStop);
+    }
+
+    public SAMRecord hardClipByReferenceCoordinatesRightTail(int refStart) {
+        return hardClipByReferenceCoordinates(refStart, -1);
+    }
+
+    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);