diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
index 951ab265c..47ce8165c 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
@@ -432,25 +432,37 @@ public class ClippingOp {
     }
 
     private int calculateAlignmentStartShift(Cigar oldCigar, Cigar newCigar) {
-        int shift = 0;
+        int newShift = 0;
+        int oldShift = 0;
+        int deletionShift = 0;
 
-        // Rewind to previous start (by counting everything that was already clipped in this read)
-        for (CigarElement cigarElement : oldCigar.getCigarElements()) {
-            if (!cigarElement.getOperator().consumesReferenceBases())
-                shift -= cigarElement.getLength();
-            else
-                break;
-        }
-
-        // Advance to new start (by counting everything new that has been clipped )
         for (CigarElement cigarElement : newCigar.getCigarElements()) {
-            if (!cigarElement.getOperator().consumesReferenceBases())
-                shift += cigarElement.getLength();
+            if (cigarElement.getOperator() == CigarOperator.HARD_CLIP || cigarElement.getOperator() == CigarOperator.SOFT_CLIP)
+                newShift += cigarElement.getLength();
             else
                 break;
         }
 
-        return shift;
+        for (CigarElement cigarElement : oldCigar.getCigarElements()) {
+            if (cigarElement.getOperator() == CigarOperator.HARD_CLIP || cigarElement.getOperator() == CigarOperator.SOFT_CLIP )
+                oldShift += Math.min(cigarElement.getLength(), newShift - oldShift);
+            else
+                break;
+        }
+
+        int basesClipped = 0;
+        for (CigarElement cigarElement : oldCigar.getCigarElements()) {
+            if (basesClipped > newShift)                                        // are we beyond the clipped region?
+                break;
+
+            else if (cigarElement.getOperator() == CigarOperator.DELETION)      // if this is a deletion, we have to adjust the starting shift
+                deletionShift += cigarElement.getLength();
+
+            else
+                basesClipped += cigarElement.getLength();
+        }
+
+        return newShift - oldShift + deletionShift;
     }
 
     private int calculateHardClippingAlignmentShift(CigarElement cigarElement, int clippedLength) {
@@ -462,8 +474,8 @@ public class ClippingOp {
                 return -clippedLength;
         }
 
-        if (cigarElement.getOperator() == CigarOperator.DELETION)
-            return cigarElement.getLength();
+//        if (cigarElement.getOperator() == CigarOperator.DELETION)
+//            return cigarElement.getLength();
 
         return 0;
     }
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 9b9ce4fdf..d0e7f8371 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
@@ -71,21 +71,21 @@ public class ReadClipper {
 
     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 + numDeletions(read))
+        if (start < 0 || stop > read.getReadLength() - 1)
             throw new ReviewedStingException("Trying to clip before the start or after the end of a read");
 
-        // TODO add check in the Hardclip function
-        if ( start > stop )
-            stop = ReadUtils.getReadCoordinateForReferenceCoordinate(read, ReadUtils.getRefCoordSoftUnclippedEnd(read));
-
+        if ( start > stop ) {
+//            stop = ReadUtils.getReadCoordinateForReferenceCoordinate(read, ReadUtils.getRefCoordSoftUnclippedEnd(read));
+            throw new ReviewedStingException("START > STOP -- this should never happen -- call Mauricio!");
+        }
 
         //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);
+//        stop -= numDeletions(read);
+//        if ( start > stop )
+//            start -= numDeletions(read);
 
 
         //System.out.println("Clipping start/stop: " + start + "/" + stop);
@@ -145,7 +145,7 @@ public class ReadClipper {
                     cutLeft = readIndex + cigarElement.getLength() - 1;
                 }
             }
-            else
+            else if (cigarElement.getOperator() != CigarOperator.HARD_CLIP)
                 rightTail = true;
 
             if (cigarElement.getOperator().consumesReadBases())
diff --git a/public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
index a8e6593b1..35c6a4993 100644
--- a/public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
@@ -105,7 +105,6 @@ public class VCFWriterUnitTest extends BaseTest {
     public static VCFHeader createFakeHeader(Set<VCFHeaderLine> metaData, Set<String> additionalColumns) {
         metaData.add(new VCFHeaderLine(VCFHeaderVersion.VCF4_0.getFormatString(), VCFHeaderVersion.VCF4_0.getVersionString()));
         metaData.add(new VCFHeaderLine("two", "2"));
-        additionalColumns.add("FORMAT");
         additionalColumns.add("extra1");
         additionalColumns.add("extra2");
         return new VCFHeader(metaData, additionalColumns);
@@ -159,6 +158,6 @@ public class VCFWriterUnitTest extends BaseTest {
             Assert.assertTrue(additionalColumns.contains(key));
             index++;
         }
-        Assert.assertEquals(index+1, additionalColumns.size()  /* for the header field we don't see */);
+        Assert.assertEquals(index, additionalColumns.size());
     }
 }