Pushing the RR bug fix that I puished into unstable into stable, as requested by Tim

protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElement.java

@@ -39,16 +39,27 @@ public class HeaderElement {
      *
      * @param location the reference location for the new element
      */
-    public HeaderElement(int location) {
+    public HeaderElement(final int location) {
         this(new BaseAndQualsCounts(), new BaseAndQualsCounts(), 0, 0, location, new LinkedList<Integer>());
     }
 
+    /**
+     * Creates a new HeaderElement with the following default values: - empty consensusBaseCounts - empty
+     * filteredBaseCounts - empty mappingQuality list
+     *
+     * @param location the reference location for the new element
+     */
+    public HeaderElement(final int location, final int insertionsToTheRight) {
+        this(new BaseAndQualsCounts(), new BaseAndQualsCounts(), insertionsToTheRight, 0, location, new LinkedList<Integer>());
+    }
+
     /**
      * Creates a new HeaderElement with all given parameters
      *
      * @param consensusBaseCounts  the BaseCounts object for the running consensus synthetic read
      * @param filteredBaseCounts   the BaseCounts object for the filtered data synthetic read
      * @param insertionsToTheRight number of insertions to the right of this HeaderElement
+     * @param nSoftClippedBases    number of softclipped bases of this HeaderElement
      * @param location             the reference location of this reference element
      * @param mappingQuality       the list of mapping quality values of all reads that contributed to this
      *                             HeaderElement
@@ -151,6 +162,14 @@ public class HeaderElement {
             throw new ReviewedStingException("Removed too many insertions, header is now negative!");
     }
 
+    public boolean hasInsertionToTheRight() {
+        return insertionsToTheRight > 0;
+    }
+
+    public int numInsertionsToTheRight() {
+        return insertionsToTheRight;
+    }
+
     /**
      * Whether or not the HeaderElement is variant due to excess insertions
      *

protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java

@@ -645,8 +645,15 @@ public class SlidingWindow {
                 }
             }
 
-            for (int i = 0; i <= lastStop; i++) // clean up the window header elements up until the end of the variant region. (we keep the last element in case the following element had a read that started with insertion)
+            // clean up the window header elements up until the end of the variant region.
-                windowHeader.remove();
+            // note that we keep the last element of the region in the event that the following element has a read that starts with insertion.
+            if ( lastStop >= 0 ) {
+                for (int i = 0; i < lastStop; i++)
+                    windowHeader.remove();
+                final HeaderElement lastOfRegion = windowHeader.remove();
+                if ( lastOfRegion.hasInsertionToTheRight() )
+                    windowHeader.addFirst(new HeaderElement(lastOfRegion.getLocation(), lastOfRegion.numInsertionsToTheRight()));
+            }
         }
         return allReads;
     }