Fix subtle bug in the ReduceReads stash reported by Adam

* The tailSet generated every time we flush the reads stash is still being affected by subsequent clears because it is just a pointer to the parent element in the original TreeSet. This is dangerous, and there is a weird  condition where the clear will affects it.
   * Fix by creating a new set, given the tailSet instead of trying to do magic with just the pointer.

public/java/src/org/broadinstitute/sting/utils/sam/AlignmentStartWithNoTiesComparator.java

@@ -36,8 +36,10 @@ public class AlignmentStartWithNoTiesComparator implements Comparator<SAMRecord>
                 result = cmpContig;
 
             else {
-                if (r1.getAlignmentStart() < r2.getAlignmentStart()) result = -1;
-                else result = 1;
+                if (r1.getAlignmentStart() < r2.getAlignmentStart())
+                    result = -1;
+                else
+                    result = 1;
             }
         }