RR bug: we need to call removeFromHeader() for reads that were used in creating a polyploid consensus or else they are reused later in creating synthetic reads. In the worst case, this bug caused the tool to create 2 copies of the reduced read.

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

@@ -719,6 +719,7 @@ public class SlidingWindow {
         }
 
         for (GATKSAMRecord read : toRemove) {
+            removeFromHeader(windowHeader, read);
             readsInWindow.remove(read);
         }
         return hetReads;