From ced652b3dd4be0ea8d1aa4450eaa2c334d828745 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Sat, 22 Sep 2012 21:50:10 -0400
Subject: [PATCH] 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.

---
 .../gatk/walkers/compression/reducereads/SlidingWindow.java      | 1 +
 1 file changed, 1 insertion(+)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
index 13d90358b..19b4826bf 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
+++ b/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;