From 0187f04a906f1b4b4b93446d2b68ccf4c8befff7 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Sun, 23 Sep 2012 00:39:19 -0400
Subject: [PATCH] Proper fix for a previous RR bug fix: only remove reads from
 the header if they were actually used in the creation of the polyploid
 consensus.

---
 .../gatk/walkers/compression/reducereads/SlidingWindow.java   | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

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 19b4826bf..997eca1ed 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
@@ -698,8 +698,11 @@ public class SlidingWindow {
                             LinkedList<HeaderElement> header = read.getReadNegativeStrandFlag() ? headersNegStrand.get(haplotype) : headersPosStrand.get(haplotype);
                             addToHeader(header, read);
                         }
+
+                        removeFromHeader(windowHeader, read);
                     }
                 }
+
                 // we remove all reads before and inside the variant region from the window
                 toRemove.add(read);
             }
@@ -719,7 +722,6 @@ public class SlidingWindow {
         }
 
         for (GATKSAMRecord read : toRemove) {
-            removeFromHeader(windowHeader, read);
             readsInWindow.remove(read);
         }
         return hetReads;