From ef680e1e13864bead13767c82b20bdd6e304237f Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 24 Sep 2012 11:14:18 -0400
Subject: [PATCH] RR fix: push the header removal all the way into the inner
 loops so that we literally remove a read from the general header only if it
 was added to the polyploid header.  Add comments.

---
 .../gatk/walkers/compression/reducereads/SlidingWindow.java  | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

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 997eca1ed..d55560a70 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
@@ -696,10 +696,11 @@ public class SlidingWindow {
                                 currentHaplotype++;
                             }
                             LinkedList<HeaderElement> header = read.getReadNegativeStrandFlag() ? headersNegStrand.get(haplotype) : headersPosStrand.get(haplotype);
+                            // add to the polyploid header
                             addToHeader(header, read);
+                            // remove from the standard header so that we don't double count it
+                            removeFromHeader(windowHeader, read);
                         }
-
-                        removeFromHeader(windowHeader, read);
                     }
                 }