From 5bb069388810f1c0858801379b1fbdc3d56fb8aa Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Thu, 28 Jun 2012 12:57:51 -0400
Subject: [PATCH] Bug fix for HC GGA mode. Shouldn't try to add an indel into
 the haplotype if that haplotype already contains the event of interest. Misc
 minor assembly param changes. Turning off capping of base qualities by base
 indel qualities until we can evaluate that change.

---
 .../broadinstitute/sting/utils/activeregion/ActiveRegion.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
index 7c956b855..18276f932 100644
--- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
+++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
@@ -46,7 +46,7 @@ public class ActiveRegion implements HasGenomeLocation, Comparable<ActiveRegion>
     }
     
     public void hardClipToActiveRegion() {
-        final ArrayList<GATKSAMRecord> clippedReads = ReadClipper.hardClipToRegion( reads, activeRegionLoc.getStart(), activeRegionLoc.getStop() );
+        final ArrayList<GATKSAMRecord> clippedReads = ReadClipper.hardClipToRegion( reads, extendedLoc.getStart(), extendedLoc.getStop() );
         reads.clear();
         reads.addAll(clippedReads);
     }