From 9306041cf45a5f71e031ff6b6d96849486dcbda0 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 24 Feb 2010 16:42:56 +0000
Subject: [PATCH] Since IntervalCleaner is gone for good, it is sensible to
 update the package to refer to the new IndelRealigner instead

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2883 348d0f76-0448-11de-a6fe-93d51630548a
---
 packages/LocalRealignmentAroundIndels.xml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/packages/LocalRealignmentAroundIndels.xml b/packages/LocalRealignmentAroundIndels.xml
index ba035d3cf..46960e69f 100644
--- a/packages/LocalRealignmentAroundIndels.xml
+++ b/packages/LocalRealignmentAroundIndels.xml
@@ -6,8 +6,7 @@
     <dependencies>
       <!-- Local realignment around indels -->
       <class name="org.broadinstitute.sting.gatk.walkers.indels.RealignerTargetCreator" />
-      <class name="org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker" />
-      <class name="org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector" />
+      <class name="org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner" />
     </dependencies>
   </executable>
 </package>