From bbddeb693ff817a0efd661ce5dbf56032b592d4d Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 27 Jan 2010 03:45:15 +0000
Subject: [PATCH] Updated the package to use RealignerTargetCreator.  Also,
 removed IndelGenotyper since it's still experimental.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2698 348d0f76-0448-11de-a6fe-93d51630548a
---
 packages/LocalRealignmentAroundIndels.xml | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/packages/LocalRealignmentAroundIndels.xml b/packages/LocalRealignmentAroundIndels.xml
index a3cb273a1..ba035d3cf 100644
--- a/packages/LocalRealignmentAroundIndels.xml
+++ b/packages/LocalRealignmentAroundIndels.xml
@@ -5,14 +5,9 @@
     <resource-bundle file="StingText.properties" />
     <dependencies>
       <!-- Local realignment around indels -->
-      <class name="org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector" />
-      <class name="org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker" />
+      <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.IntervalMergerWalker" />
-      <class name="org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker" />
-      <class name="org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker" />
-      <class name="org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker" />
-      <class name="org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker" /> 
+      <class name="org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector" />
     </dependencies>
   </executable>
 </package>