From e2ec703a327366b6d457bd62b24b403b931e2b48 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 24 Jul 2009 16:20:38 +0000
Subject: [PATCH] Added indel cleaner and quality scores recalibrator to the
 GATK package.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1311 348d0f76-0448-11de-a6fe-93d51630548a
---
 packages/CreatePackager.xsl   |  3 +++
 packages/GenomeAnalysisTK.xml | 11 +++++++++++
 2 files changed, 14 insertions(+)

diff --git a/packages/CreatePackager.xsl b/packages/CreatePackager.xsl
index 5a9b5825e..fa85bac80 100644
--- a/packages/CreatePackager.xsl
+++ b/packages/CreatePackager.xsl
@@ -22,6 +22,9 @@
       <jar jarfile="{concat($package.dir,$project.name,'.jar')}">
         <classfileset dir="{$staging.dir}">
           <root classname="{main-class}"/>
+          <xsl:for-each select="dependencies/package">
+            <rootfileset dir="{$staging.dir}" includes="{concat(translate(current(),'.','/'),'/','*.class')}" />
+          </xsl:for-each>
           <xsl:for-each select="dependencies/class">
             <root classname="{current()}" />
           </xsl:for-each>
diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index f3a4b3600..fdd23fc32 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -3,12 +3,23 @@
   <name>GenomeAnalysisTK</name>
   <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
   <dependencies>
+    <package>org.broadinstitute.sting.gatk.filters</package>
     <class>org.broadinstitute.sting.gatk.walkers.CountLociWalker</class>
     <class>org.broadinstitute.sting.gatk.walkers.CountReadsWalker</class>
     <class>org.broadinstitute.sting.gatk.walkers.DepthOfCoverageWalker</class>
     <class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
     <class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
     <class>org.broadinstitute.sting.gatk.walkers.ValidatingPileupWalker</class>
+    <!-- Quality scores recalibration -->
+    <class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
+    <class>org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker</class>
+    <!-- Local realignment around indels -->
+    <class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
+    <class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>
+    <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker</class>
+    <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker</class>
+    <class>org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker</class>
+    <class>org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker</class>
   </dependencies>
   <resources>
     <file>java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java</file>