From fe8809d12ae7b26d7ec42684d1c8eb24efa797be Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 25 Nov 2009 18:59:21 +0000
Subject: [PATCH] Added Covariate classes to the Early Access binary

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2159 348d0f76-0448-11de-a6fe-93d51630548a
---
 packages/GenomeAnalysisTK.xml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index 25c732968..f7658ac98 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -13,6 +13,15 @@
     <!-- Quality scores recalibration -->
     <class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
     <class>org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker</class>
+    <!-- Recalibration Covariates -->
+    <class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
+    <class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
+    <class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
+    <class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
+    <class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
+    <class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
+    <class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
+    <class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
     <!-- Local realignment around indels -->
     <class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
     <class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>