From 93842abb4a3996080608033f860037a8f1e30a17 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 2 Dec 2009 19:09:53 +0000
Subject: [PATCH] Let the packages know about the changes made for
 AnalyzeCovariates.jar

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2222 348d0f76-0448-11de-a6fe-93d51630548a
---
 packages/AnalyzeCovariates.xml | 17 +++++++++++++++++
 packages/GenomeAnalysisTK.xml  |  7 ++-----
 2 files changed, 19 insertions(+), 5 deletions(-)
 create mode 100644 packages/AnalyzeCovariates.xml

diff --git a/packages/AnalyzeCovariates.xml b/packages/AnalyzeCovariates.xml
new file mode 100644
index 000000000..9fdfb1d37
--- /dev/null
+++ b/packages/AnalyzeCovariates.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<package>
+  <name>AnalyzeCovariates</name>
+  <main-class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</main-class>
+  <dependencies>
+    <!-- Recalibration analysis script -->
+    <class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</class>
+    <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>
+  </dependencies>
+</package>
diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index a4c9c34d2..51814abcd 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -62,10 +62,7 @@
     <file>testdata/exampleFASTA.fasta.fai</file>
     <file>testdata/exampleFASTA.dict</file>
     <!-- Supplemental scripts for graph generation, etc. -->
-    <file>python/analyzeRecalQuals_1KG.py</file>
-    <file>testdata/recalConfig_1KG.cfg</file>
-    <file>R/plot_q_emp_stated_hst.R</file>
-    <file>R/plot_qual_diff_v_cycle.R</file>
-    <file>R/plot_qual_diff_v_dinuc.R</file>
+    <file>R/plot_residualError_OtherCovariate.R</file>
+    <file>R/plot_residualError_QualityScoreCovariate.R</file>
   </resources>
 </package>