From e6827424b9907614aeb0b1c9f3bf07084572f0a7 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 15 Sep 2009 14:17:36 +0000
Subject: [PATCH] Added support python and R scripts for generating covariate
 output graphs.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1625 348d0f76-0448-11de-a6fe-93d51630548a
---
 packages/GenomeAnalysisTK.xml | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index c94d9d4b9..eeaad6a18 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -35,6 +35,7 @@
     <class>org.broadinstitute.sting.playground.gatk.walkers.variants.VECClusteredSnps</class>
   </dependencies>
   <resources>
+    <!-- GATK sample code and build scripts -->
     <file>java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java</file>
     <file>java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java</file>
     <file>java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java</file>
@@ -43,10 +44,20 @@
     <file>java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java</file>
     <file>java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java</file>
     <file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file>
+    <!-- Sample reads and reference files -->
     <file>testdata/exampleBAM.bam</file>
     <file>testdata/exampleBAM.bam.bai</file>
     <file>testdata/exampleFASTA.fasta</file>
     <file>testdata/exampleFASTA.fasta.fai</file>
     <file>testdata/exampleFASTA.dict</file>
+    <!-- Supplemental scripts for graph generation, etc. -->
+    <file>python/analyzeRecalQuals.py</file>
+    <file>python/analyzeRecalQuals_1KG.py</file>
+    <file>testdata/defaultGATKConfig.cfg</file>
+    <file>testdata/recalConfig_1KG.cfg</file>
+    <file>R/logistic_regression.R</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>
   </resources>
 </package>