From de21943acdc0c07176f689fc724dc13bf7695f28 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 21 Jan 2010 22:12:16 +0000
Subject: [PATCH] A few more bug fixes based on extended testing.  Sorry, Eric.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2656 348d0f76-0448-11de-a6fe-93d51630548a
---
 packages/AnalyzeCovariates.xml          | 10 +++++-----
 packages/GATK-Picard.xml                | 10 +++++-----
 packages/QualityScoresRecalibration.xml | 14 +++++++-------
 3 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/packages/AnalyzeCovariates.xml b/packages/AnalyzeCovariates.xml
index 87f055f83..3a3cae54e 100644
--- a/packages/AnalyzeCovariates.xml
+++ b/packages/AnalyzeCovariates.xml
@@ -6,11 +6,11 @@
     <dependencies>
       <!-- Recalibration analysis script -->
       <class name="org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates" />
-      <class name=">org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate" />
-      <class name=">org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate" />
-      <class name=">org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate" />
-      <class name=">org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate" />
-      <class name=">org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" />
+      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate" />
+      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate" />
+      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate" />
+      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate" />
+      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" />
     </dependencies>
   </executable>
   <resources>
diff --git a/packages/GATK-Picard.xml b/packages/GATK-Picard.xml
index 207e2c0a6..29057d398 100644
--- a/packages/GATK-Picard.xml
+++ b/packages/GATK-Picard.xml
@@ -8,11 +8,11 @@
     <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
     <resource-bundle file="StingText.properties" />
     <modules>
-      <module name="QualityScoresRecalibration.xml" />
-      <module name="LocalRealignmentAroundIndels.xml" />
-      <module name="UnifiedGenotyper.xml" />
-      <module name="VariantFiltration.xml" />
-      <module name="VariantAnnotator.xml" />
+      <module file="QualityScoresRecalibration.xml" />
+      <module file="LocalRealignmentAroundIndels.xml" />
+      <module file="UnifiedGenotyper.xml" />
+      <module file="VariantFiltration.xml" />
+      <module file="VariantAnnotator.xml" />
     </modules>
     <dependencies>
       <!-- Filters -->
diff --git a/packages/QualityScoresRecalibration.xml b/packages/QualityScoresRecalibration.xml
index 3b43158f2..95e8b7c63 100644
--- a/packages/QualityScoresRecalibration.xml
+++ b/packages/QualityScoresRecalibration.xml
@@ -5,14 +5,14 @@
     <resource-bundle file="StingText.properties" />
     <dependencies>
       <!-- Quality scores recalibration -->
-      <class file="org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker" />
-      <class file=">org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker" />
       <!-- Recalibration Covariates -->
-      <class file=">org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate" />
-      <class file=">org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate" />
-      <class file=">org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate" />
-      <class file=">org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate" />
-      <class file=">org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" />
+      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate" />
+      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate" />
+      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate" />
+      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate" />
+      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" />
     </dependencies>
   </executable>
 </package>