From 4e116760f4f8577bfaf677ed7711cfc599a6c90d Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 12 Sep 2011 15:09:25 -0400
Subject: [PATCH] Removing some old cruft from the packages dir.  Updating
 AnalyzeCovariates to include all Covariates.

---
 public/packages/AnalyzeCovariates.xml         |  5 +---
 .../packages/FindContaminatingReadGroups.xml  | 10 -------
 public/packages/GATKResources.xml             | 20 --------------
 public/packages/IndelGenotyper.xml            | 11 --------
 .../packages/LocalRealignmentAroundIndels.xml | 12 ---------
 .../packages/QualityScoresRecalibration.xml   | 18 -------------
 public/packages/RMDIndexer.xml                | 13 ----------
 public/packages/UnifiedGenotyper.xml          | 11 --------
 public/packages/VariantAnnotator.xml          | 26 -------------------
 public/packages/VariantEval.xml               | 18 -------------
 public/packages/VariantFiltration.xml         | 13 ----------
 public/packages/VariantRecalibration.xml      | 12 ---------
 12 files changed, 1 insertion(+), 168 deletions(-)
 delete mode 100644 public/packages/FindContaminatingReadGroups.xml
 delete mode 100755 public/packages/GATKResources.xml
 delete mode 100644 public/packages/IndelGenotyper.xml
 delete mode 100644 public/packages/LocalRealignmentAroundIndels.xml
 delete mode 100644 public/packages/QualityScoresRecalibration.xml
 delete mode 100644 public/packages/RMDIndexer.xml
 delete mode 100644 public/packages/UnifiedGenotyper.xml
 delete mode 100644 public/packages/VariantAnnotator.xml
 delete mode 100644 public/packages/VariantEval.xml
 delete mode 100644 public/packages/VariantFiltration.xml
 delete mode 100644 public/packages/VariantRecalibration.xml

diff --git a/public/packages/AnalyzeCovariates.xml b/public/packages/AnalyzeCovariates.xml
index 7e31934df..a6675a63d 100644
--- a/public/packages/AnalyzeCovariates.xml
+++ b/public/packages/AnalyzeCovariates.xml
@@ -6,10 +6,7 @@
     <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.*" />
     </dependencies>
   </executable>
   <resources>
diff --git a/public/packages/FindContaminatingReadGroups.xml b/public/packages/FindContaminatingReadGroups.xml
deleted file mode 100644
index 880f64a81..000000000
--- a/public/packages/FindContaminatingReadGroups.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package name="FindContaminatingReadGroups">
-  <executable name="FindContaminatingReadGroups">
-    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
-    <resource-bundle file="StingText.properties" />
-    <dependencies>
-      <class name="org.broadinstitute.sting.playground.gatk.walkers.contamination.FindContaminatingReadGroupsWalker" />
-    </dependencies>
-  </executable>
-</package>
diff --git a/public/packages/GATKResources.xml b/public/packages/GATKResources.xml
deleted file mode 100755
index 87e6e0e50..000000000
--- a/public/packages/GATKResources.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package name="GATKResources">
-  <resources>
-    <file name="/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" />
-    <file name="/humgen/gsa-scr1/GATK_Data/dbsnp_129_b37.rod" />
-    <file name="/humgen/gsa-scr1/GATK_Data/dbsnp_130_b36.rod" />
-    <file name="/humgen/1kg/reference/human_b36_both.fasta" />
-    <file name="/humgen/1kg/reference/human_b36_both.dict" />
-    <file name="/humgen/1kg/reference/human_b36_both.fasta.fai" />
-    <file name="/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod" />
-    <file name="/humgen/gsa-scr1/GATK_Data/dbsnp_130_hg18.rod" />
-    <file name="/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" />
-    <file name="/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.dict" />
-    <file name="/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta.fai" />
-    <file name="/humgen/gsa-scr1/GATK_Data/dbsnp_130_b37.rod" />
-    <file name="/humgen/1kg/reference/human_g1k_v37.fasta" />
-    <file name="/humgen/1kg/reference/human_g1k_v37.dict" />
-    <file name="/humgen/1kg/reference/human_g1k_v37.fasta.fai" />
-   </resources>
-</package>
diff --git a/public/packages/IndelGenotyper.xml b/public/packages/IndelGenotyper.xml
deleted file mode 100644
index c9e3ae0f6..000000000
--- a/public/packages/IndelGenotyper.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package name="IndelGenotyper">
-  <executable name="IndelGenotyper">
-    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
-    <resource-bundle file="StingText.properties" />
-    <dependencies>
-      <!-- Local realignment around indels -->
-      <class name="org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker" />
-    </dependencies>
-  </executable>
-</package>
diff --git a/public/packages/LocalRealignmentAroundIndels.xml b/public/packages/LocalRealignmentAroundIndels.xml
deleted file mode 100644
index 46960e69f..000000000
--- a/public/packages/LocalRealignmentAroundIndels.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package name="LocalRealignmentAroundIndels">
-  <executable name="LocalRealignmentAroundIndels">
-    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
-    <resource-bundle file="StingText.properties" />
-    <dependencies>
-      <!-- Local realignment around indels -->
-      <class name="org.broadinstitute.sting.gatk.walkers.indels.RealignerTargetCreator" />
-      <class name="org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner" />
-    </dependencies>
-  </executable>
-</package>
diff --git a/public/packages/QualityScoresRecalibration.xml b/public/packages/QualityScoresRecalibration.xml
deleted file mode 100644
index 95e8b7c63..000000000
--- a/public/packages/QualityScoresRecalibration.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package name="QualityScoresRecalibration">
-  <executable name="QualityScoresRecalibration">
-    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
-    <resource-bundle file="StingText.properties" />
-    <dependencies>
-      <!-- Quality scores recalibration -->
-      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker" />
-      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker" />
-      <!-- Recalibration Covariates -->
-      <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>
diff --git a/public/packages/RMDIndexer.xml b/public/packages/RMDIndexer.xml
deleted file mode 100644
index 5d40876de..000000000
--- a/public/packages/RMDIndexer.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package name="RMDIndexer">
-  <executable name="RMDIndexer">
-    <main-class name="org.broadinstitute.sting.gatk.refdata.indexer.RMDIndexer" />
-    <resource-bundle file="StingText.properties" />
-    <dependencies>
-      <package name="org.broad.tribble.*" />
-      <package name="org.broadinstitute.sting.gatk.refdata.features.*" />
-      <!-- the class itself -->
-      <class name="org.broadinstitute.sting.gatk.refdata.indexer.RMDIndexer" />
-    </dependencies>
-  </executable>
-</package>
diff --git a/public/packages/UnifiedGenotyper.xml b/public/packages/UnifiedGenotyper.xml
deleted file mode 100644
index 67a17640c..000000000
--- a/public/packages/UnifiedGenotyper.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package name="UnifiedGenotyper">
-  <executable name="UnifiedGenotyper">
-    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
-    <resource-bundle file="StingText.properties" />
-    <dependencies>
-      <!-- Unified genotyper -->
-      <class name="org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper" />
-    </dependencies>
-  </executable>
-</package>
diff --git a/public/packages/VariantAnnotator.xml b/public/packages/VariantAnnotator.xml
deleted file mode 100644
index 88c0701f0..000000000
--- a/public/packages/VariantAnnotator.xml
+++ /dev/null
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package name="VariantAnnotator">
-  <executable name="VariantAnnotator">
-    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
-    <resource-bundle file="StingText.properties" />
-    <dependencies>
-      <!-- Variant annotator -->
-      <class name="org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator" />
-      <!-- The interfacess -->
-      <class name="org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType" />
-      <class name="org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation" />
-      <class name="org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation" />
-      <class name="org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation" />
-      <!-- The annotations -->
-      <class name="org.broadinstitute.sting.gatk.walkers.annotator.DepthPerAlleleBySample" />
-      <class name="org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage" />
-      <class name="org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun" />
-      <class name="org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero" />
-      <class name="org.broadinstitute.sting.gatk.walkers.annotator.QualByDepth" />
-      <class name="org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality" />
-      <class name="org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions" />
-      <class name="org.broadinstitute.sting.gatk.walkers.annotator.HaplotypeScore" />
-      <class name="org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts" />
-    </dependencies>
-  </executable>
-</package>
diff --git a/public/packages/VariantEval.xml b/public/packages/VariantEval.xml
deleted file mode 100644
index 791066fb7..000000000
--- a/public/packages/VariantEval.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package name="VariantEval">
-  <executable name="VariantEval">
-    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
-    <resource-bundle file="StingText.properties" />
-    <dependencies>
-      <class name="org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker" />
-      <class name="org.broadinstitute.sting.gatk.walkers.varianteval.CountVariants" />
-      <class name="org.broadinstitute.sting.gatk.walkers.varianteval.CompOverlap" />
-      <class name="org.broadinstitute.sting.gatk.walkers.varianteval.GenotypeConcordance" />
-      <class name="org.broadinstitute.sting.gatk.walkers.varianteval.MendelianViolationEvaluator" />
-      <class name="org.broadinstitute.sting.gatk.walkers.varianteval.TiTvVariantEvaluator" />
-      <class name="org.broadinstitute.sting.gatk.walkers.varianteval.ValidationRate" />
-      <class name="org.broadinstitute.sting.gatk.walkers.varianteval.VariantQualityScore" />
-      <class name="org.broadinstitute.sting.gatk.walkers.varianteval.CountFunctionalClasses" />
-    </dependencies>
-  </executable>
-</package>
diff --git a/public/packages/VariantFiltration.xml b/public/packages/VariantFiltration.xml
deleted file mode 100644
index 48fa0ff37..000000000
--- a/public/packages/VariantFiltration.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package name="VariantFiltration">
-  <executable name="VariantFiltration">
-    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
-    <resource-bundle file="StingText.properties" />
-    <dependencies>
-      <!-- Workaround - depend on the logger impl required by JEXL -->
-      <package name="org.apache.commons.logging.impl" />
-      <!-- Variant filtration -->
-      <class name="org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker" />
-    </dependencies>
-  </executable>
-</package>
diff --git a/public/packages/VariantRecalibration.xml b/public/packages/VariantRecalibration.xml
deleted file mode 100644
index 6fe6b1eff..000000000
--- a/public/packages/VariantRecalibration.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package name="VariantRecalibration">
-  <executable name="VariantRecalibration">
-    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
-    <resource-bundle file="StingText.properties" />
-    <dependencies>
-      <!-- Variant recalibration -->
-      <class name="org.broadinstitute.sting.gatk.walkers.variantrecalibration.GenerateVariantClustersWalker" />
-      <class name="org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator" />
-    </dependencies>
-  </executable>
-</package>