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Removing some old cruft from the packages dir. Updating AnalyzeCovariates to include all Covariates.

This commit is contained in:
Eric Banks 2011-09-12 15:09:25 -04:00
parent ec4b30de6d
commit 4e116760f4
12 changed files with 1 additions and 168 deletions
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5
public/packages/AnalyzeCovariates.xml
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@ -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>

10
public/packages/FindContaminatingReadGroups.xml
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@ -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>

20
public/packages/GATKResources.xml
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@ -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>

11
public/packages/IndelGenotyper.xml
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@ -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>

12
public/packages/LocalRealignmentAroundIndels.xml
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@ -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>

18
public/packages/QualityScoresRecalibration.xml
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@ -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>

13
public/packages/RMDIndexer.xml
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@ -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>

11
public/packages/UnifiedGenotyper.xml
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@ -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>

26
public/packages/VariantAnnotator.xml
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@ -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>

18
public/packages/VariantEval.xml
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@ -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>

13
public/packages/VariantFiltration.xml
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@ -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>

12
public/packages/VariantRecalibration.xml
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@ -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>