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A rethink of some of the modules from last night -- make the modules stand alone. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2637 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-01-20 00:59:21 +00:00
parent ff66023d83
commit 2f3fbc145d
9 changed files with 9 additions and 0 deletions
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1
packages/AnalyzeCovariatesModule.xml
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@ -4,6 +4,7 @@
<executable> <executable>
<name>AnalyzeCovariates</name> <name>AnalyzeCovariates</name>
<main-class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</main-class> <main-class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</main-class>
<properties>StingText.properties</properties>
<dependencies> <dependencies>
<!-- Recalibration analysis script --> <!-- Recalibration analysis script -->
<class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</class> <class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</class>

1
packages/FindContaminatingReadGroupsModule.xml
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@ -4,6 +4,7 @@
<executable> <executable>
<name>FindContaminatingReadGroups</name> <name>FindContaminatingReadGroups</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class> <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<properties>StingText.properties</properties>
<dependencies> <dependencies>
<class>org.broadinstitute.sting.playground.gatk.walkers.contamination.FindContaminatingReadGroupsWalker</class> <class>org.broadinstitute.sting.playground.gatk.walkers.contamination.FindContaminatingReadGroupsWalker</class>
</dependencies> </dependencies>

1
packages/LocalRealignmentAroundIndelsModule.xml
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@ -4,6 +4,7 @@
<executable> <executable>
<name>LocalRealignmentAroundIndels</name> <name>LocalRealignmentAroundIndels</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class> <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<properties>StingText.properties</properties>
<dependencies> <dependencies>
<!-- Local realignment around indels --> <!-- Local realignment around indels -->
<class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class> <class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>

1
packages/QualityScoresRecalibrationModule.xml
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@ -4,6 +4,7 @@
<executable> <executable>
<name>QualityScoresRecalibration</name> <name>QualityScoresRecalibration</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class> <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<properties>StingText.properties</properties>
<dependencies> <dependencies>
<!-- Quality scores recalibration --> <!-- Quality scores recalibration -->
<class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class> <class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>

1
packages/UnifiedGenotyperModule.xml
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@ -4,6 +4,7 @@
<executable> <executable>
<name>UnifiedGenotyper</name> <name>UnifiedGenotyper</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class> <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<properties>StingText.properties</properties>
<dependencies> <dependencies>
<!-- Unified genotyper --> <!-- Unified genotyper -->
<class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class> <class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>

1
packages/VCFValidatorModule.xml
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@ -4,6 +4,7 @@
<executable> <executable>
<name>VCFValidator</name> <name>VCFValidator</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class> <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<properties>StingText.properties</properties>
<dependencies> <dependencies>
<!-- VCF validator --> <!-- VCF validator -->
<class>org.broadinstitute.sting.gatk.walkers.qc.VCFValidator</class> <class>org.broadinstitute.sting.gatk.walkers.qc.VCFValidator</class>

1
packages/VariantAnnotatorModule.xml
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@ -4,6 +4,7 @@
<executable> <executable>
<name>VariantAnnotator</name> <name>VariantAnnotator</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class> <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<properties>StingText.properties</properties>
<dependencies> <dependencies>
<!-- Variant annotator --> <!-- Variant annotator -->
<class>org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator</class> <class>org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator</class>

1
packages/VariantEvalModule.xml
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@ -4,6 +4,7 @@
<executable> <executable>
<name>VariantEval</name> <name>VariantEval</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class> <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<properties>StingText.properties</properties>
<dependencies> <dependencies>
<class>org.broadinstitute.sting.playground.gatk.walkers.varianteval.VariantEvalWalker</class> <class>org.broadinstitute.sting.playground.gatk.walkers.varianteval.VariantEvalWalker</class>
</dependencies> </dependencies>

1
packages/VariantFiltrationModule.xml
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@ -4,6 +4,7 @@
<executable> <executable>
<name>VariantFiltration</name> <name>VariantFiltration</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class> <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<properties>StingText.properties</properties>
<dependencies> <dependencies>
<!-- Variant filtration --> <!-- Variant filtration -->
<class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class> <class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class>