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Create package that contains just what Picard needs. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2282 348d0f76-0448-11de-a6fe-93d51630548a
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alecw 2009-12-07 21:22:07 +00:00
parent a3e88c0b1c
commit 2cf21317f9
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packages/GATK-Picard.xml 100644
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<?xml version="1.0" encoding="UTF-8"?>
<package>
<name>GATK-Picard</name>
<executable>
<name>GATK-Picard</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<dependencies>
<package>org.broadinstitute.sting.gatk.filters</package>
<class>org.broadinstitute.sting.gatk.walkers.CountLociWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.CountReadsWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker</class>
<!-- Quality scores recalibration -->
<class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker</class>
<!-- Recalibration Covariates -->
<class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</class>
<!-- Local realignment around indels -->
<class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker</class>
<!-- Unified genotyper -->
<class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>
<!-- Variant filtration -->
<class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class>
<!-- Variant annotator -->
<class>org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator</class>
<!-- And the annotations -->
<class>org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
</dependencies>
</executable>
<executable>
<name>AnalyzeCovariates</name>
<main-class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</main-class>
<dependencies>
<!-- Recalibration analysis script -->
<class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
</dependencies>
</executable>
<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/coverage/DepthOfCoverageWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/qc/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>R/plot_residualError_OtherCovariate.R</file>
<file>R/plot_residualError_QualityScoreCovariate.R</file>
</resources>
</package>