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gatk-3.8/packages/GenomeAnalysisTK.xml

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Plumbed packaging support into build.xml and added package for GATK. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1012 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 03:41:16 +08:00
<?xml version="1.0" encoding="UTF-8"?>
<package>
<name>GenomeAnalysisTK</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<dependencies>
Added indel cleaner and quality scores recalibrator to the GATK package. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1311 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-25 00:20:38 +08:00
<package>org.broadinstitute.sting.gatk.filters</package>
Adding more walkers to the base GATK package. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1241 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 04:40:52 +08:00
<class>org.broadinstitute.sting.gatk.walkers.CountLociWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.CountReadsWalker</class>
Oops. Specified incorrect classname in packgae for depth of coverage walker. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1161 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-03 05:40:40 +08:00
<class>org.broadinstitute.sting.gatk.walkers.DepthOfCoverageWalker</class>
Plumbed packaging support into build.xml and added package for GATK. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1012 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 03:41:16 +08:00
<class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
Adding more walkers to the base GATK package. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1241 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 04:40:52 +08:00
<class>org.broadinstitute.sting.gatk.walkers.ValidatingPileupWalker</class>
Added indel cleaner and quality scores recalibrator to the GATK package. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1311 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-25 00:20:38 +08:00
<!-- Quality scores recalibration -->
<class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker</class>
Added Covariate classes to the Early Access binary git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2159 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-26 02:59:21 +08:00
<!-- 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>
Added indel cleaner and quality scores recalibrator to the GATK package. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1311 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-25 00:20:38 +08:00
<!-- 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>
moving IndelGenotyper out from playground git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1731 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-26 03:43:53 +08:00
<class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker</class>
added IndelGenotyperV2Walker git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1937 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 04:07:31 +08:00
<class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker</class>
Updated package for early access git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2158 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-26 02:08:12 +08:00
<!-- Unified genotyper -->
<class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>
Added VariantFiltrationWalker to GATK early release. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1502 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 10:17:50 +08:00
<!-- Variant filtration -->
Package tool doesn't provide an error if classes listed in the package are not found, and classes were moved from playground to core. This step: correct the classes listed in the package. Next step: update the packaging tool to fail if class is not found. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1680 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-22 23:06:45 +08:00
<class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class>
Updated package for early access git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2158 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-26 02:08:12 +08:00
<!-- 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>
Plumbed packaging support into build.xml and added package for GATK. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1012 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 03:41:16 +08:00
</dependencies>
First step in replacing the Hello, World! document. Revamped the HelloWalker and checked it into the source tree, created a special build file for it, and added it to the packaging tool. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1135 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 05:59:54 +08:00
<resources>
Added support python and R scripts for generating covariate output graphs. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1625 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-15 22:17:36 +08:00
<!-- GATK sample code and build scripts -->
Packaging cleanup. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1242 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 05:00:02 +08:00
<file>java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java</file>
Cleanup pileup and depth of coverage in preparation for release. Add pileup, depth of coverage, and print reads to package for distribution. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1159 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 22:54:01 +08:00
<file>java/src/org/broadinstitute/sting/gatk/walkers/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>
Adding more walkers to the base GATK package. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1241 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 04:40:52 +08:00
<file>java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java</file>
First step in replacing the Hello, World! document. Revamped the HelloWalker and checked it into the source tree, created a special build file for it, and added it to the packaging tool. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1135 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 05:59:54 +08:00
<file>java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file>
Added support python and R scripts for generating covariate output graphs. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1625 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-15 22:17:36 +08:00
<!-- Sample reads and reference files -->
added the example files to the distro git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1152 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 07:16:42 +08:00
<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>
Added support python and R scripts for generating covariate output graphs. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1625 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-15 22:17:36 +08:00
<!-- Supplemental scripts for graph generation, etc. -->
Let the packages know about the changes made for AnalyzeCovariates.jar git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2222 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 03:09:53 +08:00
<file>R/plot_residualError_OtherCovariate.R</file>
<file>R/plot_residualError_QualityScoreCovariate.R</file>
First step in replacing the Hello, World! document. Revamped the HelloWalker and checked it into the source tree, created a special build file for it, and added it to the packaging tool. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1135 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 05:59:54 +08:00
</resources>
Plumbed packaging support into build.xml and added package for GATK. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1012 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 03:41:16 +08:00
</package>