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Port VariantEval and FindContaminatingReadGroups to modules. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2634 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-01-19 22:10:33 +00:00
parent 8dafd26100
commit 96a053c769
3 changed files with 24 additions and 3 deletions
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11
packages/FindContaminatingReadGroupsModule.xml 100644
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@ -0,0 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<package>
<name>FindContaminatingReadGroups</name>
<executable>
<name>FindContaminatingReadGroups</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<dependencies>
<class>org.broadinstitute.sting.playground.gatk.walkers.contamination.FindContaminatingReadGroupsWalker</class>
</dependencies>
</executable>
</package>

5
packages/GATK-GSA-Pipeline.xml
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@ -12,12 +12,11 @@
<module>UnifiedGenotyperModule.xml</module> <module>UnifiedGenotyperModule.xml</module>
<module>VariantFiltrationModule.xml</module> <module>VariantFiltrationModule.xml</module>
<module>VariantAnnotatorModule.xml</module> <module>VariantAnnotatorModule.xml</module>
<module>VariantEvalModule.xml</module>
<module>FindContaminatingReadGroupsModule.xml</module>
<dependencies> <dependencies>
<!-- Filters --> <!-- Filters -->
<package>org.broadinstitute.sting.gatk.filters</package> <package>org.broadinstitute.sting.gatk.filters</package>
<!-- From playground -->
<class>org.broadinstitute.sting.playground.gatk.walkers.varianteval.VariantEvalWalker</class>
<class>org.broadinstitute.sting.playground.gatk.walkers.contamination.FindContaminatingReadGroupsWalker</class>
</dependencies> </dependencies>
</executable> </executable>
</package> </package>

11
packages/VariantEvalModule.xml 100644
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@ -0,0 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<package>
<name>VariantEval</name>
<executable>
<name>VariantEval</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<dependencies>
<class>org.broadinstitute.sting.playground.gatk.walkers.varianteval.VariantEvalWalker</class>
</dependencies>
</executable>
</package>