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A few more bug fixes based on extended testing. Sorry, Eric. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2656 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-01-21 22:12:16 +00:00
parent c1e09efb23
commit de21943acd
3 changed files with 17 additions and 17 deletions
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10
packages/AnalyzeCovariates.xml
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@ -6,11 +6,11 @@
<dependencies> <dependencies>
<!-- Recalibration analysis script --> <!-- Recalibration analysis script -->
<class name="org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates" /> <class name="org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates" />
<class name=">org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate" /> <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.QualityScoreCovariate" />
<class name=">org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate" /> <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.ReadGroupCovariate" />
<class name=">org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" /> <class name="org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" />
</dependencies> </dependencies>
</executable> </executable>
<resources> <resources>

10
packages/GATK-Picard.xml
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@ -8,11 +8,11 @@
<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" /> <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
<resource-bundle file="StingText.properties" /> <resource-bundle file="StingText.properties" />
<modules> <modules>
<module name="QualityScoresRecalibration.xml" /> <module file="QualityScoresRecalibration.xml" />
<module name="LocalRealignmentAroundIndels.xml" /> <module file="LocalRealignmentAroundIndels.xml" />
<module name="UnifiedGenotyper.xml" /> <module file="UnifiedGenotyper.xml" />
<module name="VariantFiltration.xml" /> <module file="VariantFiltration.xml" />
<module name="VariantAnnotator.xml" /> <module file="VariantAnnotator.xml" />
</modules> </modules>
<dependencies> <dependencies>
<!-- Filters --> <!-- Filters -->

14
packages/QualityScoresRecalibration.xml
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@ -5,14 +5,14 @@
<resource-bundle file="StingText.properties" /> <resource-bundle file="StingText.properties" />
<dependencies> <dependencies>
<!-- Quality scores recalibration --> <!-- Quality scores recalibration -->
<class file="org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker" /> <class name="org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker" />
<class file=">org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker" /> <class name="org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker" />
<!-- Recalibration Covariates --> <!-- Recalibration Covariates -->
<class file=">org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate" /> <class name="org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate" />
<class file=">org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate" /> <class name="org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate" />
<class file=">org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate" /> <class name="org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate" />
<class file=">org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate" /> <class name="org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate" />
<class file=">org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" /> <class name="org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" />
</dependencies> </dependencies>
</executable> </executable>
</package> </package>