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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
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rpoplin 2009-12-02 19:09:53 +00:00
parent c524b8e84b
commit 93842abb4a
2 changed files with 19 additions and 5 deletions
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17
packages/AnalyzeCovariates.xml 100644
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@ -0,0 +1,17 @@
<?xml version="1.0" encoding="UTF-8"?>
<package>
<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>
</package>

7
packages/GenomeAnalysisTK.xml
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@ -62,10 +62,7 @@
<file>testdata/exampleFASTA.fasta.fai</file>
<file>testdata/exampleFASTA.dict</file>
<!-- Supplemental scripts for graph generation, etc. -->
<file>python/analyzeRecalQuals_1KG.py</file>
<file>testdata/recalConfig_1KG.cfg</file>
<file>R/plot_q_emp_stated_hst.R</file>
<file>R/plot_qual_diff_v_cycle.R</file>
<file>R/plot_qual_diff_v_dinuc.R</file>
<file>R/plot_residualError_OtherCovariate.R</file>
<file>R/plot_residualError_QualityScoreCovariate.R</file>
</resources>
</package>