<?xml version="1.0" encoding="UTF-8"?>
<package name="AnalyzeCovariates">
  <executable name="AnalyzeCovariates">
    <main-class name="org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates" />
    <resource-bundle file="StingText.properties" />
    <dependencies>
      <!-- Recalibration analysis script -->
      <class name="org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates" />
      <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.CycleCovariate" />
      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate" />
      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" />
    </dependencies>
  </executable>
  <resources>
    <!-- Supplemental scripts for graph generation, etc. -->
    <file name="R/plot_residualError_OtherCovariate.R" />
    <file name="R/plot_residualError_QualityScoreCovariate.R" />
  </resources>
</package>
