<?xml version="1.0" encoding="UTF-8"?>
<package name="QualityScoresRecalibration">
  <executable name="QualityScoresRecalibration">
    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
    <resource-bundle file="StingText.properties" />
    <dependencies>
      <!-- Quality scores recalibration -->
      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker" />
      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker" />
      <!-- Recalibration Covariates -->
      <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>
</package>
