<?xml version="1.0" encoding="UTF-8"?>
        <!-- In order to update this file, copy GenomeAnalysisTK.xml, change the name of the
        package and executable to GATK-Picard, and add TileCovariate to the list of dependencies.
        Remove the AnalyzeCovariates executable. -->
<package name="GATK-Picard">
  <version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
  <executable name="GATK-Picard">
    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
    <resource-bundle file="StingText.properties" />
    <modules>
      <module file="QualityScoresRecalibration.xml" />
      <module file="LocalRealignmentAroundIndels.xml" />
      <module file="UnifiedGenotyper.xml" />
      <module file="VariantFiltration.xml" />
      <module file="VariantAnnotator.xml" />
    </modules>
    <dependencies>
      <!-- Filters -->
      <package name="org.broadinstitute.sting.gatk.filters" />
      <class name="org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker" />
      <class name="org.broadinstitute.sting.gatk.walkers.PileupWalker" />
      <class name="org.broadinstitute.sting.gatk.walkers.PrintReadsWalker" />
      <class name="org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker" />
      <class name="org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker" />
      <class name="org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker" />
      <!-- Recalibration Covariates -->
      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate" />
      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate" />
      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate" />
      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate" />
      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate" />
    </dependencies>
  </executable>
  <resources>
    <!-- GATK sample code and build scripts -->
    <file name="java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java" />
    <file name="java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java" />
    <file name="java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java" />
    <file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java" />
    <file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java" />
    <file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java" />
    <file name="java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java" />
    <file name="java/src/org/broadinstitute/sting/gatk/examples/build.xml" />
    <!-- Sample reads and reference files -->
    <file name="testdata/exampleBAM.bam" />
    <file name="testdata/exampleBAM.bam.bai" />
    <file name="testdata/exampleFASTA.fasta" />
    <file name="testdata/exampleFASTA.fasta.fai" />
    <file name="testdata/exampleFASTA.dict" />
  </resources>
</package>
