<?xml version="1.0" encoding="UTF-8"?>
<package name="GenomeAnalysisTK">
  <version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
  <executable name="GenomeAnalysisTK">
    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
    <resource-bundle file="StingText.properties" />
    <modules>
      <module file="QualityScoresRecalibration.xml" />
      <module file="VariantRecalibration.xml" />
      <module file="LocalRealignmentAroundIndels.xml" />
      <module file="UnifiedGenotyper.xml" />
      <module file="VariantEval.xml" />
      <module file="VariantFiltration.xml" />
      <module file="VariantAnnotator.xml" />
      <module file="IndelGenotyper.xml" />
    </modules>
    <dependencies>
      <!-- Filters -->
      <package name="org.broadinstitute.sting.gatk.filters" />
      <!-- Tribble codecs -->
      <package name="org.broad.tribble.*" />
      <!-- Basic qc walkers -->
      <class name="org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker" />
      <class name="org.broadinstitute.sting.gatk.walkers.coverage.DoCOutputMultiplexer" />

      <class name="org.broadinstitute.sting.gatk.refdata.tracks.builders.RODTrackBuilder" />
      <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" />
      <!-- Other misc walkers -->
      <class name="org.broadinstitute.sting.gatk.walkers.sequenom.SequenomValidationConverter" />
      <class name="org.broadinstitute.sting.gatk.walkers.variantutils.CombineVariants" />
      <class name="org.broadinstitute.sting.gatk.walkers.VariantsToVCF" />
    </dependencies>
  </executable>
  <modules>
    <module file="AnalyzeCovariates.xml"/>
  </modules>
  <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>
  <release>
    <executable directory="/humgen/gsa-hpprojects/GATK/bin" symlink="current" />
    <archive directory="/web/ftp/pub/gsa/GenomeAnalysisTK" symlink="GenomeAnalysisTK-latest.tar.bz2" />
  </release>
</package>
