<?xml version="1.0" encoding="UTF-8"?>
<package name="VariantAnnotator">
  <executable name="VariantAnnotator">
    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
    <resource-bundle file="StingText.properties" />
    <dependencies>
      <!-- Variant annotator -->
      <class name="org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator" />
      <!-- The interfacess -->
      <class name="org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType" />
      <class name="org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation" />
      <class name="org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation" />
      <class name="org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation" />
      <!-- The annotations -->
      <class name="org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance" />
      <class name="org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage" />
      <class name="org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun" />
      <class name="org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero" />
      <class name="org.broadinstitute.sting.gatk.walkers.annotator.QualByDepth" />
      <class name="org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality" />
      <class name="org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions" />
      <class name="org.broadinstitute.sting.gatk.walkers.annotator.HaplotypeScore" />
    </dependencies>
  </executable>
</package>
