<commit_before><?xml version="1.0" encoding="UTF-8"?>
<package name="LocalRealignmentAroundIndels">
  <executable name="LocalRealignmentAroundIndels">
    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
    <resource-bundle file="StingText.properties" />
    <dependencies>
      <!-- Local realignment around indels -->
      <class name="org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector" />
      <class name="org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker" />
      <class name="org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker" />
      <class name="org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker" />
      <class name="org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker" />
      <class name="org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker" />
      <class name="org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker" />
      <class name="org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker" /> 
    </dependencies>
  </executable>
</package><commit_msg>Updated the package to use RealignerTargetCreator.  Also, removed IndelGenotyper since it's still experimental.<commit_after><?xml version="1.0" encoding="UTF-8"?>
<package name="LocalRealignmentAroundIndels">
  <executable name="LocalRealignmentAroundIndels">
    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
    <resource-bundle file="StingText.properties" />
    <dependencies>
      <!-- Local realignment around indels -->
      <class name="org.broadinstitute.sting.gatk.walkers.indels.RealignerTargetCreator" />
      <class name="org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker" />
      <class name="org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector" />
    </dependencies>
  </executable>
</package>
{'fraction_non_alphanumeric': 0.13851891315929676, 'fraction_numerical': 0.0037293553542887587, 'mean_word_length': 4.7784615384615385, 'pattern_counts': {'":': 0, '<': 34, '<?xml version=': 2, '>': 34, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1356488', 'n_tokens_mistral': 644, 'n_tokens_neox': 620, 'n_words': 71}