old_contents: import argparse, sys
  import svtools.lsort
  import svtools.vcfpaste
  import svtools.afreq
  
  def svtools_cli_parser():
      parser = argparse.ArgumentParser(description='Comprehensive utilities to explore structural variation in genomes', prog='svtools')
      subparsers = parser.add_subparsers(title='subcommands')
  
      lsort = subparsers.add_parser('lsort', help=svtools.lsort.description())
      svtools.lsort.add_arguments_to_parser(lsort)
      
      vcf_paste = subparsers.add_parser('vcfpaste', help=svtools.vcfpaste.description())
      svtools.vcfpaste.add_arguments_to_parser(vcf_paste)
      
      afreq = subparsers.add_parser('afreq', help=svtools.afreq.description())
      svtools.afreq.add_arguments_to_parser(afreq)
  
      return parser
  
  if __name__ == '__main__':
      parser = svtools_cli_parser()
      args = parser.parse_args()
      sys.exit(args.entry_point(args))
  
  
  
new_contents: import argparse, sys
  import svtools.lsort
  import svtools.vcfpaste
  import svtools.afreq
  
  def svtools_cli_parser():
      parser = argparse.ArgumentParser(description='Comprehensive utilities to explore structural variation in genomes', prog='svtools')
      subparsers = parser.add_subparsers(title=None, metavar='subcommand', help='description')
  
      lsort = subparsers.add_parser('lsort', help=svtools.lsort.description())
      svtools.lsort.add_arguments_to_parser(lsort)
      
      vcf_paste = subparsers.add_parser('vcfpaste', help=svtools.vcfpaste.description())
      svtools.vcfpaste.add_arguments_to_parser(vcf_paste)
      
      afreq = subparsers.add_parser('afreq', help=svtools.afreq.description())
      svtools.afreq.add_arguments_to_parser(afreq)
  
      return parser
  
  if __name__ == '__main__':
      parser = svtools_cli_parser()
      args = parser.parse_args()
      sys.exit(args.entry_point(args))
  
  
  
subject: clean up help formatting a bit more