old_contents: import argparse, sys
  import svtools.lsort
  import svtools.lmerge
  import svtools.vcfpaste
  import svtools.copynumber
  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)
  
      lmerge = subparsers.add_parser('lmerge', help=svtools.lmerge.description())
      svtools.lmerge.add_arguments_to_parser(lmerge)
      
      vcf_paste = subparsers.add_parser('vcfpaste', help=svtools.vcfpaste.description())
      svtools.vcfpaste.add_arguments_to_parser(vcf_paste)
  
      copynumber = subparsers.add_parser('copynumber', help=svtools.copynumber.description())
      svtools.copynumber.add_arguments_to_parser(copynumber)
      
      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.lmerge
  import svtools.vcfpaste
  import svtools.copynumber
  import svtools.afreq
  import svtools.bedpetobed12
  import svtools.bedpetovcf
  import svtools.vcftobedpe
  import svtools.vcfsort
  import svtools.bedpesort
  
  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)
  
      lmerge = subparsers.add_parser('lmerge', help=svtools.lmerge.description())
      svtools.lmerge.add_arguments_to_parser(lmerge)
      
      vcf_paste = subparsers.add_parser('vcfpaste', help=svtools.vcfpaste.description())
      svtools.vcfpaste.add_arguments_to_parser(vcf_paste)
  
      copynumber = subparsers.add_parser('copynumber', help=svtools.copynumber.description())
      svtools.copynumber.add_arguments_to_parser(copynumber)
      
      afreq = subparsers.add_parser('afreq', help=svtools.afreq.description())
      svtools.afreq.add_arguments_to_parser(afreq)
  
      bedpetobed12 = subparsers.add_parser('bedpetobed12', help=svtools.bedpetobed12.description())
      svtools.bedpetobed12.add_arguments_to_parser(bedpetobed12)
  
      bedpetovcf = subparsers.add_parser('bedpetovcf', help=svtools.bedpetovcf.description())
      svtools.bedpetovcf.add_arguments_to_parser(bedpetovcf)
  
      vcftobedpe = subparsers.add_parser('vcftobedpe', help=svtools.vcftobedpe.description())
      svtools.vcftobedpe.add_arguments_to_parser(vcftobedpe)
  
      vcfsort = subparsers.add_parser('vcfsort', help=svtools.vcfsort.description())
      svtools.vcfsort.add_arguments_to_parser(vcfsort)
  
      bedpesort = subparsers.add_parser('bedpesort', help=svtools.bedpesort.description())
      svtools.bedpesort.add_arguments_to_parser(bedpesort)
      
      return parser
  
  if __name__ == '__main__':
      parser = svtools_cli_parser()
      args = parser.parse_args()
      sys.exit(args.entry_point(args))
  
  
  
subject: add in newest batch of tools