code: def bedpe(args):
      
      from jcvi.assembly.coverage import bed_to_bedpe
  
      p = OptionParser(bedpe.__doc__)
      p.add_option("--span", default=False, action="store_true",
                   help="Write span bed file [default: %default]")
      p.add_option("--strand", default=False, action="store_true",
              help="Write the strand columns [default: %default]")
      p.add_option("--mates", help="Check the library stats from .mates file")
      opts, args = p.parse_args(args)
  
      if len(args) != 1:
          sys.exit(not p.print_help())
  
      bedfile, = args
      pf = bedfile.rsplit(".", 1)[0]
      bedpefile = pf + ".bedpe"
      bedspanfile = pf + ".spans.bed" if opts.span else None
      bed_to_bedpe(bedfile, bedpefile, \
                   pairsbedfile=bedspanfile, matesfile=opts.mates, \
                   strand=opts.strand)
      return bedpefile, bedspanfile
docs: %prog bedpe bedfile
  
      Convert to bedpe format. Use --span to write another bed file that contain
      the span of the read pairs.