code: def posmap(args):
      p = OptionParser(posmap.__doc__)
      opts, args = p.parse_args(args)
      if len(args) != 3:
          sys.exit(p.print_help())
      frgscffile, fastafile, scf = args
      cmd = "faOneRecord {0} {1}".format(fastafile, scf)
      scffastafile = scf + ".fasta"
      if not op.exists(scffastafile):
          sh(cmd, outfile=scffastafile)
      sizesfile = scffastafile + ".sizes"
      sizes = Sizes(scffastafile).mapping
      scfsize = sizes[scf]
      logging.debug("`{0}` has length of {1}.".format(scf, scfsize))
      gapsbedfile = scf + ".gaps.bed"
      if not op.exists(gapsbedfile):
          args = [scffastafile, "--bed", "--mingap=100"]
          gaps(args)
      posmapfile = scf + ".posmap"
      if not op.exists(posmapfile):
          args = [frgscffile, scf]
          query(args)
      bedfile = scf + ".bed"
      if not op.exists(bedfile):
          args = [posmapfile]
          bed(args)
      bedpefile = scf + ".bedpe"
      pairsbedfile = scf + ".pairs.bed"
      if not (op.exists(bedpefile) and op.exists(pairsbedfile)):
          bed_to_bedpe(bedfile, bedpefile, pairsbedfile=pairsbedfile, ca=True)
      Coverage(bedfile, sizesfile)
      Coverage(pairsbedfile, sizesfile)