code: def count(args):
      
      p = OptionParser(count.__doc__)
      opts, args = p.parse_args(args)
  
      if len(args) != 2:
          sys.exit(not p.print_help())
  
      coveragefile, fastafile = args
  
      countsfile = coveragefile.split(".")[0] + ".bin"
      if op.exists(countsfile):
          logging.error("`{0}` file exists. Remove before proceed."\
                  .format(countsfile))
          return
  
      fastasize, sizes, offsets = get_offsets(fastafile)
      logging.debug("Initialize array of uint8 with size {0}".format(fastasize))
      ar = np.zeros(fastasize, dtype=np.uint8)
  
      update_array(ar, coveragefile, sizes, offsets)
  
      ar.tofile(countsfile)
      logging.debug("Array written to `{0}`".format(countsfile))
docs: %prog count t.coveragePerBase fastafile
  
      Serialize the genomeCoverage results. The coordinate system of the count array
      will be based on the fastafile.