docs: def run_plink(in_prefix, out_prefix, extract_filename):
      """Runs Plink with the geno option.
  
      :param in_prefix: the input prefix.
      :param out_prefix: the output prefix.
      :param extract_filename: the name of the file containing markers to
                               extract.
  
      :type in_prefix: str
      :type out_prefix: str
      :param extract_filename: str
  
      """
      # The plink command
      plink_command = [
          "plink",
          "--noweb",
          "--bfile", in_prefix,
          "--extract", extract_filename,
          "--freq",
          "--out", out_prefix,
      ]
      output = None
      try:
          output = subprocess.check_output(plink_command,
                                           stderr=subprocess.STDOUT, shell=False)
      except subprocess.CalledProcessError as exc:
          msg = "plink: couldn't run plink\n{}".format(exc.output)
          raise ProgramError(msg)