code: def run_bafRegress(filenames, out_prefix, extract_filename, freq_filename,
                     options):
      
      # The command
      command = [
          "bafRegress.py",
          "estimate",
          "--freqfile", freq_filename,
          "--freqcol", "2,5",
          "--extract", extract_filename,
          "--colsample", options.colsample,
          "--colmarker", options.colmarker,
          "--colbaf", options.colbaf,
          "--colab1", options.colab1,
          "--colab2", options.colab2,
      ]
      command.extend(filenames)
  
      output = None
      try:
          output = subprocess.check_output(command, stderr=subprocess.STDOUT,
                                           shell=False)
      except subprocess.CalledProcessError as exc:
          raise ProgramError("bafRegress.py: couldn't run "
                             "bafRegress.py\n{}".format(exc.output))
  
      # Saving the output
      try:
          with open(out_prefix + ".bafRegress", "w") as o_file:
              o_file.write(output)
      except IOError:
          raise ProgramError("{}: cannot write file".format(
              out_prefix + ".bafRegress",
          ))
docs: Runs the bafRegress function.
  
      :param filenames: the set of all sample files.
      :param out_prefix: the output prefix.
      :param extract_filename: the name of the markers to extract.
      :param freq_filename: the name of the file containing the frequency.
      :param options: the other options.
  
      :type filenames: set
      :type out_prefix: str
      :type extract_filename: str
      :type freq_filename: str
      :type options: argparse.Namespace