docs: def compareBIMfiles(beforeFileName, afterFileName, outputFileName):
      """Compare two BIM files for differences.
  
      :param beforeFileName: the name of the file before modification.
      :param afterFileName: the name of the file after modification.
      :param outputFileName: the name of the output file (containing the
                             differences between the ``before`` and the ``after``
                             files.
  
      :type beforeFileName: str
      :type afterFileName: str
      :type outputFileName: str
  
      :returns: the number of differences between the two files.
  
      The ``bim`` files contain the list of markers in a given dataset. The
      ``before`` file should have more markers than the ``after`` file. The
      ``after`` file should be a subset of the markers in the ``before`` file.
  
      """
      # Creating the options
      options = Dummy()
      options.before = beforeFileName
      options.after = afterFileName
      options.out = outputFileName
  
      # Checking the options
      CompareBIM.checkArgs(options)
  
      # Reading the BIM files
      beforeBIM = CompareBIM.readBIM(options.before)
      afterBIM = CompareBIM.readBIM(options.after)
  
      # Finding the differences
      CompareBIM.compareSNPs(beforeBIM, afterBIM, options.out)
  
      return beforeBIM - afterBIM