docs: def checkArgs(args):
      """Checks the arguments and options.
  
      :param args: an object containing the options of the program.
  
      :type args: argparse.Namespace
  
      :returns: ``True`` if everything was OK.
  
      If there is a problem with an option, an exception is raised using the
      :py:class:`ProgramError` class, a message is printed to the
      :class:`sys.stderr` and the program exists with code 1.
  
      """
      # Check if we have the tped and the tfam files
      for fileName in [args.bfile + i for i in [".bed", ".bim", ".fam"]]:
          if not os.path.isfile(fileName):
              msg = "%(fileName)s: no such file" % locals()
              raise ProgramError(msg)
  
      # Check the plate bias file
      if not os.path.isfile(args.loop_assoc):
          msg = "%s: no such file" % args.loop_assoc
          raise ProgramError(msg)
  
      return True