code: def checkArgs(args):
      
      # Check if we have the binary files
      for prefix in [args.bfile, args.gold_bfile]:
          if prefix is None:
              msg = "no input file"
              raise ProgramError(msg)
          for fileName in [prefix + i for i in [".bed", ".bim", ".fam"]]:
              if not os.path.isfile(fileName):
                  msg = "{}: no such file".format(fileName)
                  raise ProgramError(msg)
  
      # Check for the same sample file
      if not os.path.isfile(args.same_samples):
          msg = "{}: no such file".format(args.same_samples)
          raise ProgramError(msg)
  
      # Check we have either a manifest or a allele file
      if (args.source_manifest is None) and (args.source_alleles is None):
          msg = ("need an allele file (either an Illumina manifest "
                 "[--source-manifest] or a file containing alleles for each "
                 "marker [--source-alleles]")
          raise ProgramError(msg)
      if ((args.source_manifest is not None) and
              (args.source_alleles is not None)):
          msg = ("use either --source-manifest or --source-alleles, not both")
          raise ProgramError(msg)
      # Check for the manifests
      if args.source_manifest is not None:
          if not os.path.isfile(args.source_manifest):
              msg = "{}: no such file".format(args.source_manifest)
              raise ProgramError(msg)
      if args.source_alleles is not None:
          if not os.path.isfile(args.source_alleles):
              msg = "{}: no such file".format(args.source_alleles)
              raise ProgramError(msg)
  
      return True
docs: Checks the arguments and options.
  
      :param args: a :py:class:`Namespace` object containing the options of the
                   program.
      :type args: :py:class:`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.