Note that the root and input files need seperate reader options.
@@ -46,6 +46,7 @@ def add_arguments_extended(parser: KGTKArgumentParser, parsed_shared_args: Names
KgtkReader.add_debug_arguments(parser, expert=_expert)
KgtkReaderOptions.add_arguments(parser, mode_options=True, expert=_expert)
KgtkReaderOptions.add_arguments(parser, mode_options=True, who="input", expert=_expert, defaults=False)
+ KgtkReaderOptions.add_arguments(parser, mode_options=True, who="root", expert=_expert, defaults=False)
KgtkValueOptions.add_arguments(parser, expert=_expert)
def run(input_file: KGTKFiles,
@@ -107,6 +108,7 @@ def run(input_file: KGTKFiles,
error_file: typing.TextIO = sys.stdout if errors_to_stdout else sys.stderr
# Build the option structures.
+ # TODO: build seperate reader options for input and root.
reader_options: KgtkReaderOptions = KgtkReaderOptions.from_dict(kwargs)
value_options: KgtkValueOptions = KgtkValueOptions.from_dict(kwargs)
