def main(args: List[str] = None) -> None:
"""
Main entrypoint for the CLI.
"""
Logger.setup_root_logger()
logger = Logger.get_logger("main")
funcs = [
add_oxog_filters,
create_dtoxog_maf,
create_oxog_intervals,
dtoxog_maf_to_vcf,
extract_oxoq_from_sqlite,
filter_contigs,
filter_nonstandard_variants,
filter_somatic_score,
format_gdc_vcf,
format_pindel_vcf,
format_sanger_pindel_vcf,
position_filter_dkfz,
]
defopt.run(
funcs,
argv=args if args is not None else sys.argv[1:],
version=True,
argparse_kwargs={'prog': 'gdc_filtration_tools'},
)
logger.info("Finished!")
def captured_output():
"""Captures stderr and stdout and returns them"""
new_out, new_err = StringIO(), StringIO()
old_out, old_err = sys.stdout, sys.stderr
try:
sys.stdout, sys.stderr = new_out, new_err
Logger.setup_root_logger()
yield sys.stdout, sys.stderr
finally:
sys.stdout, sys.stderr = old_out, old_err