def _add_common_chunk_options(p): # Order matters! U.add_debug_option(p) add_max_nchunks_option(p) p = _add_chunk_output_dir_option(p) p = add_output_chunk_json_report_option(p) return p
def _add_run_random_fastq_options(p): U.add_debug_option(p) p.add_argument('--max-records', type=int, default=1000, help="Max number of Fasta record to write.") U.add_fastq_output(p) return p
def _add_run_random_fofn_options(p): U.add_debug_option(p) U.add_output_dir_option(p) p.add_argument('--nfofns', type=int, default=10, help="Number of mock/random Fofns to write.") U.add_fofn_output(p) return p
def _add_run_fasta_filter_options(p): U.add_debug_option(p) p.add_argument('--min-length', type=int, default=150, help='Min Length of Sequence to filter') U.add_fasta_input(p) U.add_fasta_output(p) return p
def get_parser(): desc = "Transform pbreport Report to HTML file." p = get_default_argparser(__version__, desc) U.add_debug_option(p) U.add_output_dir_option(p) _add_report_option(p) _add_output_file_option(p) _add_ccs_js_extras_option(p) p.set_defaults(func=_args_to_render_report) return p
def _add_base_options(p): return _add_manifest_json_option(U.add_debug_option(p))
def _f(p): U.add_debug_option(p) f = __gather_options(output_file_msg, input_file_msg, validate_file, chunk_key_func) return f(p)
def add_args_run_diagnstic(p): _add_required_preset_xml_option(p) TU.add_debug_option(p) TU.add_output_dir_option(p) _add_simple_mode_option(p) return p
def _add_run_dataset_report(p): U.add_debug_option(p) U.add_subread_input(p) U.add_report_output(p) return p