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_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 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_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 _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_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_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_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_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