def add_ice_partial_split_arguments(parser): """Add arguments for ice_partial split.""" parser = add_cluster_root_dir_as_positional_argument(parser) parser = add_nfl_fa_argument(parser, positional=True) helpstr = "Split non-full-length reads into N chunks, N < 100." parser.add_argument("N", help=helpstr, type=int)
def add_ice_polish_arguments(parser): """Set up argument parser.""" parser = add_cluster_root_dir_as_positional_argument(parser) parser = add_nfl_fa_argument(parser, positional=True) parser = add_fofn_arguments(parser, ccs_fofn=True, bas_fofn=True, fasta_fofn=True) parser = add_ice_post_quiver_hq_lq_arguments(parser) parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True, sge_env_name=True, sge_queue=True) return parser