Пример #1
0
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
Пример #2
0
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)