INNER CODE UNIT · Python

add_args

nloyfer/wgbs_tools · src/python/add_cpg_counts.py:186

def add_args(parser):
    parser.add_argument('bam', nargs='+')
    add_GR_args(parser, bed_file=True)
    parser.add_argument('--out_dir', '-o', default='.')
    parser.add_argument('--min_cpg', type=int, default=1,
                help='Reads covering less than MIN_CPG sites are removed [1]')
    parser.add_argument('--debug', '-d', action='store_true')
    parser.add_argument('--force', '-f', action='store_true', help='overwrite existing files if exists')
    parser.add_argument('--verbose', '-v', action='store_true')
    add_samtools_view_flags(parser)
    parser.add_argument('--clip', type=int, default=0,
                        help='Clip for each read the first and last CLIP characters [0]')
    add_multi_thread_args(parser)

    return parser


def main():

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