INNER CODE UNIT · Python
add_cpg_args
nloyfer/wgbs_tools · src/python/add_cpg_counts.py:176
def add_cpg_args(parser):
parser.add_argument('--drop_singles', action='store_true',
help='For paired bam only - if mate is not exists drop single read')
parser.add_argument('--suffix', default='counts',
help='The output file suffix. The output file will be [in_file].[suffix].bam. By default the '
'suffix is "counts".')
parser.add_argument('--add_pat', action='store_true',
help='Indicates whether to add the methylation pattern of the read (pair).')
return parser
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')