#!/usr/bin/env python

from mirror_seq import hmc_calling

if __name__=='__main__':
    import argparse
    import os

    parser = argparse.ArgumentParser(
        description='Mirror-seq hydroxymethylation calling from alignment files.'
    )
    parser.add_argument(
        '-b',
        dest='bam_filename',
        required=True,
        help='The BAM filename.'
    )
    parser.add_argument(
        '--nts-in-regions',
        dest='nts_in_regions',
        default=100000000,
        type=int,
        help='''Number of total nucleotides in an iter of regions.
        It is an rough number so it is possible to get more than the number. default is 100M.'''
    )
    parser.add_argument(
        '--bed',
        dest='create_bed_file',
        action='store_true',
        help='If set, create a gzipped bed file for genomer browser.'
    )
    parser.add_argument(
        '-o',
        dest='out_prefix',
        default=None,
        help='''The output preifx of all output files. With absolute path is recommended.
        If None (default), use the pathname of bam file without extension.'''
    )
    args = parser.parse_args()

    if args.out_prefix:
        out_prefix = args.out_prefix
    else:
        out_prefix = os.path.splitext(args.bam_filename)[0]

    main(
        args.bam_filename,
        out_prefix,
        args.create_bed_file,
        args.nts_in_regions,
    )
