INNER CODE UNIT · Python

main

nloyfer/wgbs_tools · src/python/add_cpg_counts.py:203

def main():
    """
    Add to bam file an extra field, YI:Z:{nr_meth},{nr_unmeth},
    to count Cytosine retention at CpG context.
    """
    parser = argparse.ArgumentParser(description=main.__doc__)
    parser = add_args(parser)
    parser = add_cpg_args(parser)
    args = parser.parse_args()
    validate_local_exe(add_cpg_count_tool)
    if not check_samtools_version(minor=15, verbose=args.verbose):
        eprint('[wt add_cpg_counts] Error: add_cpg_counts only works with samtools version >=1.15.\n'
                '                    Please update samtools.\n'
                '                    Run wgbstools add_cpg_counts with --verbose for more information')
        return
    for bam in args.bam:
        if not validate_bam(bam):
            eprint(f'[wt add_cpg_counts] Skipping {bam}')

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