INNER CODE UNIT · Python

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nloyfer/wgbs_tools · src/python/bam2pat.py:37

    start = max(1, start - by)
    end += by
    return f'{chrom}:{start}-{end}'


def subprocess_wrap(cmd, debug):
    if debug:
        eprint(cmd)
        return
    subprocess.check_call(cmd, shell=True, executable='/bin/bash')


def set_regions(bam_path, gr, tmp_dir=None):
    # if user specified a region, just use it
    if gr.region_str:
        return [gr.region_str]

    # get all chromosomes from the reference genome:

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