INNER CODE UNIT · Python

validate_bam

nloyfer/wgbs_tools · src/python/bam2pat.py:212

def validate_bam(bam):

    # validate bam path:
    eprint('[wt bam2pat] bam:', bam)
    if not (op.isfile(bam) and bam.endswith(('.bam', '.cram'))):
        eprint(f'[wt bam2pat] Invalid bam: {bam}')
        return False
    return True


def is_bam_sorted(bam):

    # check if bam is sorted by coordinate:
    peek_cmd = f'samtools view -H {bam}| head -1'
    hd_line = subprocess.check_output(peek_cmd, shell=True).decode()
    if hd_line.startswith('@HD') and 'coordinate' not in hd_line:
        eprint(f'[wt bam2pat] WARNING: based on the @HD, bam file is not sorted: {bam}')
        return False

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