hints_db.py 文件源码

def bam_is_paired(bam_path, num_reads=20000, paired_cutoff=0.75):
    """
    Infers the paired-ness of a bam file.
    """
    sam = pysam.Samfile(bam_path)
    count = 0
    for rec in itertools.islice(sam, num_reads):
        if rec.is_paired:
            count += 1
    if tools.mathOps.format_ratio(count, num_reads) > 0.75:
        return True
    elif tools.mathOps.format_ratio(count, num_reads) < 1 - paired_cutoff:
        return False
    else:
        raise UserException("Unable to infer pairing from bamfile {}".format(bam_path))