util.py 文件源码

def get_ref_len_from_bam(bam_path, target_contig):
    """
    Fetch the length of a given reference sequence from a :py:class:`pysam.AlignmentFile`.

    Parameters
    ----------
    bam_path : str
        Path to the BAM alignment

    target_contig : str
        The name of the contig for which to recover haplotypes.

    Returns
    -------
    end_pos : int
        The 1-indexed genomic position at which to stop considering variants.
    """
    bam = pysam.AlignmentFile(bam_path)
    end = bam.lengths[bam.get_tid(target_contig)]
    bam.close()

    return end