utils.py 文件源码

def get_full_alignment_base_quality_scores(read):
    """
    Returns base quality scores for the full read alignment, inserting zeroes for deletions and removing
    inserted and soft-clipped bases. Therefore, only returns quality for truly aligned sequenced bases.

    Args:
        read (pysam.AlignedSegment): read to get quality scores for

    Returns:
        np.array: numpy array of quality scores

    """

    quality_scores = np.fromstring(read.qual, dtype=np.byte) - tk_constants.ILLUMINA_QUAL_OFFSET

    start_pos = 0

    for operation,length in read.cigar:
        operation = cr_constants.cigar_numeric_to_category_map[operation]

        if operation == 'D':
            quality_scores = np.insert(quality_scores, start_pos, [0] * length)
        elif operation == 'I' or operation == 'S':
            quality_scores = np.delete(quality_scores, np.s_[start_pos:start_pos + length])

        if not operation == 'I' and not operation == 'S':
            start_pos += length

    return start_pos, quality_scores