demultiplex.py 文件源码

def align_one(ssw, qProfile, rNum, nRLen, nOpen, nExt, nFlag, nMaskLen):
    """
    align one pair of sequences
    @param  qProfile   query profile
    @param  rNum   number array for reference
    @param  nRLen   length of reference sequence
    @param  nFlag   alignment flag
    @param  nMaskLen   mask length
    """
    res = ssw.ssw_align(qProfile, rNum, ct.c_int32(nRLen), nOpen, nExt, nFlag, 0, 0, nMaskLen)

    nScore = res.contents.nScore
    nScore2 = res.contents.nScore2
    nRefBeg = res.contents.nRefBeg
    nRefEnd = res.contents.nRefEnd
    nQryBeg = res.contents.nQryBeg
    nQryEnd = res.contents.nQryEnd
    nRefEnd2 = res.contents.nRefEnd2
    lCigar = [res.contents.sCigar[idx] for idx in range(res.contents.nCigarLen)]
    nCigarLen = res.contents.nCigarLen
    ssw.align_destroy(res)

    return (nScore, nScore2, nRefBeg, nRefEnd, nQryBeg, nQryEnd, nRefEnd2, nCigarLen, lCigar)