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src/c/o/cogent-1.5.3/cogent/align/dp_calculation.py   cogent(Download)
        assert bprobs
        R = SiteClassTransitionMatrix(switch, bprobs)
        TM = R.nestTransitionMatricies(tms)
    assert min(TM.Matrix.flat) >=0, bin_data
    return EP.makePairHMM(TM)

src/p/y/pycogent-HEAD/cogent/align/dp_calculation.py   pycogent(Download)
        assert bprobs
        R = SiteClassTransitionMatrix(switch, bprobs)
        TM = R.nestTransitionMatricies(tms)
    assert min(TM.Matrix.flat) >=0, bin_data
    return EP.makePairHMM(TM)