diff --git a/python/tests/beagle.py b/python/tests/beagle.py index dca93e5801..feef12e08c 100644 --- a/python/tests/beagle.py +++ b/python/tests/beagle.py @@ -107,7 +107,7 @@ def get_mismatch_prob(pos, miscall_rate): Set mismatch probabilities at genotyped markers. In BEAGLE, the mismatch probability is dominated by the allelic miscall rate. - By default, it is set to 0.0001. Also, it is capped at 0.5. + By default, it is set to 0.0001 and capped at 0.50. :param numpy.ndarray pos: Site positions. :param float miscall_rate: Allelic miscall rate. @@ -115,7 +115,8 @@ def get_mismatch_prob(pos, miscall_rate): :rtype: numpy.ndarray """ assert isinstance(miscall_rate, float) - assert 0 <= miscall_rate <= 0.5 + if miscall_rate >= 0.5: + miscall_rate = 0.5 mu = np.zeros(len(pos), dtype=np.float64) + miscall_rate return mu @@ -239,6 +240,7 @@ def compute_backward_probability_matrix(ref_h, query_h, rho, mu): sum_site = np.sum(bm[i, :]) scale = (1 - rho[i + 1]) / sum_site shift = rho[i + 1] / h + print(str(sum_site) + " " + str(scale) + " " + str(shift)) for j in np.arange(h): bm[i, j] = scale * bm[i, j] + shift return bm