Minor refactor

python/tests/beagle.py

@@ -107,15 +107,16 @@ 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.
     :return: Mismatch probabilities.
     :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