Minor refactor and cleanup

python/tests/beagle.py

@@ -226,17 +226,15 @@ def compute_backward_probability_matrix(ref_h, query_h, rho, mu):
     assert m == len(rho)
     assert m == len(mu)
     assert 0 <= np.min(rho) and np.max(rho) <= 1
-    # BEAGLE caps mismatch probabilities at 0.5.
     assert 0 <= np.min(mu) and np.max(mu) <= 0.5
     bm = np.zeros((m, h), dtype=np.float64)
-    # Initialise the last column
-    bm[-1, :] = 1.0 / h
+    bm[-1, :] = 1.0 / h  # Initialise the last column
     for i in np.arange(m - 2, -1, -1):
         query_a = query_h[i + 1]
         for j in np.arange(h):
             ref_a = ref_h[i + 1, j]
             em_prob = mu[i + 1] if ref_a != query_a else 1.0 - mu[i + 1]
-            # Note that BEAGLE only keeps the values at one site at a time.
+            # Note that BEAGLE keeps the values at one site at a time.
             bm[i, j] = bm[i + 1, j] * em_prob
         sum_site = np.sum(bm[i, :])
         scale = (1 - rho[i + 1]) / sum_site