Take out compute_emission_probability from njit functions

Author: szhan

python/tests/beagle_numba.py

@@ -377,9 +377,9 @@ def compute_forward_matrix(
             # Get allele at genotyped position i on reference haplotype j.
             ref_a = ref_h[i, j]
             # Get emission probability.
-            em_prob = compute_emission_probability(
-                mismatch_probs[i], query_a == ref_a, num_alleles=num_alleles
-            )
+            em_prob = mismatch_probs[i]
+            if query_a == ref_a:
+                em_prob = 1.0 - (num_alleles - 1) * mismatch_probs[i]
             fwd_mat[i, j] = em_prob
             if i > 0:
                 fwd_mat[i, j] *= scale * fwd_mat[i - 1, j] + shift
@@ -421,11 +421,9 @@ def compute_backward_matrix(
         query_a = query_h[iP1]
         for j in range(h):
             ref_a = ref_h[iP1, j]
-            em_prob = compute_emission_probability(
-                mismatch_probs[iP1],
-                query_a == ref_a,
-                num_alleles=num_alleles,
-            )
+            em_prob = mismatch_probs[iP1]
+            if query_a == ref_a:
+                em_prob = 1.0 - (num_alleles - 1) * mismatch_probs[iP1]
             bwd_mat[iP1, j] *= em_prob
         site_sum = np.sum(bwd_mat[iP1, :])
         scale = (1 - trans_probs[iP1]) / site_sum