Rename get_mutation_rates to get_mismatch_probs

python/tests/beagle_numba.py

@@ -150,14 +150,16 @@ def convert_to_genetic_map_positions(pos, genetic_map=None):
     return est_cm
 
 
-def get_mutation_rates(pos, error_rate):
+def get_mismatch_probs(pos, error_rate):
     """
-    Set mutation rates at genotyped positions.
+    Compute mismatch probabilities at genotyped positions.
 
-    Mutation rates should be dominated by the allele error rate.
+    Mutation rates should be dominated by the rate of allele error,
+    which should be the main source of mismatch between query and
+    reference haplotypes.
 
-    In BEAGLE 4.1/5.4, the default value is set to 0.0001 and capped at 0.50.
-    In IMPUTE5, the default value is also set to 0.0001.
+    In BEAGLE 4.1/5.4, the default value is set to 1e-4 and capped at 0.50.
+    In IMPUTE5, the default value is also set to 1e-4.
 
     When using `_tskit.LsHmm`, this is `mu`.
 
@@ -169,8 +171,8 @@ def get_mutation_rates(pos, error_rate):
     MAX_ERROR_RATE = 0.5
     if error_rate >= MAX_ERROR_RATE:
         error_rate = MAX_ERROR_RATE
-    mu = np.zeros(len(pos), dtype=np.float64) + error_rate
-    return mu
+    mismatch_probs = np.zeros(len(pos), dtype=np.float64) + error_rate
+    return mismatch_probs
 
 
 def get_recombination_rates(cm, h, ne):
@@ -472,7 +474,7 @@ def run_interpolation_beagle(
     # Get rates at genotyped markers.
     h = ref_h.shape[1]
     rho = get_recombination_rates(typed_cm, h=h, ne=ne)
-    mu = get_mutation_rates(typed_pos, error_rate=error_rate)
+    mu = get_mismatch_probs(typed_pos, error_rate=error_rate)
     # Compute matrices at genotyped markers.
     fm = compute_forward_matrix(ref_h_typed, query_h_typed, rho, mu)
     bm = compute_backward_matrix(ref_h_typed, query_h_typed, rho, mu)