Improve docs for get_mismatch_prob

python/tests/beagle_numba.py

@@ -122,21 +122,23 @@ def get_weights(genotyped_pos, ungenotyped_pos, genotyped_cm, ungenotyped_cm):
     return (weights, marker_interval_start)
 
 
-def get_mismatch_prob(pos, miscall_rate):
+def get_mismatch_prob(pos, error_rate):
     """
-    Set mismatch probabilities at genotyped markers.
+    Set mismatch probabilities at genotyped positions.
 
-    In BEAGLE, the mismatch probability is dominated by the allelic miscall rate.
-    By default, it is set to 0.0001 and capped at 0.50.
+    Mutation rates (per meiosis) should be dominated by the genotyping error rate.
+    Note that in BEAGLE 4.1, the default value is set to 0.0001 and capped at 0.50.
 
-    :param numpy.ndarray pos: Physical positions.
+    In terms of using `_tskit.LsHmm`, this mismatch probability is `mu`.
+
+    :param numpy.ndarray pos: Physical positions (bp).
     :param float miscall_rate: Allelic miscall rate.
     :return: Mismatch probabilities.
     :rtype: numpy.ndarray
     """
-    if miscall_rate >= 0.5:
-        miscall_rate = 0.5
-    mu = np.zeros(len(pos), dtype=np.float32) + miscall_rate
+    if error_rate >= 0.5:
+        error_rate = 0.5
+    mu = np.zeros(len(pos), dtype=np.float32) + error_rate
     return mu