Remove minimum denominator for weight calculations

tskit-dev · Dec 18, 2023 · 017edd2 · 017edd2
1 parent 3c6a546
commit 017edd2
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Showing 2 changed files with 3 additions and 7 deletions.
diff --git a/python/tests/beagle.py b/python/tests/beagle.py
@@ -80,8 +80,6 @@ def get_weights(genotyped_pos, ungenotyped_pos, genetic_map=None):
     m = len(genotyped_pos)
     x = len(ungenotyped_pos)
     assert len(np.union1d(genotyped_pos, ungenotyped_pos)) == m + x
-    # Set min genetic distance.
-    MIN_CM_DIST = 0.005
     if genetic_map is None:
         genotyped_cm = convert_to_genetic_map_position(genotyped_pos)
         ungenotyped_cm = convert_to_genetic_map_position(ungenotyped_pos)
@@ -105,7 +103,8 @@ def get_weights(genotyped_pos, ungenotyped_pos, genetic_map=None):
             # Ungenotyped marker is between genotyped markers k and k + 1.
             k = np.max(np.where(ungenotyped_pos[i] > genotyped_pos)[0])  # Inefficient
             cm_mP1_x = genotyped_cm[k + 1] - ungenotyped_cm[i]
-            cm_mP1_m = np.max([genotyped_cm[k + 1] - genotyped_cm[k], MIN_CM_DIST])
+            cm_mP1_m = genotyped_cm[k + 1] - genotyped_cm[k]
+            assert cm_mP1_m > 0, "Division by zero in weight calculation."
             weights[i] = cm_mP1_x / cm_mP1_m
         marker_interval_start[i] = k
     assert 0 <= np.min(weights)

diff --git a/python/tests/beagle_numba.py b/python/tests/beagle_numba.py
@@ -46,7 +46,6 @@ def get_weights(genotyped_pos, ungenotyped_pos, genotyped_cm, ungenotyped_cm):
     :return: Weights and marker interval start indices.
     :rtype: tuple(numpy.ndarray, numpy.ndarray)
     """
-    _MIN_CM = 0.005
     m = len(genotyped_pos)
     x = len(ungenotyped_pos)
     # Calculate weights for ungenotyped markers.
@@ -67,9 +66,7 @@ def get_weights(genotyped_pos, ungenotyped_pos, genotyped_cm, ungenotyped_cm):
         else:
             # Between two genotyped markers.
             cm_mP1_x = genotyped_cm[idx_m + 1] - ungenotyped_cm[idx_x]
-            cm_mP1_m = max(
-                genotyped_cm[idx_m + 1] - genotyped_cm[idx_m], _MIN_CM
-            )  # Set min.
+            cm_mP1_m = genotyped_cm[idx_m + 1] - genotyped_cm[idx_m]
             weights[idx_x] = cm_mP1_x / cm_mP1_m
         marker_interval_start[idx_x] = idx_m
     return (weights, marker_interval_start)