Fix memory bug.

Initialise total_weights to 0 and avoid an extra loop through arrays.

c/tskit/trees.c

@@ -2931,7 +2931,6 @@ genetic_relatedness_weighted_summary_func(size_t state_dim, const double *state,
     double meanx, ni, nj;
 
     meanx = state[state_dim - 1] / args.total_weights[state_dim - 1];
-    ;
     for (k = 0; k < result_dim; k++) {
         i = args.index_tuples[2 * k];
         j = args.index_tuples[2 * k + 1];
@@ -2954,33 +2953,28 @@ tsk_treeseq_genetic_relatedness_weighted(const tsk_treeseq_t *self,
     indexed_weight_stat_params_t args;
     const double *row;
     double *new_row;
-    double *total_weights = malloc((num_weights + 1) * sizeof(*total_weights));
+    double *total_weights = calloc((num_weights + 1), sizeof(*total_weights));
     double *new_weights = malloc((num_weights + 1) * num_samples * sizeof(*new_weights));
 
     if (total_weights == NULL || new_weights == NULL) {
         ret = TSK_ERR_NO_MEMORY;
         goto out;
     }
 
-    // add a column of ones to W
-    for (k = 0; k < num_samples; k++) {
-        row = GET_2D_ROW(weights, num_weights, k);
-        new_row = GET_2D_ROW(new_weights, num_weights + 1, k);
-        for (j = 0; j < num_weights; j++) {
-            new_row[j] = row[j];
+    // Add a column of ones to W
+    for (j = 0; j < num_samples; j++) {
+        row = GET_2D_ROW(weights, num_weights, j);
+        new_row = GET_2D_ROW(new_weights, num_weights + 1, j);
+        for (k = 0; k < num_weights; k++) {
+            new_row[k] = row[k];
+            total_weights[k] += row[k];
         }
         new_row[num_weights] = 1.0;
     }
+    total_weights[num_weights] = num_samples;
 
     /* TODO: sanity check indexes */
 
-    for (j = 0; j < num_samples; j++) {
-        row = GET_2D_ROW(new_weights, num_weights + 1, j);
-        for (k = 0; k < num_weights + 1; k++) {
-            total_weights[k] += row[k];
-        }
-    }
-
     args.total_weights = total_weights;
     args.index_tuples = index_tuples;
 

python/tests/test_lowlevel.py

@@ -1577,6 +1577,15 @@ def test_window_errors(self):
             with pytest.raises(_tskit.LibraryError):
                 f(windows=bad_window, **params)
 
+    def test_polarisation(self):
+        ts, f, params = self.get_example()
+        with pytest.raises(TypeError):
+            f(polarised="sdf", **params)
+        x1 = f(polarised=False, **params)
+        x2 = f(polarised=True, **params)
+        # Basic check just to run both code paths
+        assert x1.shape == x2.shape
+
     def test_windows_output(self):
         ts, f, params = self.get_example()
         del params["windows"]
@@ -1992,6 +2001,20 @@ def test_output_dims(self):
         out = method(weights[:, [0, 0, 0]], mode=mode, **params)
         assert out.shape == (1, N, 1)
 
+    def test_set_index_errors(self):
+        ts, method, params = self.get_example()
+        del params["indexes"]
+
+        def f(indexes):
+            method(indexes=indexes, **params)
+
+        for bad_array in ["wer", {}, [[[], []], [[], []]]]:
+            with pytest.raises(ValueError):
+                f(bad_array)
+        for bad_dim in [[[]], [[1], [1]]]:
+            with pytest.raises(ValueError):
+                f(bad_dim)
+
 
 class ThreeWaySampleStatsMixin(SampleSetMixin):
     """