diff --git a/c/tskit/trees.c b/c/tskit/trees.c
index 10cce4ab68..35fbb4f6e7 100644
--- a/c/tskit/trees.c
+++ b/c/tskit/trees.c
@@ -2564,9 +2564,8 @@ tsk_treeseq_two_site_general_stat(const tsk_treeseq_t *self, tsk_size_t state_di
     const double *sample_weights, tsk_size_t result_dim, general_stat_func_t *f,
     sample_count_stat_params_t *f_params, norm_func_t *norm_f,
     const double *TSK_UNUSED(left_window), const double *TSK_UNUSED(right_window),
-    tsk_flags_t options, tsk_size_t num_result, double *result)
+    tsk_flags_t options, tsk_size_t *result_size, double **result)
 {
-    // TODO: implement windows!
     int ret = 0;
     const tsk_size_t num_sites = self->tables->sites.num_rows;
     const tsk_size_t num_samples = self->num_samples;
@@ -2612,9 +2611,9 @@ tsk_treeseq_two_site_general_stat(const tsk_treeseq_t *self, tsk_size_t state_di
     }
 
     // Number of pairs w/ replacement (sites)
-    num_result = (num_sites * (1 + num_sites)) >> (tsk_size_t) 1;
+    *result_size = (num_sites * (1 + num_sites)) >> (tsk_size_t) 1;
+    *result = tsk_calloc(*result_size * result_dim, sizeof(*result));
 
-    result = tsk_calloc(num_result * result_dim, sizeof(*result));
     tsk_bit_array_t *sample_bits
         = tsk_calloc(num_sample_chunks * state_dim, sizeof(*sample_bits));
 
@@ -2631,19 +2630,19 @@ tsk_treeseq_two_site_general_stat(const tsk_treeseq_t *self, tsk_size_t state_di
         polarised = true;
     }
 
-    tsk_size_t inner = 0, site_a_offset = 0, site_b_offset = 0, result_offset = 0;
+    // TODO: implement windows!
+    tsk_size_t inner = 0;
+    tsk_size_t result_offset = 0;
     for (tsk_size_t site_a = 0; site_a < num_sites; site_a++) {
-        site_a_offset = site_offsets[site_a];
         for (tsk_size_t site_b = inner; site_b < num_sites; site_b++) {
-            site_b_offset = site_offsets[site_b];
-            ret = compute_general_two_site_stat_result(site_a, site_a_offset, site_b,
-                site_b_offset, num_sample_chunks, num_alleles, allele_samples, state_dim,
-                sample_bits, result_dim, f, f_params, norm_f, polarised,
-                &(result[result_offset]));
+            ret = compute_general_two_site_stat_result(site_a, site_offsets[site_a],
+                site_b, site_offsets[site_b], num_sample_chunks, num_alleles,
+                allele_samples, state_dim, sample_bits, result_dim, f, f_params, norm_f,
+                polarised, &((*result)[result_offset]));
             if (ret != 0) {
                 goto out;
             }
-            result_offset++;
+            result_offset += state_dim;
         }
         inner++;
     }
@@ -2671,7 +2670,7 @@ tsk_treeseq_two_locus_general_stat(const tsk_treeseq_t *self, tsk_size_t num_sam
     tsk_size_t result_dim, const tsk_id_t *set_indexes, general_stat_func_t *f,
     norm_func_t *norm_f, tsk_size_t num_left_windows, const double *left_windows,
     tsk_size_t num_right_windows, const double *right_windows, tsk_flags_t options,
-    tsk_size_t num_result, double *result)
+    tsk_size_t *result_size, double **result)
 {
     int ret = 0;
     bool stat_site = !!(options & TSK_STAT_SITE);
@@ -2749,7 +2748,8 @@ tsk_treeseq_two_locus_general_stat(const tsk_treeseq_t *self, tsk_size_t num_sam
     if (stat_site) {
         // TODO: assert 1 window left/right
         ret = tsk_treeseq_two_site_general_stat(self, state_dim, weights, result_dim, f,
-            &f_params, norm_f, left_windows, right_windows, options, num_result, result);
+            &f_params, norm_f, left_windows, right_windows, options, result_size,
+            result);
     } else {
         // TODO: branch statistics
         ret = TSK_ERR_GENERIC;
@@ -3585,7 +3585,7 @@ tsk_treeseq_D(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const tsk_size_t *sample_set_sizes, const tsk_id_t *sample_sets,
     tsk_size_t num_left_windows, const double *left_windows,
     tsk_size_t num_right_windows, const double *right_windows, tsk_flags_t options,
-    tsk_size_t result_size, double *result)
+    tsk_size_t *result_size, double **result)
 {
     options |= TSK_STAT_POLARISED; // TODO: allow user to pick?
     return tsk_treeseq_two_locus_general_stat(self, num_sample_sets, sample_set_sizes,
@@ -3622,7 +3622,7 @@ tsk_treeseq_D2(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const tsk_size_t *sample_set_sizes, const tsk_id_t *sample_sets,
     tsk_size_t num_left_windows, const double *left_windows,
     tsk_size_t num_right_windows, const double *right_windows, tsk_flags_t options,
-    tsk_size_t result_size, double *result)
+    tsk_size_t *result_size, double **result)
 {
     return tsk_treeseq_two_locus_general_stat(self, num_sample_sets, sample_set_sizes,
         sample_sets, num_sample_sets, NULL, D2_summary_func, norm_total_weighted,
@@ -3664,7 +3664,7 @@ tsk_treeseq_r2(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const tsk_size_t *sample_set_sizes, const tsk_id_t *sample_sets,
     tsk_size_t num_left_windows, const double *left_windows,
     tsk_size_t num_right_windows, const double *right_windows, tsk_flags_t options,
-    tsk_size_t result_size, double *result)
+    tsk_size_t *result_size, double **result)
 {
     return tsk_treeseq_two_locus_general_stat(self, num_sample_sets, sample_set_sizes,
         sample_sets, num_sample_sets, NULL, r2_summary_func, norm_hap_weighted,
@@ -3704,7 +3704,7 @@ tsk_treeseq_D_prime(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const tsk_size_t *sample_set_sizes, const tsk_id_t *sample_sets,
     tsk_size_t num_left_windows, const double *left_windows,
     tsk_size_t num_right_windows, const double *right_windows, tsk_flags_t options,
-    tsk_size_t result_size, double *result)
+    tsk_size_t *result_size, double **result)
 {
     options |= TSK_STAT_POLARISED; // TODO: allow user to pick?
     return tsk_treeseq_two_locus_general_stat(self, num_sample_sets, sample_set_sizes,
@@ -3747,7 +3747,7 @@ tsk_treeseq_r(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const tsk_size_t *sample_set_sizes, const tsk_id_t *sample_sets,
     tsk_size_t num_left_windows, const double *left_windows,
     tsk_size_t num_right_windows, const double *right_windows, tsk_flags_t options,
-    tsk_size_t result_size, double *result)
+    tsk_size_t *result_size, double **result)
 {
     options |= TSK_STAT_POLARISED; // TODO: allow user to pick?
     return tsk_treeseq_two_locus_general_stat(self, num_sample_sets, sample_set_sizes,
@@ -3785,7 +3785,7 @@ tsk_treeseq_Dz(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const tsk_size_t *sample_set_sizes, const tsk_id_t *sample_sets,
     tsk_size_t num_left_windows, const double *left_windows,
     tsk_size_t num_right_windows, const double *right_windows, tsk_flags_t options,
-    tsk_size_t result_size, double *result)
+    tsk_size_t *result_size, double **result)
 {
     return tsk_treeseq_two_locus_general_stat(self, num_sample_sets, sample_set_sizes,
         sample_sets, num_sample_sets, NULL, Dz_summary_func, norm_total_weighted,
@@ -3819,7 +3819,7 @@ tsk_treeseq_pi2(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const tsk_size_t *sample_set_sizes, const tsk_id_t *sample_sets,
     tsk_size_t num_left_windows, const double *left_windows,
     tsk_size_t num_right_windows, const double *right_windows, tsk_flags_t options,
-    tsk_size_t result_size, double *result)
+    tsk_size_t *result_size, double **result)
 {
     return tsk_treeseq_two_locus_general_stat(self, num_sample_sets, sample_set_sizes,
         sample_sets, num_sample_sets, NULL, pi2_summary_func, norm_total_weighted,
diff --git a/c/tskit/trees.h b/c/tskit/trees.h
index a031166cd0..e3129e40d4 100644
--- a/c/tskit/trees.h
+++ b/c/tskit/trees.h
@@ -1011,37 +1011,37 @@ int tsk_treeseq_D(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const tsk_size_t *sample_set_sizes, const tsk_id_t *sample_sets,
     tsk_size_t num_left_windows, const double *left_windows,
     tsk_size_t num_right_windows, const double *right_windows, tsk_flags_t options,
-    tsk_size_t result_size, double *result);
+    tsk_size_t *result_size, double **result);
 int tsk_treeseq_D2(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const tsk_size_t *sample_set_sizes, const tsk_id_t *sample_sets,
     tsk_size_t num_left_windows, const double *left_windows,
     tsk_size_t num_right_windows, const double *right_windows, tsk_flags_t options,
-    tsk_size_t result_size, double *result);
+    tsk_size_t *result_size, double **result);
 int tsk_treeseq_r2(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const tsk_size_t *sample_set_sizes, const tsk_id_t *sample_sets,
     tsk_size_t num_left_windows, const double *left_windows,
     tsk_size_t num_right_windows, const double *right_windows, tsk_flags_t options,
-    tsk_size_t result_size, double *result);
+    tsk_size_t *result_size, double **result);
 int tsk_treeseq_D_prime(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const tsk_size_t *sample_set_sizes, const tsk_id_t *sample_sets,
     tsk_size_t num_left_windows, const double *left_windows,
     tsk_size_t num_right_windows, const double *right_windows, tsk_flags_t options,
-    tsk_size_t result_size, double *result);
+    tsk_size_t *result_size, double **result);
 int tsk_treeseq_r(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const tsk_size_t *sample_set_sizes, const tsk_id_t *sample_sets,
     tsk_size_t num_left_windows, const double *left_windows,
     tsk_size_t num_right_windows, const double *right_windows, tsk_flags_t options,
-    tsk_size_t result_size, double *result);
+    tsk_size_t *result_size, double **result);
 int tsk_treeseq_Dz(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const tsk_size_t *sample_set_sizes, const tsk_id_t *sample_sets,
     tsk_size_t num_left_windows, const double *left_windows,
     tsk_size_t num_right_windows, const double *right_windows, tsk_flags_t options,
-    tsk_size_t result_size, double *result);
+    tsk_size_t *result_size, double **result);
 int tsk_treeseq_pi2(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const tsk_size_t *sample_set_sizes, const tsk_id_t *sample_sets,
     tsk_size_t num_left_windows, const double *left_windows,
     tsk_size_t num_right_windows, const double *right_windows, tsk_flags_t options,
-    tsk_size_t result_size, double *result);
+    tsk_size_t *result_size, double **result);
 
 /* Three way sample set stats */
 int tsk_treeseq_Y3(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,