removed min number sample sets requirement

petrelharp · petrelharp · commit 7f485420442c · 2025-09-11T17:58:23.000-07:00
diff --git a/c/tests/test_stats.c b/c/tests/test_stats.c
@@ -881,9 +881,6 @@ verify_two_way_stat_func_errors(
     ret = method(ts, 0, sample_set_sizes, samples, 1, set_indexes, 0, NULL,
         options | TSK_STAT_SITE, &result);
     CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_INSUFFICIENT_SAMPLE_SETS);
-    ret = method(ts, 1, sample_set_sizes, samples, 1, set_indexes, 0, NULL,
-        options | TSK_STAT_SITE, &result);
-    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_INSUFFICIENT_SAMPLE_SETS);
 
     ret = method(ts, 2, sample_set_sizes, samples, 0, set_indexes, 0, NULL,
         options | TSK_STAT_SITE, &result);
@@ -938,12 +935,6 @@ verify_three_way_stat_func_errors(tsk_treeseq_t *ts, general_sample_stat_method
     ret = method(ts, 0, sample_set_sizes, samples, 1, set_indexes, 0, NULL,
         TSK_STAT_SITE, &result);
     CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_INSUFFICIENT_SAMPLE_SETS);
-    ret = method(ts, 1, sample_set_sizes, samples, 1, set_indexes, 0, NULL,
-        TSK_STAT_SITE, &result);
-    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_INSUFFICIENT_SAMPLE_SETS);
-    ret = method(ts, 2, sample_set_sizes, samples, 1, set_indexes, 0, NULL,
-        TSK_STAT_SITE, &result);
-    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_INSUFFICIENT_SAMPLE_SETS);
 
     ret = method(ts, 3, sample_set_sizes, samples, 0, set_indexes, 0, NULL,
         TSK_STAT_SITE, &result);
@@ -972,15 +963,6 @@ verify_four_way_stat_func_errors(tsk_treeseq_t *ts, general_sample_stat_method *
     ret = method(ts, 0, sample_set_sizes, samples, 1, set_indexes, 0, NULL,
         TSK_STAT_SITE, &result);
     CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_INSUFFICIENT_SAMPLE_SETS);
-    ret = method(ts, 1, sample_set_sizes, samples, 1, set_indexes, 0, NULL,
-        TSK_STAT_SITE, &result);
-    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_INSUFFICIENT_SAMPLE_SETS);
-    ret = method(ts, 2, sample_set_sizes, samples, 1, set_indexes, 0, NULL,
-        TSK_STAT_SITE, &result);
-    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_INSUFFICIENT_SAMPLE_SETS);
-    ret = method(ts, 3, sample_set_sizes, samples, 1, set_indexes, 0, NULL,
-        TSK_STAT_SITE, &result);
-    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_INSUFFICIENT_SAMPLE_SETS);
 
     ret = method(ts, 4, sample_set_sizes, samples, 0, set_indexes, 0, NULL,
         TSK_STAT_SITE, &result);
diff --git a/c/tskit/trees.c b/c/tskit/trees.c
@@ -4510,12 +4510,12 @@ tsk_treeseq_pi2_unbiased(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
  ***********************************/
 
 static int
-check_sample_stat_inputs(tsk_size_t num_sample_sets, tsk_size_t min_num_sample_sets,
-    tsk_size_t tuple_size, tsk_size_t num_index_tuples, const tsk_id_t *index_tuples)
+check_sample_stat_inputs(tsk_size_t num_sample_sets, tsk_size_t tuple_size,
+    tsk_size_t num_index_tuples, const tsk_id_t *index_tuples)
 {
     int ret = 0;
 
-    if (num_sample_sets < min_num_sample_sets) {
+    if (num_sample_sets < 1) {
         ret = tsk_trace_error(TSK_ERR_INSUFFICIENT_SAMPLE_SETS);
         goto out;
     }
@@ -4560,7 +4560,7 @@ tsk_treeseq_divergence(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const double *windows, tsk_flags_t options, double *result)
 {
     int ret = 0;
-    ret = check_sample_stat_inputs(num_sample_sets, 2, 2, num_index_tuples, index_tuples);
+    ret = check_sample_stat_inputs(num_sample_sets, 2, num_index_tuples, index_tuples);
     if (ret != 0) {
         goto out;
     }
@@ -4625,7 +4625,7 @@ tsk_treeseq_genetic_relatedness(const tsk_treeseq_t *self, tsk_size_t num_sample
 {
     int ret = 0;
     // we want to allow self comparisons
-    ret = check_sample_stat_inputs(num_sample_sets, 1, 2, num_index_tuples, index_tuples);
+    ret = check_sample_stat_inputs(num_sample_sets, 2, num_index_tuples, index_tuples);
     if (ret != 0) {
         goto out;
     }
@@ -4770,7 +4770,7 @@ tsk_treeseq_Y2(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const double *windows, tsk_flags_t options, double *result)
 {
     int ret = 0;
-    ret = check_sample_stat_inputs(num_sample_sets, 2, 2, num_index_tuples, index_tuples);
+    ret = check_sample_stat_inputs(num_sample_sets, 2, num_index_tuples, index_tuples);
     if (ret != 0) {
         goto out;
     }
@@ -4811,7 +4811,7 @@ tsk_treeseq_f2(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const double *windows, tsk_flags_t options, double *result)
 {
     int ret = 0;
-    ret = check_sample_stat_inputs(num_sample_sets, 2, 2, num_index_tuples, index_tuples);
+    ret = check_sample_stat_inputs(num_sample_sets, 2, num_index_tuples, index_tuples);
     if (ret != 0) {
         goto out;
     }
@@ -5051,7 +5051,7 @@ tsk_treeseq_Y3(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const double *windows, tsk_flags_t options, double *result)
 {
     int ret = 0;
-    ret = check_sample_stat_inputs(num_sample_sets, 3, 3, num_index_tuples, index_tuples);
+    ret = check_sample_stat_inputs(num_sample_sets, 3, num_index_tuples, index_tuples);
     if (ret != 0) {
         goto out;
     }
@@ -5094,7 +5094,7 @@ tsk_treeseq_f3(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const double *windows, tsk_flags_t options, double *result)
 {
     int ret = 0;
-    ret = check_sample_stat_inputs(num_sample_sets, 3, 3, num_index_tuples, index_tuples);
+    ret = check_sample_stat_inputs(num_sample_sets, 3, num_index_tuples, index_tuples);
     if (ret != 0) {
         goto out;
     }
@@ -5143,7 +5143,7 @@ tsk_treeseq_f4(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
     const double *windows, tsk_flags_t options, double *result)
 {
     int ret = 0;
-    ret = check_sample_stat_inputs(num_sample_sets, 4, 4, num_index_tuples, index_tuples);
+    ret = check_sample_stat_inputs(num_sample_sets, 4, num_index_tuples, index_tuples);
     if (ret != 0) {
         goto out;
     }
diff --git a/python/tests/test_lowlevel.py b/python/tests/test_lowlevel.py
@@ -1871,17 +1871,13 @@ def test_ld_matrix_multipop(self, stat_method_name):
             stat_method(
                 bad_ss_sizes, bad_ss, indexes, None, None, row_pos, col_pos, "branch"
             )
-        with pytest.raises(
-            _tskit.LibraryError, match="TSK_ERR_INSUFFICIENT_SAMPLE_SETS"
-        ):
+        with pytest.raises(_tskit.LibraryError, match="TSK_ERR_BAD_SAMPLE_SET_INDEX"):
             bad_ss = np.array([], dtype=np.int32)
             bad_ss_sizes = np.array([0], dtype=np.uint32)
             stat_method(
                 bad_ss_sizes, bad_ss, indexes, row_sites, col_sites, None, None, "site"
             )
-        with pytest.raises(
-            _tskit.LibraryError, match="TSK_ERR_INSUFFICIENT_SAMPLE_SETS"
-        ):
+        with pytest.raises(_tskit.LibraryError, match="TSK_ERR_BAD_SAMPLE_SET_INDEX"):
             bad_ss = np.array([], dtype=np.int32)
             bad_ss_sizes = np.array([0], dtype=np.uint32)
             stat_method(

Original file line number	Diff line number	Diff line change
`@@ -4510,12 +4510,12 @@ tsk_treeseq_pi2_unbiased(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,`
`4510`	`4510`	`***********************************/`
`4511`	`4511`
`4512`	`4512`	`static int`
`4513`		`-check_sample_stat_inputs(tsk_size_t num_sample_sets, tsk_size_t min_num_sample_sets,`
`4514`		`- tsk_size_t tuple_size, tsk_size_t num_index_tuples, const tsk_id_t *index_tuples)`
	`4513`	`+check_sample_stat_inputs(tsk_size_t num_sample_sets, tsk_size_t tuple_size,`
	`4514`	`+ tsk_size_t num_index_tuples, const tsk_id_t *index_tuples)`
`4515`	`4515`	`{`
`4516`	`4516`	`int ret = 0;`
`4517`	`4517`
`4518`		`- if (num_sample_sets < min_num_sample_sets) {`
	`4518`	`+ if (num_sample_sets < 1) {`
`4519`	`4519`	`ret = tsk_trace_error(TSK_ERR_INSUFFICIENT_SAMPLE_SETS);`
`4520`	`4520`	`goto out;`
`4521`	`4521`	`}`
`@@ -4560,7 +4560,7 @@ tsk_treeseq_divergence(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,`
`4560`	`4560`	`const double windows, tsk_flags_t options, double result)`
`4561`	`4561`	`{`
`4562`	`4562`	`int ret = 0;`
`4563`		`- ret = check_sample_stat_inputs(num_sample_sets, 2, 2, num_index_tuples, index_tuples);`
	`4563`	`+ ret = check_sample_stat_inputs(num_sample_sets, 2, num_index_tuples, index_tuples);`
`4564`	`4564`	`if (ret != 0) {`
`4565`	`4565`	`goto out;`
`4566`	`4566`	`}`
`@@ -4625,7 +4625,7 @@ tsk_treeseq_genetic_relatedness(const tsk_treeseq_t *self, tsk_size_t num_sample`
`4625`	`4625`	`{`
`4626`	`4626`	`int ret = 0;`
`4627`	`4627`	`// we want to allow self comparisons`
`4628`		`- ret = check_sample_stat_inputs(num_sample_sets, 1, 2, num_index_tuples, index_tuples);`
	`4628`	`+ ret = check_sample_stat_inputs(num_sample_sets, 2, num_index_tuples, index_tuples);`
`4629`	`4629`	`if (ret != 0) {`
`4630`	`4630`	`goto out;`
`4631`	`4631`	`}`
`@@ -4770,7 +4770,7 @@ tsk_treeseq_Y2(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,`
`4770`	`4770`	`const double windows, tsk_flags_t options, double result)`
`4771`	`4771`	`{`
`4772`	`4772`	`int ret = 0;`
`4773`		`- ret = check_sample_stat_inputs(num_sample_sets, 2, 2, num_index_tuples, index_tuples);`
	`4773`	`+ ret = check_sample_stat_inputs(num_sample_sets, 2, num_index_tuples, index_tuples);`
`4774`	`4774`	`if (ret != 0) {`
`4775`	`4775`	`goto out;`
`4776`	`4776`	`}`
`@@ -4811,7 +4811,7 @@ tsk_treeseq_f2(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,`
`4811`	`4811`	`const double windows, tsk_flags_t options, double result)`
`4812`	`4812`	`{`
`4813`	`4813`	`int ret = 0;`
`4814`		`- ret = check_sample_stat_inputs(num_sample_sets, 2, 2, num_index_tuples, index_tuples);`
	`4814`	`+ ret = check_sample_stat_inputs(num_sample_sets, 2, num_index_tuples, index_tuples);`
`4815`	`4815`	`if (ret != 0) {`
`4816`	`4816`	`goto out;`
`4817`	`4817`	`}`
`@@ -5051,7 +5051,7 @@ tsk_treeseq_Y3(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,`
`5051`	`5051`	`const double windows, tsk_flags_t options, double result)`
`5052`	`5052`	`{`
`5053`	`5053`	`int ret = 0;`
`5054`		`- ret = check_sample_stat_inputs(num_sample_sets, 3, 3, num_index_tuples, index_tuples);`
	`5054`	`+ ret = check_sample_stat_inputs(num_sample_sets, 3, num_index_tuples, index_tuples);`
`5055`	`5055`	`if (ret != 0) {`
`5056`	`5056`	`goto out;`
`5057`	`5057`	`}`
`@@ -5094,7 +5094,7 @@ tsk_treeseq_f3(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,`
`5094`	`5094`	`const double windows, tsk_flags_t options, double result)`
`5095`	`5095`	`{`
`5096`	`5096`	`int ret = 0;`
`5097`		`- ret = check_sample_stat_inputs(num_sample_sets, 3, 3, num_index_tuples, index_tuples);`
	`5097`	`+ ret = check_sample_stat_inputs(num_sample_sets, 3, num_index_tuples, index_tuples);`
`5098`	`5098`	`if (ret != 0) {`
`5099`	`5099`	`goto out;`
`5100`	`5100`	`}`
`@@ -5143,7 +5143,7 @@ tsk_treeseq_f4(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,`
`5143`	`5143`	`const double windows, tsk_flags_t options, double result)`
`5144`	`5144`	`{`
`5145`	`5145`	`int ret = 0;`
`5146`		`- ret = check_sample_stat_inputs(num_sample_sets, 4, 4, num_index_tuples, index_tuples);`
	`5146`	`+ ret = check_sample_stat_inputs(num_sample_sets, 4, num_index_tuples, index_tuples);`
`5147`	`5147`	`if (ret != 0) {`
`5148`	`5148`	`goto out;`
`5149`	`5149`	`}`