Catch case when windows do not span entire sequence

tskit-dev · Sep 19, 2024 · 702385c · 702385c
1 parent dcee409
commit 702385c
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Showing 2 changed files with 15 additions and 9 deletions.
diff --git a/c/tskit/trees.c b/c/tskit/trees.c
@@ -9651,6 +9651,7 @@ tsk_treeseq_pair_coalescence_counts(const tsk_treeseq_t *self,
     tsk_size_t num_windows, const double *windows, tsk_size_t num_bins,
     const tsk_id_t *node_bin_map, tsk_flags_t options, double *result)
 {
+    options |= TSK_REQUIRE_FULL_SPAN;
     return tsk_treeseq_pair_coalescence_stat(self, num_sample_sets, sample_set_sizes,
         sample_sets, num_set_indexes, set_indexes, num_windows, windows, num_bins,
         node_bin_map, pair_coalescence_weights, num_bins, NULL, options, result);
@@ -9767,7 +9768,7 @@ tsk_treeseq_pair_coalescence_quantiles(const tsk_treeseq_t *self,
     if (ret != 0) {
         goto out;
     }
-    options |= TSK_STAT_SPAN_NORMALISE | TSK_STAT_PAIR_NORMALISE;
+    options |= TSK_STAT_SPAN_NORMALISE | TSK_STAT_PAIR_NORMALISE | TSK_REQUIRE_FULL_SPAN;
     ret = tsk_treeseq_pair_coalescence_stat(self, num_sample_sets, sample_set_sizes,
         sample_sets, num_set_indexes, set_indexes, num_windows, windows, num_bins,
         node_bin_map, pair_coalescence_quantiles, num_quantiles, params, options,
@@ -9885,7 +9886,7 @@ tsk_treeseq_pair_coalescence_rates(const tsk_treeseq_t *self, tsk_size_t num_sam
     if (ret != 0) {
         goto out;
     }
-    options |= TSK_STAT_SPAN_NORMALISE | TSK_STAT_PAIR_NORMALISE;
+    options |= TSK_STAT_SPAN_NORMALISE | TSK_STAT_PAIR_NORMALISE | TSK_REQUIRE_FULL_SPAN;
     ret = tsk_treeseq_pair_coalescence_stat(self, num_sample_sets, sample_set_sizes,
         sample_sets, num_set_indexes, set_indexes, num_windows, windows,
         num_time_windows, node_time_window, pair_coalescence_rates, num_time_windows,

diff --git a/python/tests/test_lowlevel.py b/python/tests/test_lowlevel.py
@@ -4402,8 +4402,8 @@ def test_c_tsk_err_node_out_of_bounds(self, bad_node):
     def test_c_tsk_err_bad_windows(self):
         ts = self.example_ts()
         L = ts.get_sequence_length()
-        with pytest.raises(_tskit.LibraryError, match="BAD_WINDOWS"):
-            self.pair_coalescence_counts(ts, windows=[-1.0, L])
+        with pytest.raises(tskit.LibraryError, match="TSK_ERR_BAD_WINDOWS"):
+            self.pair_coalescence_counts(ts, windows=[1.0, L])
 
     def test_c_tsk_err_bad_node_bin_map(self):
         ts = self.example_ts()
@@ -4526,6 +4526,11 @@ def test_c_tsk_err_unsorted_times(self):
         with pytest.raises(_tskit.LibraryError, match="TSK_ERR_UNSORTED_TIMES"):
             self.pair_coalescence_quantiles(ts, node_bin_map=node_bin_map)
 
+    def test_c_tsk_err_bad_windows(self):
+        ts = self.example_ts()
+        with pytest.raises(tskit.LibraryError, match="TSK_ERR_BAD_WINDOWS"):
+            self.pair_coalescence_quantiles(ts, windows=[1.0, ts.get_sequence_length()])
+
     @pytest.mark.parametrize("bad_ss_size", [-1, 1000])
     def test_cpy_bad_sample_sets(self, bad_ss_size):
         ts = self.example_ts()
@@ -4654,6 +4659,11 @@ def test_c_tsk_err_bad_sample_pair_times(self):
         with pytest.raises(_tskit.LibraryError, match="TSK_ERR_BAD_SAMPLE_PAIR_TIMES"):
             self.pair_coalescence_rates(ts, time_windows=np.array([-1.0, np.inf]))
 
+    def test_c_tsk_err_bad_windows(self):
+        ts = self.example_ts()
+        with pytest.raises(tskit.LibraryError, match="TSK_ERR_BAD_WINDOWS"):
+            self.pair_coalescence_rates(ts, windows=[1.0, ts.get_sequence_length()])
+
     @pytest.mark.parametrize("bad_ss_size", [-1, 1000])
     def test_cpy_bad_sample_sets(self, bad_ss_size):
         ts = self.example_ts()
@@ -4665,11 +4675,6 @@ def test_cpy_bad_sample_sets(self, bad_ss_size):
                 ts, sample_set_sizes=[bad_ss_size, ts.get_num_samples()]
             )
 
-    def test_cpy_bad_windows(self):
-        ts = self.example_ts()
-        with pytest.raises(ValueError, match="at least 2"):
-            self.pair_coalescence_rates(ts, windows=[0.0])
-
     @pytest.mark.parametrize("indexes", [[(0, 0, 0)], np.zeros((0, 2), dtype=np.int32)])
     def test_cpy_bad_indexes(self, indexes):
         ts = self.example_ts()