Test nonsuccinct case

python/tests/test_coalrate.py

@@ -55,6 +55,46 @@ def naive_pair_coalescence_counts(ts, sample_set_0, sample_set_1):
     return output
 
 
+def convert_to_nonsuccinct(ts):
+    """
+    Give the edges and internal nodes in each tree distinct IDs
+    """
+    tables = tskit.TableCollection(sequence_length=ts.sequence_length)
+    for _ in range(ts.num_populations):
+        tables.populations.add_row()
+    nodes_count = 0
+    for n in ts.samples():
+        tables.nodes.add_row(
+            time=ts.nodes_time[n],
+            flags=ts.nodes_flags[n],
+            population=ts.nodes_population[n],
+        )
+        nodes_count += 1
+    for t in ts.trees():
+        nodes_map = {n: n for n in ts.samples()}
+        for n in t.nodes():
+            if t.num_samples(n) > 1:
+                tables.nodes.add_row(
+                    time=ts.nodes_time[n],
+                    flags=ts.nodes_flags[n],
+                    population=ts.nodes_population[n],
+                )
+                nodes_map[n] = nodes_count
+                nodes_count += 1
+        for n in t.nodes():
+            if t.edge(n) != tskit.NULL:
+                tables.edges.add_row(
+                    parent=nodes_map[t.parent(n)],
+                    child=nodes_map[n],
+                    left=t.interval.left,
+                    right=t.interval.right,
+                )
+    tables.sort()
+    ts_unroll = tables.tree_sequence()
+    assert nodes_count == ts_unroll.num_nodes
+    return ts_unroll
+
+
 class TestCoalescingPairsOneTree:
     """
     Test against worked example (single tree)
@@ -473,6 +513,15 @@ def test_windows_inside_trees(self):
         self._check_total_pairs(ts, windows)
         self._check_subset_pairs(ts, windows)
 
+    def test_nonsuccinct_sequence(self):
+        """
+        test case where each tree has distinct nodes
+        """
+        ts = convert_to_nonsuccinct(self.example_ts())
+        windows = np.linspace(0, ts.sequence_length, 9)
+        self._check_total_pairs(ts, windows)
+        self._check_subset_pairs(ts, windows)
+
     def test_span_normalise(self):
         ts = self.example_ts()
         windows = np.array([0.0, 0.33, 1.0]) * ts.sequence_length