stick test

stick test

Author: petrelharp

c/tskit/tables.c

@@ -4566,7 +4566,8 @@ tsk_table_sorter_run(tsk_table_sorter_t *self, tsk_bookmark_t *start)
         if (start->sites == self->tables->sites.num_rows
             && start->mutations == self->tables->mutations.num_rows) {
             skip_sites = true;
-        } else {
+        } else if (start->sites != 0
+                   || start->mutations != 0) {
             ret = TSK_ERR_SORT_OFFSET_NOT_SUPPORTED;
             goto out;
         }

python/tests/test_topology.py

@@ -3223,6 +3223,76 @@ def test_single_binary_tree_keep_roots_mutations(self):
             keep_input_roots=True,
         )
 
+    def test_map_mutations_with_and_without_roots(self):
+        nodes_before = """\
+        id      is_sample   time
+        0       1           0
+        1       0           1
+        """
+        edges_before = """\
+        left    right   parent  child
+        0       2       1       0
+        """
+        sites = """\
+        id  position    ancestral_state
+        0   1.0         0
+        """
+        mutations_before = """\
+        site    node    derived_state
+        0       0       2
+        0       1       1
+        """
+        # expected result without keep_input_roots
+        nodes_after = """\
+        id      is_sample   time
+        0       1           0
+        """
+        edges_after = """\
+        left    right   parent  child
+        """
+        mutations_after = """\
+        site    node    derived_state
+        0       0       2
+        0       0       1
+        """
+        # expected result with keep_input_roots
+        nodes_after_keep = nodes_before
+        edges_after_keep = """\
+        left    right   parent  child
+        0       2       1       0
+        """
+        mutations_after_keep = """\
+        site    node    derived_state
+        0       0       2
+        0       0       1
+        """
+        self.verify_simplify(
+            samples=[0],
+            nodes_before=nodes_before,
+            edges_before=edges_before,
+            sites_before=sites,
+            mutations_before=mutations_before,
+            nodes_after=nodes_after,
+            edges_after=edges_after,
+            sites_after=sites,
+            mutations_after=mutations_after,
+            keep_input_roots=False,
+            debug=True
+        )
+        self.verify_simplify(
+            samples=[0],
+            nodes_before=nodes_before,
+            edges_before=edges_before,
+            sites_before=sites,
+            mutations_before=mutations_before,
+            nodes_after=nodes_after_keep,
+            edges_after=edges_after_keep,
+            sites_after=sites,
+            mutations_after=mutations_after_keep,
+            keep_input_roots=True,
+            debug=True
+        )
+
     def test_overlapping_edges(self):
         nodes = """\
         id      is_sample   time