Initial steps for internal pedigree samples

Author: jeromekelleher

algorithms.py

@@ -1011,10 +1011,12 @@ def initialise(self, ts):
                             root_segments_tail[root] = seg
         self.S[self.L] = -1
 
+        # FIXME should determine start_time from the youngest roots. See the C code.
+        start_time = 0
         # Insert the segment chains into the algorithm state.
         for node in range(ts.num_nodes):
             lineage = root_lineages[node]
-            if lineage is not None:
+            if lineage is not None and ts.nodes_time[node] == start_time:
                 seg = lineage.head
                 left_end = seg.left
                 while seg is not None:
@@ -1617,6 +1619,7 @@ def process_pedigree_common_ancestors(self, ind, ploid):
         material among its parent ploids.
         """
         common_ancestors = ind.common_ancestors[ploid]
+        node = ind.nodes[ploid]
         if len(common_ancestors) == 0:
             # No ancestral material inherited on this ploid of this individual
             return
@@ -1632,7 +1635,6 @@ def process_pedigree_common_ancestors(self, ind, ploid):
         # monoploid genome for this ploid of this individual.
         # If any coalescences occur, they use the corresponding node ID.
         # FIXME update the population/label here
-        node = ind.nodes[ploid]
         genome = self.merge_ancestors(common_ancestors, 0, 0, node)
         if ind.parents[ploid] == tskit.NULL:
             # If this individual is a founder we need to make sure that all

tests/test_algorithms.py

@@ -423,6 +423,23 @@ def test_pedigree_trio(self, r):
         input_tables.nodes.assert_equals(output_tables.nodes[: len(input_tables.nodes)])
         assert len(output_tables.edges) >= 2
 
+    @pytest.mark.parametrize("r", [0, 0.1, 1])
+    def test_pedigree_internal_sample(self, r):
+        input_tables = simulate_pedigree(num_founders=4, num_generations=4)
+        flags = input_tables.nodes.flags
+        flags[8:12] = tskit.NODE_IS_SAMPLE  # Make inds 4 and 5 samples
+        input_tables.nodes.flags = flags
+        print(input_tables)
+        with tempfile.TemporaryDirectory() as tmpdir:
+            # ts_path = pathlib.Path(tmpdir) / "pedigree.trees"
+            ts_path = "pedigree.trees"
+            input_tables.dump(ts_path)
+            ts = self.run_script(f"0 --from-ts {ts_path} -r {r} --model=fixed_pedigree")
+        output_tables = ts.dump_tables()
+        input_tables.individuals.assert_equals(output_tables.individuals)
+        input_tables.nodes.assert_equals(output_tables.nodes[: len(input_tables.nodes)])
+        assert len(output_tables.edges) >= 2
+
     @pytest.mark.parametrize("num_founders", [1, 2, 20])
     def test_one_gen_pedigree(self, num_founders):
         tables = simulate_pedigree(num_founders=num_founders, num_generations=1)