Extra test for node extent

Author: benjeffery

python/tests/test_genotypes.py

@@ -1835,6 +1835,33 @@ def test_nexus_impute_missing(self):
         )
 
 
+class TestAlignmentsPartialIsolation:
+    def build_ts(self):
+        # sequence length 10, sample node covers only [3,7)
+        tables = tskit.TableCollection(10)
+        parent = tables.nodes.add_row(time=1)
+        child = tables.nodes.add_row(flags=tskit.NODE_IS_SAMPLE, time=0)
+        tables.edges.add_row(left=3, right=7, parent=parent, child=child)
+        # Add a site inside the covered region with a mutation on the child
+        site_id = tables.sites.add_row(position=5, ancestral_state="A")
+        tables.mutations.add_row(site=site_id, node=child, derived_state="G")
+        tables.sort()
+        return tables.tree_sequence()
+
+    def test_whole_window_missing_at_ends(self):
+        ts = self.build_ts()
+        ref = "0123456789"
+        # Node is isolated outside [3,7): expect missing there; inside use ref, with site overlay at 5
+        got = list(ts.alignments(samples=[1], reference_sequence=ref))
+        assert got == ["NNN34G6NNN"]
+
+    def test_subwindow(self):
+        ts = self.build_ts()
+        ref = "0123456789"
+        # Request [2,8): expect missing at 2 and 7, ref inside, site overlay at 5
+        got = list(ts.alignments(samples=[1], reference_sequence=ref[2:8], left=2, right=8))
+        assert got == ["N34G6N"]
+
 class TestMultiRootExample:
     # 1.00┊  4   5  ┊
     #     ┊ ┏┻┓ ┏┻┓ ┊