Merge pull request #509 from jeromekelleher/robust-to-interval-change

Tolerate coordinate shifts

Author: jeromekelleher

sc2ts/info.py

@@ -1026,12 +1026,20 @@ def node_info(node, label):
             parent_left = hmm_match["path"][0]["parent"]
             parent_right = hmm_match["path"][1]["parent"]
 
+            edges_right = self.ts.edges_right[self.ts.edges_child == u]
+            interval_right = int(edges_right.min())
+            if interval_right != interval[0][1]:
+                logger.warning(
+                    f"RE: {u} interval right shifted from {interval[0][1]} "
+                    f"to {interval_right}"
+                )
+
             datum = {
                 "num_descendant_samples": self.nodes_max_descendant_samples[u],
                 "num_samples": len(samples),
                 "distinct_sample_pango": len(set(causal_lineages.values())),
                 "interval_left": interval[0][0],
-                "interval_right": interval[0][1],
+                "interval_right": interval_right,
                 "num_mutations": len(hmm_match["mutations"]),
                 "Viridian_amplicon_scheme": self.nodes_metadata[v].get(
                     "Viridian_amplicon_scheme", "Unknown"

tests/test_info.py

@@ -223,6 +223,21 @@ def test_recombinants_summary_example_2(self, fx_recombinant_example_2):
         assert row["diffs"] == 6
         assert row["max_run_length"] == 2
 
+    def test_recombinants_summary_example_2_bp_shift(self, fx_recombinant_example_2):
+        tables = fx_recombinant_example_2.dump_tables()
+        sample = 55
+        row = tables.nodes[sample]
+        md = row.metadata
+        # Shift the bp one base right
+        md["sc2ts"]["breakpoint_intervals"] = [[114, 29826]]
+        tables.nodes[sample] = row.replace(metadata=md)
+        ts = tables.tree_sequence()
+        ti = info.TreeInfo(ts, show_progress=False)
+        df1 = ti.recombinants_summary(characterise_copying=True, show_progress=False)
+        ti = info.TreeInfo(fx_recombinant_example_2, show_progress=False)
+        df2 = ti.recombinants_summary(characterise_copying=True, show_progress=False)
+        pd.testing.assert_frame_equal(df1, df2)
+
 
 class TestSampleGroupInfo:
     def test_draw_svg(self, fx_ti_2020_02_13):