Fixup metadata for reversion push/coalesce

jeromekelleher · Dec 6, 2024 · f456ed2 · f456ed2
1 parent bde243e
commit f456ed2
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Showing 3 changed files with 9 additions and 8 deletions.
diff --git a/sc2ts/inference.py b/sc2ts/inference.py
@@ -1110,7 +1110,7 @@ def add_matching_results(
     tables.compute_mutation_parents()
     ts = tables.tree_sequence()
     ts = tree_ops.push_up_reversions(ts, attach_nodes, date)
-    ts = tree_ops.coalesce_mutations(ts, attach_nodes)
+    ts = tree_ops.coalesce_mutations(ts, attach_nodes, date)
     ts = delete_immediate_reversion_nodes(ts, attach_nodes)
     return ts, added_groups
 

diff --git a/sc2ts/info.py b/sc2ts/info.py
@@ -781,14 +781,14 @@ def _node_summary(self, u, child_mutations=True):
         else:
             md = md["sc2ts"]
             if flags == 1 << 21:
-                if "overlap" in md:
-                    strain = f"Overlap {len(md['overlap'])} mut {len(md['sibs'])} sibs"
-                else:
+                try:
+                    strain = f"Overlap added={md['date_added']} {md['mutations']}"
+                except KeyError:
                     strain = "Overlap debug missing"
             elif flags == 1 << 22:
-                if "sites" in md:
-                    strain = f"Push {len(md['sites'])} reversions"
-                else:
+                try:
+                    strain = f"Push added={md['date_added']} {md['mutations']}"
+                except KeyError:
                     strain = "Push debug missing"
             elif "group_id" in md:
                 strain = md["group_id"]

diff --git a/sc2ts/tree_ops.py b/sc2ts/tree_ops.py
@@ -276,7 +276,7 @@ def update_tables(tables, edges_to_delete, mutations_to_delete):
     return tables.tree_sequence()
 
 
-def coalesce_mutations(ts, samples=None):
+def coalesce_mutations(ts, samples=None, date="1999-01-01"):
     """
     Examine all time-0 samples and their (full-sequence) sibs and create
     new nodes to represent overlapping sets of mutations. The algorithm
@@ -380,6 +380,7 @@ def coalesce_mutations(ts, samples=None):
                 "sc2ts": {
                     "mutations": md_overlap,
                     "sibs": md_sibs,
+                    "date_added": date,
                 }
             },
         )