Minor tweaks

jeromekelleher · Dec 7, 2024 · b221fd4 · b221fd4
1 parent 43a3ef4
commit b221fd4
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/sc2ts/core.py b/sc2ts/core.py
@@ -109,7 +109,7 @@ def decode_flags(f):
 
 
 def flags_summary(f):
-    return "".join([v.short if (v.value & f) > 0 else "-" for v in flag_values])
+    return "".join([v.short if (v.value & f) > 0 else "_" for v in flag_values])
 
 
 class FastaReader(collections.abc.Mapping):

diff --git a/sc2ts/info.py b/sc2ts/info.py
@@ -753,7 +753,7 @@ def _node_summary(self, u, child_mutations=True):
         flags = self.ts.nodes_flags[u]
 
         strain = ""
-        if (flags & tskit.NODE_IS_SAMPLE) != 0:
+        if flags & (tskit.NODE_IS_SAMPLE | core.NODE_IS_REFERENCE) > 0:
             strain = md["strain"]
         else:
             md = md["sc2ts"]
@@ -763,7 +763,9 @@ def _node_summary(self, u, child_mutations=True):
                 except KeyError:
                     strain = "debug missing"
             elif "group_id" in md:
-                strain = md["group_id"]
+                # FIXME clipping this artificially for now
+                # see https://github.com/jeromekelleher/sc2ts/issues/434
+                strain = md["group_id"][:8]
 
         pango = md.get(self.pango_source, None)
         imputed_pango = md.get("Imputed_" + self.pango_source, None)