fix: make legacy mapping use {clade} (Omicron) by default

Resolves #471
I forgot to update the clade-legacy-mapping.yml with the last clade update (24C). As a result, the Nextstrain_clade output for 24C was wrong (`?` instead of `24C (Omicron)`).

To reduce maintenance effort, we now use `{value} (Omicron)` as the default mapping. This means one less file to update when clades are updated. If there's ever a non-Omicron again, we'd have to updated `clade-legacy-mapping.yml` but WHO has stopped giving variant names and there's nothing left that's not Omicron. So this should work into the indefinite future (until Emma stops using `Nextstrain_clade` - she's possibly the only user of that backwards-compat column)

bin/join-metadata-and-clades

@@ -93,7 +93,6 @@ def main():
     metadata = pd.read_csv(args.metadata, index_col=METADATA_JOIN_COLUMN_NAME,
                            sep='\t', low_memory=False, na_filter = False)
 
-    # Read and rename clade column to be more descriptive
     clades = pd.read_csv(args.nextclade_tsv, index_col=NEXTCLADE_JOIN_COLUMN_NAME,
                          usecols=[NEXTCLADE_JOIN_COLUMN_NAME, *(set(column_map.keys()) - clades_21L_columns)],
                          sep='\t', low_memory=True, dtype="object", na_filter = False) \
@@ -113,7 +112,11 @@ def main():
     # Add clade_legacy column as Nextstrain_clade
     # Use yml mapping
     with open(args.clade_legacy_mapping, 'r') as legacy_mapping_file:
-         clade_legacy_mapping = yaml.safe_load(legacy_mapping_file)
+        clade_legacy_mapping_dict: dict[str, str] = yaml.safe_load(legacy_mapping_file)
+
+    def clade_legacy_mapping(clade_nextstrain: str) -> str:
+        return clade_legacy_mapping_dict.get(clade_nextstrain, f"{clade_nextstrain} Omicron")
+
     clades["Nextstrain_clade"] = clades["clade_nextstrain"].map(clade_legacy_mapping)
 
     # Remove immune_escape and ace2_binding when clade <21L and not recombinant

defaults/clade-legacy-mapping.yml

@@ -20,24 +20,4 @@
 21F: 21F (Iota)
 21G: 21G (Lambda)
 21H: 21H (Mu)
-21K: 21K (Omicron)
-21L: 21L (Omicron)
-21M: 21M (Omicron)
-22A: 22A (Omicron)
-22B: 22B (Omicron)
-22C: 22C (Omicron)
-22D: 22D (Omicron)
-22E: 22E (Omicron)
-22F: 22F (Omicron)
-23A: 23A (Omicron)
-23B: 23B (Omicron)
-23C: 23C (Omicron)
-23D: 23D (Omicron)
-23E: 23E (Omicron)
-23F: 23F (Omicron)
-23G: 23G (Omicron)
-23H: 23H (Omicron)
-23I: 23I (Omicron)
-24A: 24A (Omicron)
-24B: 24B (Omicron)
 recombinant: recombinant