Quick hacky version hard-coding metadata filtering

sc2ts/inference.py

@@ -551,7 +551,12 @@ def extend(
         f"mutations={base_ts.num_mutations};date={base_ts.metadata['sc2ts']['date']}"
     )
 
-    metadata_matches = list(metadata_db.get(date))
+    additional_metadata_clause = None
+    # Quick hack
+    if date > "2020-03-01":
+        additional_metadata_clause = "Viridian_cons_het == '0' AND Viridian_cons_het != '.'"
+
+    metadata_matches = list(metadata_db.get(date, additional_metadata_clause))
 
     logger.info(f"Got {len(metadata_matches)} metadata matches")
     # first check for samples that are in the alignment_store

sc2ts/metadata.py

@@ -75,9 +75,12 @@ def query(self, sql, args=None):
             for row in self.conn.execute(sql):
                 yield row
 
-    def get(self, date):
+    def get(self, date, additional_clause=None):
         sql = "SELECT * FROM samples WHERE date==?"
+        if additional_clause is not None:
+            sql = f"{sql} AND {additional_clause}"
         with self.conn:
+            logger.debug(f"Running {sql}")
             for row in self.conn.execute(sql, [date]):
                 yield row