. and PASS are now PASS

snakecnv/bin/filter.py

@@ -96,7 +96,8 @@ def UnifiedPassAnnotation(SVSet):
         filters = [f for f in record.filter]
         # We make the assumption when a "." is present no other filter
         # are present
-        if "." in filters:
+        # if no filter or "." is present in filters
+        if len(filters) == 0 or "." in filters:
             record.filter.clear()
             record.filter.add("PASS")