Merge pull request #206 from nextstrain/feat/warn-dataset-ref-mismatch

scripts/rebuild

@@ -126,6 +126,7 @@ def index_one_dataset(args, pathogen_json_path: str, dataset: object, tag: str,
   path = relpath(dataset_dir, args.input_dir)
 
   ref = get_ref_seq(pathogen_json, dataset_dir)
+  check_ref_seq_mismatch(ref, pathogen_json, dataset_dir)
 
   versions, last_version = dataset_get_versions(dataset)
 
@@ -163,6 +164,20 @@ def get_ref_seq(pathogen_json, dataset_dir):
     raise ValueError(f"When reading reference sequence") from e
 
 
+def check_ref_seq_mismatch(standalone_ref, pathogen_json, dataset_dir):
+  tree_filename = dict_get(pathogen_json, ["files", "treeJson"])
+  tree_json_path = join(dataset_dir, tree_filename) if tree_filename else None
+  if tree_json_path is not None and isfile(tree_json_path):
+    tree_json = json_read(tree_json_path)
+    tree_ref = dict_get(tree_json, ["root_sequence", "nuc"])
+    if tree_ref is not None:
+      if standalone_ref.seq != tree_ref:
+        l.warn(
+          "Reference sequence provided does not exactly match reference (root) sequence in Auspice JSON. This warning "
+          "signals that there is a potential for failures if the mismatch is not intended."
+        )
+
+
 def get_new_dataset_order(datasets, dataset_order):
   paths = list(map(lambda d: d["path"], datasets))