fix: upper case root sequence for ancestral reconstruction

nextstrain · Sep 26, 2023 · f9c3e19 · f9c3e19
1 parent 2ec73cd
commit f9c3e19
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/augur/ancestral.py b/augur/ancestral.py
@@ -268,7 +268,7 @@ def run(args):
         if args.root_sequence:
             for fmt in ['fasta', 'genbank']:
                 try:
-                    ref = str(SeqIO.read(args.root_sequence, fmt).seq)
+                    ref = str(SeqIO.read(args.root_sequence, fmt).seq).upper()
                     break
                 except:
                     pass