[ancestral] only export VCF if requested

This is consistent with augur's general behaviour of "request a file for
it to be produced". Moreover, the previous code would ~always result in
the VCF input file being overwritten.

This is potentially a backwards compatible change. The number of users
expected to be affected is minimal (perhaps zero).

Closes #1343.

CHANGES.md

@@ -2,6 +2,9 @@
 
 ## __NEXT__
 
+* ancestral: For VCF alignments, a VCF output file is now only created when requested via `--output-vcf`. [#1344][] (@jameshadfield)
+
+[#1344]: https://github.com/nextstrain/augur/issues/1334
 
 ## 23.1.1 (7 November 2023)
 

augur/ancestral.py

@@ -376,13 +376,9 @@ def run(args):
         SeqIO.write(records, args.output_sequences, "fasta")
         print("ancestral sequences FASTA written to", args.output_sequences, file=sys.stdout)
 
-    # If VCF, output VCF including new ancestral seqs
-    if is_vcf:
-        if args.output_vcf:
-            vcf_fname = args.output_vcf
-        else:
-            vcf_fname = '.'.join(args.alignment.split('.')[:-1]) + '.vcf'
-        write_vcf(nuc_result['tt'].get_tree_dict(keep_var_ambigs=True), vcf_fname)
-        print("ancestral sequences as vcf-file written to",vcf_fname, file=sys.stdout)
+    # If VCF output VCF including new ancestral seqs if requested to
+    if is_vcf and args.output_vcf:
+        write_vcf(nuc_result['tt'].get_tree_dict(keep_var_ambigs=True), args.output_vcf)
+        print("Mutations, including for ancestral nodes, exported as VCF to", args.output_vcf, file=sys.stdout)
 
     return 0