changelog

CHANGES.md

@@ -2,6 +2,14 @@
 
 ## __NEXT__
 
+* ancestral, translate: Major improvements to how we parse GFF and GenBank reference files. [#1351][] (@jameshadfield)
+    * For GFF files, we extract the genome/sequence coordinates by inspecting the sequence-region pragma, region type and/or source type. This information is now required.
+    * For GenBank files we now require the (mandatory) source feature to be present.
+    * translate will now always export a 'nuc' annotation in the output JSON.
+    * Gene/CDS names of 'nuc' are now forbidden.
+    * If a Gene/CDS in the GFF/GenBank file is unparsed we now print a warning.
+    * Parsing behaviour of GFF rows no longer changes with the presence of the `--genes` command line argument (but the filtering is still applied).
+* utils::load_features: This function may now raise `AugurError`. [#1351][] (@jameshadfield)
 * ancestral: For VCF alignments, a VCF output file is now only created when requested via `--output-vcf`. [#1344][] (@jameshadfield)
 * ancestral: Improvements to command line arguments. [#1344][] (@jameshadfield)
      * Incompatible arguments are now checked, especially related to VCF vs FASTA inputs. 
@@ -14,6 +22,7 @@
 
 [#1344]: https://github.com/nextstrain/augur/pull/1344
 [#1348]: https://github.com/nextstrain/augur/pull/1348
+[#1351]: https://github.com/nextstrain/augur/pull/1351
 
 ## 23.1.1 (7 November 2023)