diff --git a/CHANGES.md b/CHANGES.md index d8b68d155..778cf1d98 100644 --- a/CHANGES.md +++ b/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)