From 9d96cade7739cef5dde8eca5c88eeb65e91d8945 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Wed, 7 Feb 2024 17:09:54 -0800 Subject: [PATCH] Update CHANGELOG --- CHANGES.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGES.md b/CHANGES.md index f5d9799cd..591febe98 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -6,6 +6,9 @@ * filter: Added a new option `--query-columns` that allows specifying what columns are used in `--query` along with the expected data types. If unspecified, automatic detection of columns and types is attempted. [#1294][] (@victorlin) * `augur.io.read_metadata`: A new optional `columns` argument allows specifying a subset of columns to load. The default behavior still loads all columns, so this is not a breaking change. [#1294][] (@victorlin) +* `augur parse`: A new optional `--output-id-field` argument allows the user to select any ID field for the produced FASTA file (e.g. 'accession' instead of 'name' or 'strain'). [#1403][] (@j23414) + * When no `--output-id-field` is given and the data has both `name` and `strain` fields, continue to preferentially use `name` over `strain` as the sequence ID field; but, throw a deprecation warning that the order will be switched to prefer `strain` over `name` in the future to be consistent with the rest of Augur. + * Added entry to [DEPRECATED.md](./DEPRECATED.md). ### Bug Fixes @@ -20,6 +23,7 @@ [#1294]: https://github.com/nextstrain/augur/pull/1294 [#1389]: https://github.com/nextstrain/augur/pull/1389 [#1410]: https://github.com/nextstrain/augur/pull/1410 +[#1403]: https://github.com/nextstrain/augur/pull/1403 ## 24.1.0 (30 January 2024)