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joverlee521 committed Feb 6, 2024
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* `augur.io.read_metadata`: A new optional `dtype` argument allows custom data types for all columns. Automatic type inference still happens by default, so this is not a breaking change. [#1252][] (@victorlin)
* `augur.io.read_vcf` has been removed and usage replaced with TreeTime's function of the same name which has improved validation of the VCF file. [#1366][] (@jameshadfield)
* export v2: Add flag `--metadata-columns` to specify metadata columns to export without using them as colorings. [#1384][] (@joverlee521)

### Bug Fixes

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[#1252]: https://github.com/nextstrain/augur/pull/1252
[#1366]: https://github.com/nextstrain/augur/pull/1366
[#1384]: https://github.com/nextstrain/augur/pull/1384
[#1400]: https://github.com/nextstrain/augur/pull/1400

## 24.0.0 (22 January 2024)

### Major Changes

* ancestral, translate: For VCF inputs please ensure you are using TreeTime 0.11.2 or later. A large number of bugfixes and improvements have been added in both Augur and TreeTime. [#1355][] and [TreeTime #263][] (@jameshadfield)
* ancestral, translate: For VCF inputs please ensure you are using TreeTime 0.11.2 or later. A large number of bugfixes and improvements have been added in both Augur and TreeTime. [#1355][] and [TreeTime #263][] (@jameshadfield)
* ancestral, translate: GenBank files now require the (GFF mandatory) source feature to be present. [#1351][] (@jameshadfield)
* ancestral, translate: 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. [#1351][] (@jameshadfield)

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* If a Gene/CDS in the GFF/GenBank file is unparsed we now print a warning.
* 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.
* Incompatible arguments are now checked, especially related to VCF vs FASTA inputs.
* `--vcf-reference` and `--root-sequence` are now mutually exclusive.
* translate: Tree nodes are checked against the node-data JSON input to ensure sequences are present. [#1348][] (@jameshadfield)
* utils::load_features: This function may now raise `AugurError`. [#1351][] (@jameshadfield)
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