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Update changelog
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victorlin committed Jan 19, 2024
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* `--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)
* export v2: Automatically minify large outputs. Use `--no-minify-json` to disable this default behavior. [#1352][] (@victorlin)
* `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)

### Bug Fixes

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* ancestral, translate: Address Biopython deprecation warnings. [#1379][] (@victorlin)
* ancestral: Previously, the help text for `--genes` falsely claimed that it could accept a file. Now, it can truly claim that. [#1353][] (@victorlin)
* Deprecate `read_strains` from `augur.utils` and add it to the public API under `augur.io`. [#1353][] (@victorlin)
* filter, frequencies, refine: Speed up reading of the metadata file. [#1252][] (@victorlin)
* traits: Previously, columns with only numeric values were treated as numerical data. These are now treated as categorical data for discrete trait analysis. [#1252][] (@victorlin)


[#1252]: https://github.com/nextstrain/augur/pull/1252
[#1344]: https://github.com/nextstrain/augur/pull/1344
[#1348]: https://github.com/nextstrain/augur/pull/1348
[#1351]: https://github.com/nextstrain/augur/pull/1351
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