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chore(main): release 1.4.0 #29

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17 changes: 17 additions & 0 deletions CHANGELOG.md
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# Changelog

## [1.4.0](https://github.com/PathoGenOmics-Lab/VIPERA/compare/v1.3.1...v1.4.0) (2026-02-11)


### Features

* add low-confidence site filtering ([f447478](https://github.com/PathoGenOmics-Lab/VIPERA/commit/f447478fe409e01e64c7a9d077a18c8518f460aa))
* remove demix module from rule core ([#30](https://github.com/PathoGenOmics-Lab/VIPERA/issues/30)) ([cb01079](https://github.com/PathoGenOmics-Lab/VIPERA/commit/cb0107939b82a2d7cc0dc94ca69448f9e6cf5b83))
* use site quality filter to calculate evolutionary rate ([#33](https://github.com/PathoGenOmics-Lab/VIPERA/issues/33)) ([29d75e5](https://github.com/PathoGenOmics-Lab/VIPERA/commit/29d75e5e30d93b7c1048d93cda99dabc5a21690f))


### Bug Fixes

* deduplicate variants and handle missing annotation ([#32](https://github.com/PathoGenOmics-Lab/VIPERA/issues/32)) ([c70dfe0](https://github.com/PathoGenOmics-Lab/VIPERA/commit/c70dfe0a606705807c3f912a21a89338a9f88625))
* init missing columns ([#37](https://github.com/PathoGenOmics-Lab/VIPERA/issues/37)) ([fa5f624](https://github.com/PathoGenOmics-Lab/VIPERA/commit/fa5f6240f4eac915eda1a61c53fbce0db8370732))
* pin setuptools to avoid deprecation error in Snakemake 7 ([395696c](https://github.com/PathoGenOmics-Lab/VIPERA/commit/395696c8f1231d8e94c5eaf330a6dda59045d210))
* pin setuptools version to avoid deprecation error ([#31](https://github.com/PathoGenOmics-Lab/VIPERA/issues/31)) ([395696c](https://github.com/PathoGenOmics-Lab/VIPERA/commit/395696c8f1231d8e94c5eaf330a6dda59045d210))

## [1.3.1](https://github.com/PathoGenOmics-Lab/VIPERA/compare/v1.3.0...v1.3.1) (2025-11-24)


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2 changes: 1 addition & 1 deletion version.txt
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1.3.1
1.4.0