# Changelog
All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog ](https://keepachangelog.com/en/1.0.0 )
and this project adheres to [Semantic Versioning ](https://semver.org/spec/v2.0.0.html ).
## [Unreleased]
## [0.2.2] - 2023-01-28
### Fixed
- `Haplotype` validation ([#36](https://github.com/BioJulia/SequenceVariation.jl/issues/36)/[#37](https://github.com/BioJulia/SequenceVariation.jl/pull/37))
## [0.2.1] - 2023-01-11
### Added
- `translate` functionality for `Haplotype` s ([#31](https://github.com/BioJulia/SequenceVariation.jl/pull/31))
- More informative errors when constructing invalid `Haplotype` s ([#34](https://github.com/BioJulia/SequenceVariation.jl/pull/34))
## [0.2.0] - 2023-01-10
### Added
- Tutorial-type documentation ([#28](https://github.com/BioJulia/SequenceVariation.jl/pull/28))
- `Base.isless` implementation for `Edit` and `Variation` ([#32](https://github.com/BioJulia/SequenceVariation.jl/pull/32))
### Changed
- Code now follows [Blue style ](https://github.com/invenia/BlueStyle ) ([#28](https://github.com/BioJulia/SequenceVariation.jl/pull/28))
- :bomb: [BREAKING] Public and private API defined based on Blue style guidelines ([#28](https://github.com/BioJulia/SequenceVariation.jl/pull/28))
- :bomb: [BREAKING] Renamed type `Variant` to `Haplotype` ([#20](https://github.com/BioJulia/SequenceVariation.jl/issues/20)/[#29](https://github.com/BioJulia/SequenceVariation.jl/pull/29))
- :bomb: [BREAKING] Refactored `reconstruct` function to use `Haplotype` 's reference sequence ([#30](https://github.com/BioJulia/SequenceVariation.jl/pull/30))
### Removed
- Windows and MacOS CI tests ([#28](https://github.com/BioJulia/SequenceVariation.jl/pull/28))
## [0.1.4] - 2022-12-17
### Fixed
- Soft clips at end of alignment causing invalid `Variant` s ([#25](https://github.com/BioJulia/SequenceVariation.jl/issues/25)/[#26](https://github.com/BioJulia/SequenceVariation.jl/pull/26))
## [0.1.3] - 2022-11-22
### Changed
- Variations getter now returns type-parameterized vector ([#23](https://github.com/BioJulia/SequenceVariation.jl/pull/23))
## [0.1.2] - 2022-10-04
### Changed
- Updated dependency compats ([#21](https://github.com/BioJulia/SequenceVariation.jl/pull/21))
- BioAlignments: 2 -> 2,3
- BioSequences: 2 -> 2,3
- BioSymbols: 4 -> 4,5
## [0.1.1] - 2022-07-21
### Added
- Constructor for `Variant` based on `Variation` s ([#18](https://github.com/BioJulia/SequenceVariation.jl/pull/18))
## [0.1.0] - 2022-07-14
### Added
- Mutation types (`Substitution`, `Deletion` , `Insertion` )
- `Variant` type to store groups of mutations together
- `Variation` type to store and compare individual mutations
- `reconstruct!` function to build mutated sequences from `Variant` s
- `Variant` constructor to automatically detect mutations from a `BioAlignments.PairwiseAlignment`
- Methods to get reference and alternate bases from a `Variation`
[unreleased]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.2.2...HEAD
[0.2.2]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.2.1...v0.2.2
[0.2.1]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.2.0...v0.2.1
[0.2.0]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.4...v0.2.0
[0.1.4]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.3...v0.1.4
[0.1.3]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.2...v0.1.3
[0.1.2]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.1...v0.1.2
[0.1.1]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.0...v0.1.1
[0.1.0]: https://github.com/BioJulia/SequenceVariation.jl/releases/tag/v0.1.0
