2022-07-05 15:53:34 +00:00
# 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]
2023-01-04 17:13:38 +00:00
### Added
- Tutorial-type documentation ([#28](https://github.com/BioJulia/SequenceVariation.jl/pull/28))
2023-01-10 17:09:10 +00:00
- `Base.isless` implementation for `Edit` and `Variation` ([#31](https://github.com/BioJulia/SequenceVariation.jl/pull/31))
2023-01-04 17:13:38 +00:00
### 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))
2023-01-04 19:15:36 +00:00
- :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))
2023-01-05 18:41:46 +00:00
- :bomb: [BREAKING] Refactored `reconstruct` function to use `Haplotype` 's reference sequence ([#30](https://github.com/BioJulia/SequenceVariation.jl/pull/30))
2023-01-04 17:13:38 +00:00
### Removed
- Windows and MacOS CI tests ([#28](https://github.com/BioJulia/SequenceVariation.jl/pull/28))
## [0.1.4] - 2022-12-17
2022-11-22 16:28:01 +00:00
2022-12-06 17:26:44 +00:00
### 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))
2023-01-04 17:13:38 +00:00
## [0.1.3] - 2022-11-22
2022-12-17 22:49:01 +00:00
2023-01-04 17:13:38 +00:00
### Changed
2022-12-17 22:49:01 +00:00
- Variations getter now returns type-parameterized vector ([#23](https://github.com/BioJulia/SequenceVariation.jl/pull/23))
2022-10-04 16:48:33 +00:00
## [0.1.2] - 2022-10-04
2023-01-04 17:13:38 +00:00
### Changed
2022-10-04 16:32:11 +00:00
- Updated dependency compats ([#21](https://github.com/BioJulia/SequenceVariation.jl/pull/21))
- BioAlignments: 2 -> 2,3
- BioSequences: 2 -> 2,3
- BioSymbols: 4 -> 4,5
2022-07-21 12:59:47 +00:00
## [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
2022-07-05 15:53:34 +00:00
### 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`
2022-07-13 21:52:11 +00:00
- Methods to get reference and alternate bases from a `Variation`
2022-07-05 15:53:34 +00:00
2022-12-17 22:49:01 +00:00
[unreleased]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.4...HEAD
[0.1.4]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.3...v0.1.4
2022-11-22 17:58:16 +00:00
[0.1.3]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.2...v0.1.3
2022-10-04 16:48:33 +00:00
[0.1.2]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.1...v0.1.2
2022-07-21 12:59:47 +00:00
[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
