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# Changelog
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All notable changes to HapLink.jl will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [Unreleased]
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### Added
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- Added BAM.Reader index support for BAI object ([#56](https://github.com/BioJulia/XAM.jl/pull/56/files))
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- Added doi badge
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### Changed
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- Subtype from XAMReader and XAMWriter from common abstract types.
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- Subtype from XAMRecord.
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- Unified flag queries.
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## [0.3.1]
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### Changed
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- Upgraded to BioAlignments v3 ([#55](https://github.com/BioJulia/XAM.jl/pull/55))
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## [0.3.0] - 2022-10-10
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## Added
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- Crosschecks for SAM and BAM ([#29](https://github.com/BioJulia/XAM.jl/pull/29))
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- Improved documentation for flags ([#43](https://github.com/BioJulia/XAM.jl/pull/43))
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### Changed
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- `BAM.quality` performance improved ([#21](https://github.com/BioJulia/XAM.jl/issues/21))
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- Updated BioAlignments to v2.2 and BioSequences to v3 ([#48](https://github.com/BioJulia/XAM.jl/pull/48))
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### Fixed
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- `BAM.Record` layout now matches the BAM specs ([#26](https://github.com/BioJulia/XAM.jl/pull/26))
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[Unreleased]: https://github.com/BioJulia/XAM.jl/compare/v0.3.1...HEAD
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[0.3.1]: https://github.com/BioJulia/XAM.jl/compare/v0.3.0...v0.3.1
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[0.3.0]: https://github.com/BioJulia/XAM.jl/compare/v0.2.8...v0.3.0
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