# Changelog

All notable changes to HapLink.jl 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]

### Added
- Added BAM.Reader index support for BAI object ([#56](https://github.com/BioJulia/XAM.jl/pull/56/files))
- Added doi badge

### Changed

- Subtype from XAMReader and XAMWriter from common abstract types.
- Subtype from XAMRecord.
- Unified flag queries.

## [0.3.1]

### Changed

- Upgraded to BioAlignments v3 ([#55](https://github.com/BioJulia/XAM.jl/pull/55))

## [0.3.0] - 2022-10-10

## Added

- Crosschecks for SAM and BAM ([#29](https://github.com/BioJulia/XAM.jl/pull/29))
- Improved documentation for flags ([#43](https://github.com/BioJulia/XAM.jl/pull/43))

### Changed

- `BAM.quality` performance improved ([#21](https://github.com/BioJulia/XAM.jl/issues/21))
- Updated BioAlignments to v2.2 and BioSequences to v3 ([#48](https://github.com/BioJulia/XAM.jl/pull/48))

### Fixed

- `BAM.Record` layout now matches the BAM specs ([#26](https://github.com/BioJulia/XAM.jl/pull/26))

[Unreleased]: https://github.com/BioJulia/XAM.jl/compare/v0.3.1...HEAD
[0.3.1]: https://github.com/BioJulia/XAM.jl/compare/v0.3.0...v0.3.1
[0.3.0]: https://github.com/BioJulia/XAM.jl/compare/v0.2.8...v0.3.0