# 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).

## [2.1.0](https://github.com/mbhall88/rasusa/compare/2.0.0...2.1.0) (2024-08-19)


### Features

* [aln] add program (`@PG`) entry to header ([0123e54](https://github.com/mbhall88/rasusa/commit/0123e548a70c90fd47200ac5f842f7d844f4bfe3))
* log seed used when --seed not passed ([6e1f37d](https://github.com/mbhall88/rasusa/commit/6e1f37dfe9c2fad606670a15c2de3c2eb667d105))

## [2.0.0](https://github.com/mbhall88/rasusa/compare/1.0.0...2.0.0) (2024-05-03)


### ⚠ BREAKING CHANGES

* paired reads require --output once for each file

### Bug Fixes

* paired reads require --output once for each file ([1427a0b](https://github.com/mbhall88/rasusa/commit/1427a0bd85c1a1b731d23c4b830bbcf7eb49e125))

## [1.0.0](https://github.com/mbhall88/rasusa/compare/0.8.0...1.0.0) (2024-04-29)


### ⚠ BREAKING CHANGES

* move fastq functionality to `reads` subcommand

### Features

* add `cite` command to get citation ([db17612](https://github.com/mbhall88/rasusa/commit/db17612e35d39c2d2b26bebb0b0632de4ade7206))
* add subcommand `aln` to subsample alignments ([b92979a](https://github.com/mbhall88/rasusa/commit/b92979a3165c73c1b40d3661d6dd8ea21099b3e7))
* move fastq functionality to `reads` subcommand ([f48d47b](https://github.com/mbhall88/rasusa/commit/f48d47b5ad26aff767ca52a572f8e442690e5e1c))


### Bug Fixes

* deal with chromosomes with no alignments ([14aa15e](https://github.com/mbhall88/rasusa/commit/14aa15efeed3691adc4cfd20ac0fc4bfb8ec6f87))

## [0.8.0](https://github.com/mbhall88/rasusa/compare/0.7.1...0.8.0) (2024-01-03)


### Features

* add logging message with coverage of input before downsampling ([79445fc](https://github.com/mbhall88/rasusa/commit/79445fc8b40302ed197f8330e61a797b81a47db6))
* support ztsd ([cfa50f8](https://github.com/mbhall88/rasusa/commit/cfa50f8aca00d6e2321ca45ea09579b95da25f7f))
* use default compression level for compression output type ([cfa50f8](https://github.com/mbhall88/rasusa/commit/cfa50f8aca00d6e2321ca45ea09579b95da25f7f))


### Bug Fixes

* update logging so colour not sent to file ([bc62c3f](https://github.com/mbhall88/rasusa/commit/bc62c3fb4db2b9de903440a2d2a9ef9c7a06107f))

## [Unreleased]

## [0.7.1]

### Added

- Install script and support for more binary triple targets

### Changed

- Updated needletail dependecy due to dependency deprecation

## [0.7.0]

### Added

- Fraction (`--frac`) and number (`--num`) options. This allows users to replicate the
  functionality of `seqtk sample` [[#34][34]]

## [0.6.1]

### Added

- Warning if the actual coverage of the file(s) is less than the requested coverage
  [[#36][36]]
- JOSS manuscript

### Changed

- Use `rasusa` as the entry command for docker container [[#35][35]]

## [0.6.0]

### Addedd

- `--bases` option to allow for manually setting the target number of bases to keep
  [[#30][30]]
- `--genome-size` can now take a FASTA/Q index file and the sum of all reference
  sequences will be used as the genome size [[#31][31]]

## [0.5.0]

### Added

- Support for LZMA, Bzip, and Gzip output compression (thanks to
  [`niffler`](https://github.com/luizirber/niffler/)). This is either inferred from the
  file extension or manually via the `-O` option.
- Option to specify the compression level for the output via `-l`

### Changed

- Use a `Vec<bool>` instead of `HashSet` to store the indices of reads to keep. This
  gives a nice little speedup (see [#28][28]), A big thank you to
  [@natir](https://github.com/natir) for this.

### Fixed

- Restore compression of output files [[#27][27]]

## [0.4.2]

### Fixed

- I had stupidly forgetten to merge the fix for [#22][22] onto master 🤦

## [0.4.1]

### Fixes

- Releasing cross-compiled binaries didn't work for version 0.4.0
- Docker image is now correctly built

## [0.4.0]

### Changed

- Switch from using `snafu` and `failure` for error handling to `anyhow` and
  `thiserror`. Based on the procedure outlined in [this excellent blog
  post][error-blog].
- Switched fasta/q parsing to use [needletail](https://github.com/onecodex/needletail)
  instead of rust-bio. See [benchmark] for improvement in runtimes.
- Changed the way Illumina paired reads are subsampled. Previously, there was an
  assumption made that the reads of a pair were both the same length as the R1 read. We
  are now more careful and look at each read's length individually [[#22][22]]
- Moved container hosting to quay.io

## [0.3.0]

Version 0.3.0 may give different results to previous versions. If so, the differences
will likely be a handful of extra reads (possibly none). The reason for this is
`--coverage` is now treated as a float. Previously we immediately round coverage down to
the nearest integer. As the number of reads to keep is based on the target total number
of bases, which is coverage * genome size. So if coverage is 10.7 and genome size is
100, previously our target number of bases would have been 1000, whereas now, it would
be 1070.

### Changed

- `--coverage` is now treated as a `f32` instead of being converted immediately to an
  integer [#19][19].
- Updated `rust-bio` to version 0.31.0. This means `rasusa` now handles wrapped fastq
  files.
- Preallocate fastx records instead of using iterator. Gives marginal speedup.
- Added `bash` to the docker image b47a8b75943098bdd845b7758cf2eab01ef5a3d8

## [0.2.0]

### Added

- Support paired Illumina [#15](https://github.com/mbhall88/rasusa/issues/15)

[0.2.0]: https://github.com/mbhall88/rasusa/releases/tag/0.2.0

[0.3.0]: https://github.com/mbhall88/rasusa/releases/tag/0.3.0

[0.4.0]: https://github.com/mbhall88/rasusa/releases/tag/0.4.0

[0.4.1]: https://github.com/mbhall88/rasusa/releases/tag/0.4.1

[0.4.2]: https://github.com/mbhall88/rasusa/releases/tag/0.4.2

[0.5.0]: https://github.com/mbhall88/rasusa/releases/tag/0.5.0

[0.6.0]: https://github.com/mbhall88/rasusa/releases/tag/0.6.0

[0.6.1]: https://github.com/mbhall88/rasusa/releases/tag/0.6.1

[0.7.0]: https://github.com/mbhall88/rasusa/compare/0.6.1...0.7.0

[0.7.1]: https://github.com/mbhall88/rasusa/compare/0.7.0...0.7.1

[19]: https://github.com/mbhall88/rasusa/issues/19

[22]: https://github.com/mbhall88/rasusa/issues/22

[27]: https://github.com/mbhall88/rasusa/issues/27

[28]: https://github.com/mbhall88/rasusa/pull/28

[30]: https://github.com/mbhall88/rasusa/issues/30

[31]: https://github.com/mbhall88/rasusa/issues/31

[34]: https://github.com/mbhall88/rasusa/issues/34

[35]: https://github.com/mbhall88/rasusa/issues/35

[36]: https://github.com/mbhall88/rasusa/issues/36

[benchmark]: https://github.com/mbhall88/rasusa#benchmark

[error-blog]: https://nick.groenen.me/posts/rust-error-handling/

[unreleased]: https://github.com/mbhall88/rasusa/compare/0.7.0...HEAD