kractor 4.0.0

Extract reads from a FASTQ file based on taxonomic classification via Kraken2.
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# 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/1.1.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [4.0.0] - 2026-01-26

### Changed

- Summary output now lists identified taxon IDs in `taxons_identified` (replacing `total_taxon_count`)
- Summary output now includes zero entries for identified taxa with no direct assignments in `reads_extracted_per_taxon`

## [3.1.0] - 2025-12-12

### Added

- Attempt to detect headers in kraken report files and skip if it looks like a header. It does this by checking if there
  are 6 fields that are all strings (or more precisely if each field returns an error when parsing into an int/float).
  If so,
  it is assumed that this line is a header and is skipped. A warning message is printed in this case.
- `--no-header-detect` flag to force parsing Kraken reports from the first line without auto-skipping headers, disabling
  the new header detection behaviour described above

### Changed

- Kraken report/output parsing errors now include the line number and o line for easier debugging.

## [4.0.0] - 2026-01-26

### Changed

- Summary output now lists identified taxon IDs in `taxons_identified` (replacing `total_taxon_count`) and includes zero
  entries for identified taxa with no direct assignments in `reads_extracted_per_taxon`.

## [3.0.1] - 2025-10-16

### Fixed

- Prevent a panic when writing to output paths without an extension.

## [3.0.0] - 2025-09-26

### Added

- Able to specifiy taxon ids that are not present, without kractor stopping. These are instead logged to stderr with a
  warning. This may be useful when running kractor in a wrapper script for several fastq files and just want to extract
  a set of taxonids from them all - without caring if they are present or not.
- Include a new field `missing_taxon_ids` in the summary output.

### Changed

- Under the hood refactoring, introducing structs for the processed kraken outputs and processed kraken trees to
  simplify the returned data.

### Fixed

- Unclassified reads being skipped in the tree building stage, meaning they were unable to be extracted

## [2.0.0] - 2025-08-12

### Added

- Added a `reads_extracted_per_taxon` field to to summary report (#28)
- Added a `proportion_extracted` field to summary report (#28)
- Added the version to summary report (#28)
- Added an output format (`fasta` or `fastq`) field to the summary report (#28)
- Added a `--verbose` flag (in addition to the existing `-v`)

### Changed

- Removed `-O` for compression type, now uses `--compression-format` for clarity.
- Removed `-l` for compression level, now uses `--compression-level` for clarity.
- Renamed `--json-report` to `--summary`
- Improved the JSON report format to make it easier to read by removing `Paired` and `Single` fields and instead having
  a simple `total_reads_in` and `total_reads_out` field.

### Fixed

- Removed duplicate log message for taxon IDs identified
- Clippy warnings

## [1.0.1] - 2025-06-28

### Fixed

- Create subdirectories specified in output path if they don't exist (#24)
- Add output validation to prevent overwriting existing files (#25)

## [1.0.0] - 2025-04-16

### Added

- Better error handling with color-eyre (#16)
- Proper panic handling (#16)
- Tests for most functions
- JSON report with accurate read count information (#15)

### Changed

- Keep fastq parsing in bytes instead of converting to String (#17)
- Optimized functions to take `&str` instead of `String` (#21)
- Migrated to crossbeam scoped channels and refactored threading code
- Refactored JSON output and removed lazy_static dependency

### Fixed

- Root node no longer added to tree twice (#22)

## [0.4.0] - 2023-10-06

### Added

- JSON report included in stdout upon successful completion (can be disabled with `--no-json`)

### Changed

- Project renamed

## [0.3.0] - 2023-09-22

### Added

- Support for paired-end files
- Output FASTA file with `--output-fasta` option

### Changed

- Major refactor to use Noodles for fastq parsing
- Switched to Niffler for compression handling
- Streamlined arguments related to compression types/level

### Improved

- Logging functionality

## [0.2.3] - 2023-09-02

### Changed

- Code optimizations

## [0.2.2]

### Added

- `--no-compress` flag to output standard plaintext fastq files
- `--exclude` option to exclude specified reads (works with `--children` and `--parents`)
- Internal documentation (docstrings)

### Improved

- Increased verbosity of user outputs

## [0.2.1]

### Fixed

- Reduced memory usage

## [0.2.0]

### Added

- Automatic detection and handling of gz and plain files
- `--compression` argument to select compression type
- `--children` and `--parents` options to save children and parents based on kraken report

### Changed

- Integrated zlib-ng for faster gzip handling

## [0.1.0]

### Added

- Initial release