Readfish-summarise

Features added
HTML output
With the addition of the `readfish-summarise fastq` `--html` flag, an HTML table version of the output will be written to the given filepath. This is disabled by default.

Example:

Bugs fixed
https://github.com/LooseLab/readfish/issues/285
Will catch a KeyError when looking up a channel number greater than the number of channels the Conf was initialised with (default 512), and suggest to set the `--prom` flag.

**Full Changelog**: https://github.com/Adoni5/ReadfishSummarise/compare/v0.2.4...v0.2.5

Changes:
- Demultiplexing now happens in Rust
- All demultiplexed FASTQ is now gzipped

**Full Changelog**: https://github.com/Adoni5/ReadfishSummarise/compare/v0.2.2...v0.2.3

Features:
1. Progress bar using `alive_progress` https://github.com/rsalmei/alive-progress/tree/main
1. `--csv/--no-csv` to optionally output summary CSV
1. The default CSV name is {condition/contig}_readfish_stats.csv, with a different prefix providable by passing a `csv_prefix` to `print_summary()`

**Full Changelog**: https://github.com/Adoni5/ReadfishSummarise/compare/v0.2.1...v0.2.2

Features
1. Only map with `map-ont` preset irrespective of what was in the TOML file. This is due to the `map-ont` parameters being good defaults for long reads, which _sequenced_ reads may well be.
Bug fixes
1. Doesn't create empty fastq files for the fastq demultiplex if `--no-demultiplex` has been specified.

**Full Changelog**: https://github.com/Adoni5/ReadfishSummarise/compare/v0.2.0...v0.2.1

New features
1. De-multiplex FASTQ reads into `condition.name`_`action.name`.fastq files.
1. has click based CLI interface
1. Median and N50 correctly reported on condition summaries
1. Paf files written out as alignments are performed.
1. Correctly handles promethion flag now

**Full Changelog**: https://github.com/Adoni5/ReadfishSummarise/compare/v0.1.1...v0.2.0

1. Includes now N50 and Median for Contig summaries
1. Includes Unmapped read counts in Condition and Contig Summaries
1. More tests and CI

See man driving a german whipp 🍨

**Full Changelog**: https://github.com/Adoni5/ReadfishSummarise/compare/v0.1...v0.2