jellyfish-reader 0.1.0

# jellyfish-reader

A pure Rust library for reading [Jellyfish](https://github.com/gmarcais/Jellyfish) k-mer counting output files.

## Quick Start

```sh
cargo add jellyfish-reader
```

```rust
use jellyfish_reader::ReadMerFile;

let reader = ReadMerFile::open("output.jf")?;
for result in reader {
    let (mer, count) = result?;
    println!("{}: {}", mer, count);
}
```

## Features

- Sequential reading of binary/sorted and text/sorted Jellyfish 2.x files
- Random-access queries via memory-mapped I/O
- K-mer type (`MerDna`) with canonical form, reverse complement, and comparison
- K-mer extraction from DNA strings (`StringMers`)
- Auto-format detection from file headers
- Pure Rust — no C/C++ dependencies

See [docs/usage/](docs/usage/) for detailed usage guides, API examples, and rationale.

## Compatibility

- Jellyfish **2.x** (current: 2.3.1) — `binary/sorted` and `text/sorted` formats
- Jellyfish 1.x is not supported

## License

MIT — see [LICENSE](LICENSE) for details.

## Acknowledgements

This crate reads files produced by [Jellyfish](https://github.com/gmarcais/Jellyfish), developed by Guillaume Marçais et al. The file format and k-mer encoding are based on the Jellyfish 2.x implementation. See the original repository for the k-mer counting tool itself.

## Author

Trent Zeng ([@trentzz](https://crates.io/users/trentzz)) — dev@trentz.me