small-bwt 0.2.0

BWT construction in small space
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# BWT construction in small space

![](https://github.com/kampersanda/small-bwt/actions/workflows/rust.yml/badge.svg)
[![Documentation](https://docs.rs/small-bwt/badge.svg)](https://docs.rs/small-bwt)
[![Crates.io](https://img.shields.io/crates/v/small-bwt.svg)](https://crates.io/crates/small-bwt)

This is a Rust implementation of the BWT construction algorithm in small space,
described in Algorithm 11.8 of the book:
[Compact Data Structures - A Practical Approach](https://users.dcc.uchile.cl/~gnavarro/CDSbook/),
Gonzalo Navarro, 2016.

Given a typical text, it runs in $O(n \log n \log \log n)$ time and $O(n)$ additional bits of space,
where $n$ is the length of the input string and the alphabet size is much smaller than $n$.
See the book for more details.

## Documentation

https://docs.rs/small-bwt/

## Command line tool

`tools` provides a command line tool to construct the BWT of a file.

```shell
$ cargo run --release -p tools -- -i input.txt -o output.bwt -t
```

With a desktop PC (Intel i7, 16 GB), the DNA text of size 385 MiB from [Pizza&Chili Corpus](http://pizzachili.dcc.uchile.cl/texts.html)
was transformed in 6.8 minutes using maximum resident set size of 727 MiB.

## Benchmarks

`benches` provides benchmarks on the time performance for English texts
extracted from [Pizza&Chili Corpus](http://pizzachili.dcc.uchile.cl/texts.html).

```shell
$ cargo bench
```

## Licensing

This library is licensed under either of

 * Apache License, Version 2.0
   ([LICENSE-APACHE](LICENSE-APACHE) or http://www.apache.org/licenses/LICENSE-2.0)
 * MIT license
   ([LICENSE-MIT](LICENSE-MIT) or http://opensource.org/licenses/MIT)

at your option.

`benches/english.10MB.zst` is extracted from [Pizza&Chili Corpus](http://pizzachili.dcc.uchile.cl/texts.html) and follows [LGPL License](https://www.gnu.org/licenses/lgpl-3.0.html).