https://github.com/feldroop/libsais-rs
Rust bindings to libsais
https://github.com/feldroop/libsais-rs
algortihm bioinformatics string-analysis suffix-array
Last synced: 5 months ago
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Rust bindings to libsais
- Host: GitHub
- URL: https://github.com/feldroop/libsais-rs
- Owner: feldroop
- Created: 2025-08-10T12:06:51.000Z (10 months ago)
- Default Branch: master
- Last Pushed: 2025-08-10T14:08:24.000Z (10 months ago)
- Last Synced: 2025-08-10T14:28:14.511Z (10 months ago)
- Topics: algortihm, bioinformatics, string-analysis, suffix-array
- Language: Rust
- Homepage:
- Size: 17.6 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# libsais-rs
[](https://github.com/feldroop/libsais-rs/actions)
[](https://crates.io/crates/libsais)
[](https://docs.rs/libsais)
An idiomatic and mostly safe API wrapper for the awesome and _very_ fast library [`libsais`] by Ilya Grebnov.
⚠️ **Warning:** this crate is not yet battle-tested, there might be bugs. The API is still subject to small changes. Any kind of feedback and suggestions via the issue tracker is highly appreciated!⚠️
## Functionality
This crate exposes the whole functionality of [`libsais`]. It might be useful to also check out the [documentation of the original library](https://github.com/IlyaGrebnov/libsais).
- Suffix array construction for `u8`/`u16`/`i32`/`i64` texts and `i32`/`i64` output arrays
- Generalized suffix arrays
- Longest common prefix arrays and permuted longest common prefix arrays
- Burrows-Wheeler-Transform and reversal
- Optional multithreading support via the `openmp` feature (enabled by default)
## Usage
This crate provides generic builder-like APIs for the whole functionality listed above. The following is a simple example of how to use this library to construct a suffix array in parallel:
```rust
use libsais::{SuffixArrayConstruction, ThreadCount};
let text = b"barnabasbabblesaboutbananas";
let suffix_array: Vec = SuffixArrayConstruction::for_text(text)
.in_owned_buffer()
.multi_threaded(ThreadCount::openmp_default())
.run()
.expect("The example in the README should really work")
.into_vec();
```
Please consult the [documentation] and the [examples](./examples) for more details on how to use this library.
## Performance and benchmarks
This library only adds a few safety checks, which should not impact performance in a relevant way. A notable exception is the suffix array construction for `i32` and `i64` inputs. Please consult the [documentation](https://docs.rs/libsais/latest/libsais/suffix_array/index.html#large-alphabets) for details.
Below are the results of a small benchmark of suffix array construction algorithms available on [crates.io](https://crates.io). The input was the human genome, truncated to 2 GB. Details about this benchmark can be found [here](https://github.com/feldroop/crates-io-saca-benchmark).
The excellent performance of [`libsais`] is one of the main reasons why this API wrapper crate was created.
[`libsais`]: https://github.com/IlyaGrebnov/libsais
[documentation]: https://docs.rs/libsais/latest/libsais/