# parasail-rs
 [](https://docs.rs/parasail-rs/latest/parasail-rs/index.html) 
This crate provides safe Rust bindings and a wrapper to [parasail](https://github.com/jeffdaily/parasail/tree/master), a SIMD pairwise sequence alignment C library. Note that this crate is still under development and is unstable.
## Usage
### Installation
Run the following Cargo command in your project directory:
```bash
cargo add parasail-rs
```
Note that parasail-rs depends on libparasail-sys which will either use an already installed system parasail library or build from source. For more information, please see [libparasail-sys](https://github.com/nsbuitrago/libparasail-sys).
### Examples
#### Basic usage:
For one-off alignments:
```rust
use parasail_rs::{Aligner};
let query = b"ACGT";
let reference = b"ACGT";
let aligner = Aligner::new().build();
aligner.align(Some(query), reference);
```
Using query profile:
```rust
use parasail_rs::{Matrix, Aligner, Profile};
let query = b"ACGT";
let ref_1 = b"ACGTAACGTACA";
let ref_2 = b"TGGCAAGGTAGA";
let use_stats = true;
let query_profile = Profile::new(query, use_stats, Matrix::default());
let aligner = Aligner::new()
.profile(query_profile, 5, 2, "striped")
.semi_global()
.build();
let result_1 = aligner.align(None, ref_1);
let result_2 = aligner.align(None, ref_2);
```
## Contributing
Contributions are more than welcome. Please open an issue or send an email to nsb5 [at] rice.edu for any feedback or questions.
## Citations
If needed, please cite the following paper:
[Daily, Jeff. (2016). Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments. BMC Bioinformatics, 17(1), 1-11. doi:10.1186/s12859-016-0930-z](https://doi.org/10.1186/s12859-016-0930-z)
## License
parasail-rs and libparasail-sys are licensed under the BSD-3-Clause license. The original parasail C library is licensed under a similar Battelle style BSD license.
Nicolas S. Buitrago \<nsb5 [at] rice.edu\>