https://github.com/andreaguarracino/lib_wfa2
Rust bindings for the WFA2-lib
https://github.com/andreaguarracino/lib_wfa2
Last synced: 3 months ago
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Rust bindings for the WFA2-lib
- Host: GitHub
- URL: https://github.com/andreaguarracino/lib_wfa2
- Owner: AndreaGuarracino
- Created: 2025-02-20T10:14:33.000Z (3 months ago)
- Default Branch: main
- Last Pushed: 2025-02-26T09:48:55.000Z (3 months ago)
- Last Synced: 2025-02-26T10:36:54.980Z (3 months ago)
- Language: Rust
- Size: 34.2 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# lib_wfa2
Rust binding for [WFA2-lib](https://github.com/smarco/WFA2-lib), with support for both affine gap and dual-cost gap-affine penalties.
## Building
To use `lib_wfa2` in `your project`, you need to build `WFA2-lib` first:
```shell
git clone https://github.com/smarco/WFA2-lib
cd WFA2-lib
make clean all
```
and then:
```bash
# Point to your pre-built WFA2-lib directory
export WFA2LIB_PATH="/path/to/WFA2-lib"
# Build your project
git clone
cd
cargo build --release
```
## Examples
With affine gap penalties:
```rust
use lib_wfa2::affine_wavefront::AffineWavefronts;
pub fn main() {
let aligner = AffineWavefronts::default();
// pattern means query and text means reference
let pattern = b"TCTTTACTCGCGCGTTGGAGAAATACAATAGT";
let text = b"TCTATACTGCGCGTTTGGAGAAATAAAATAGT";
aligner.align(pattern, text);
println!("Pattern: {}", String::from_utf8_lossy(pattern));
println!("Text: {}\n", String::from_utf8_lossy(text));
println!("Score: {}", aligner.score());
println!("Cigar: {}", String::from_utf8_lossy(aligner.cigar()));
}
```
With dual-cost gap-affine penalties:
```rust
use lib_wfa2::affine_wavefront::AffineWavefronts;
pub fn main() {
// Create an aligner with affine2p penalties.
let aligner = AffineWavefronts::with_penalties_affine2p(0, 6, 4, 2, 12, 1);
// pattern means query and text means reference
let pattern = b"TCTTTACTCGCGCGTTGGAGAAATACAATAGT";
let text = b"TCTATACTGCGCGTTTGGAGAAATAAAATAGT";
aligner.align(pattern, text);
println!("Pattern: {}", String::from_utf8_lossy(pattern));
println!("Text: {}\n", String::from_utf8_lossy(text));
println!("Score: {}", aligner.score());
println!("Cigar: {}", String::from_utf8_lossy(aligner.cigar()));
}
```
Setting heuristics:
```rust
use lib_wfa2::affine_wavefront::{AffineWavefronts, HeuristicStrategy};
pub fn main() {
let mut aligner = AffineWavefronts::default();
aligner.set_heuristic(&HeuristicStrategy::BandedStatic { band_min_k: -1, band_max_k: 1 });
// pattern means query and text means reference
let pattern = b"TCTTTACTCGCGCGTTGGAGAAATACAATAGT";
let text = b"TCTATACTGCGCGTTTGGAGAAATAAAATAGT";
let _status = aligner.align(pattern, text);
println!("Pattern: {}", String::from_utf8_lossy(pattern));
println!("Text: {}\n", String::from_utf8_lossy(text));
println!("Score: {}", aligner.score());
println!("Cigar: {}", String::from_utf8_lossy(aligner.cigar()));
}
```