bsalign_sys 0.4.0

Rust bindings for the bsalign C library
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55

# bsalign-rs

A rust binding for the [bsalign](https://github.com/ruanjue/bsalign) library.

## Install

```bash
cargo install bsalign
```

## Pairwise sequence alignment

```rust
use bsalign::pairwise::{BsPairwirseAligner, BsPairwiseParam};

fn main() {
    let seq = "ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT";
    let param = BsPairwiseParam::default().set_ksize(4);
    let mut aligner = BsPairwirseAligner::new(param);
    let result = aligner.align_banded_striped_8bit(&seq, &seq);
    assert_eq!(result.aln, qseq.len() as i32);
    let alnstr = result.to_string();
    println!(
        "{}\n{}\n{}",
        alnstr.tseq().to_string(),
        alnstr.alignment().to_string(),
        alnstr.qseq().to_string(),
    );
    println!("Alignment result: {}", result);
}
```

## Multiple sequence alignment

```rust
use bsalign::{
    BitSeq,
    poa::{BsPoaAligner, BsPoaParam},
};

fn main() {
    let param = BsPoaParam::default();
    let mut poa = BsPoaAligner::new(param);
    let seq = "ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT";
    poa.add_sequence(seq);
    poa.add_sequence(seq);
    poa.add_sequence(seq);
    poa.align();

    let consensus = poa.get_consensus();
    let bitseq: BitSeq = consensus.into();
    let consensus = bitseq.to_string();
    println!("Consensus: {}", consensus);
}
```