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
|
/// Include the generated bindings into a separate module.
#[allow(non_upper_case_globals)]
#[allow(non_snake_case)]
#[allow(non_camel_case_types)]
#[allow(unused)]
mod wfa {
include!(concat!(env!("OUT_DIR"), "/bindings_wfa.rs"));
}
/// Compute the affine alignment score between `a` and `b` with the given substitution,
/// gap-open, and gap-extend penalties.
fn linear_score(a: &[i8], b: &[i8], sub: i32, indel: i32) -> i32 {
unsafe {
let mut attributes = wfa::wavefront_aligner_attr_default;
// Do not use a heuristic (enabled by default).
attributes.heuristic.strategy = wfa::wf_heuristic_strategy_wf_heuristic_none;
// Only compute the score (not a path).
attributes.alignment_scope = wfa::alignment_scope_t_compute_score;
// Set the cost model and parameters.
attributes.distance_metric = wfa::distance_metric_t_gap_affine;
attributes.affine_penalties.mismatch = mismatch as i32;
attributes.affine_penalties.gap_opening = gap_open as i32;
attributes.affine_penalties.gap_extension = gap_extend as i32;
// Initialize the aligner object.
// This should be reused for multiple queries.
let wf_aligner = wfa::wavefront_aligner_new(&mut attributes);
// Do the alignment.
let status = wfa::wavefront_align(
wf_aligner,
a.as_ptr(),
a.len() as i32,
b.as_ptr(),
b.len() as i32,
);
assert_eq!(status, 0);
let score = (*wf_aligner).cigar.score;
// Clean up memory.
wfa::wavefront_aligner_delete(wf_aligner);
score
}
}
|
