Crate block_aligner

SIMD-accelerated library for computing global and X-drop affine gap sequence alignments using an adaptive block-based algorithm.

Currently, AVX2 and WASM SIMD are supported.

Example

use block_aligner::scan_block::*;
use block_aligner::scores::*;
use block_aligner::cigar::*;

let block_size = 16;
let gaps = Gaps { open: -2, extend: -1 };
let r = PaddedBytes::from_bytes::<NucMatrix>(b"TTAAAAAAATTTTTTTTTTTT", block_size);
let q = PaddedBytes::from_bytes::<NucMatrix>(b"TTTTTTTTAAAAAAATTTTTTTTT", block_size);

// Align with traceback, but no x drop threshold.
let a = Block::<_, true, false>::align(&q, &r, &NW1, gaps, block_size..=block_size, 0);
let res = a.res();

assert_eq!(res, AlignResult { score: 7, query_idx: 24, reference_idx: 21 });
assert_eq!(a.trace().cigar(res.query_idx, res.reference_idx).to_string(), "2M6I16M3D");

When building your code that uses this library, it is important to specify the correct flags to turn on specific target features that this library uses.

For x86 AVX2:

RUSTFLAGS="-C target-cpu=native" cargo build --release

or

RUSTFLAGS="-C target-feature=+avx2" cargo build --release

For WASM SIMD:

RUSTFLAGS="-C target-feature=+simd128" cargo build --target=wasm32-wasi --release

Modules

cigar

scan_block

scores

simulate

Constants

L

Number of 16-bit lanes in a SIMD vector.