rs-abPOA

Rust bindings for the abPOA partial order aligner. Only works under *NIX systems.

Contents

There are two modules in this crate:

• abpoa.rs contains the raw bindings, generated with bindgen
• abpoa_wrapper.rs contains a "Rust-friendly" wrapper to interact with abPOA

Usage

Alignment

let mut aligner = AbpoaAligner::new_with_example_params();

let seqs: Vec<&str> = [
    "CGTCAAT",
    "CCACGTCAAT",
    "CGTCAAT",
    "CGTCAATGCTA",
].to_vec();

let aln = aligner.align_seqs(&seqs);

Consensus

let mut aligner = AbpoaAligner::new_with_example_params();

let seqs: Vec<&str> = [
    "CGTCAAT",
    "CCACGTCAAT",
    "CGTCAAT",
    "CGTCAATGCTA",
].to_vec();

let cons = aligner.consensus_from_seqs(&seqs);

Interacting with abPOA

This crate also provides an abstraction layer over abPOA, that allows for the definition of nodes labelled with seqs of any size.

let mut aligner = AbpoaAligner::new_with_example_params();

// Create this graph: "ACG" -> "AAA"
aligner.add_nodes_edges(&vec!["ACG", "AAA"], &vec![(0, 1)]);

// Align "ACG" to the graph defined above
let res = aligner.align_sequence("ACG");

TODOs

• Raw bindings and wrapper
• Find a more efficient way to abpoa_id -> graph_id
• Build abPOA from source
• Limit unsafe usage