Rust-bwa is a Rust wrapper of the BWA api from 10x Genomics, further modified by kgori (https://github.com/kgori/rust-bwa). Pass read-pair information or a vector of seq_io fastq records in, and get Rust-htslib BAM records back. Get started quickly with default settings & a reasonable paired-end model. See docs for more details on customing parameters or the paired-end model.
extern crate bwa;
extern crate seq_io;
use bwa::BwaAligner;
use seqio::fastq
fn main() {
let bwa = BwaAligner::from_path(&"tests/test_ref.fa").unwrap();
let r1 = b"GATGGCTGCGCAAGGGTTCTTACTGATCGCCACGTTTTTACTGGTGTTAATGGTGCTGGCGCGTCCTTTAGGCAGCGGG";
let q1 = b"2222222222222222222222222222222222222222222222222222222222222222222222222222222";
let r2 = b"TGCTGCGTAGCAGATCGACCCAGGCATTCCCTAGCGTGCTCATGCTCTGGCTGGTAAACGCACGGATGAGGGCAAAAAT";
let q2 = b"2222222222222222222222222222222222222222222222222222222222222222222222222222222";
let (r1_alns, _r2_alns) = bwa.align_read_pair(b"read_name", r1, q1, r2, q2).unwrap();
println!("r1 mapping -- tid: {}, pos: {}", r1_alns[0].tid(), r1_alns[0].pos());
let fastq = b"@id1
GATGGCTGCGCAAGGGTTCTTACTGATCGCCACGTTTTTACTGGTGTTAATGGTGCTGGCGCGTCCTTTAGGCAGCGGG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@id2
TGCTGCGTAGCAGATCGACCCAGGCATTCCCTAGCGTGCTCATGCTCTGGCTGGTAAACGCACGGATGAGGGCAAAAAT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII";
// collect vector of seqio::fastq records
let mut reader = fastq::Reader::new(&fastq[..]);
let seqs = reader.records().collect::<Result<Vec<_>, _>>().unwrap();
let alns = bwa.align_fastq_records(&seqs, /* paired */ false).unwrap();
println!("mapping id1 -- tid: {}, pos: {}", alns[0].tid(), alns[0].pos());
println!("mapping id2 -- tid: {}, pos: {}", alns[1].tid(), alns[1].pos());
}
Pre-built rust bindings were generated using bindgen for linux using the command:
cd bwa-sys
bindgen \
--no-doc-comments \
--allowlist-function mem_align1_core \
--allowlist-function mem_sam_pe \
--allowlist-function mem_opt_init \
--allowlist-function bwa_idx_build \
--allowlist-function bwa_idx_load \
--allowlist-function bwa_idx_destroy \
--allowlist-function mem_process_seq_pe \
--allowlist-function mem_process_seqs \
--allowlist-function bwa_fill_scmat \
--allowlist-var "BWA_IDX_.*" \
--allowlist-var "MEM_F_.*" \
wrapper.h \
-o src/lib.rs
bindgen can be installed using cargo install bindgen-cli. See the documentation here.
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