Crate rust_htslib

Rust-HTSlib provides a high level BAM API. Reading and writing BAM files is as easy as

use rust_htslib::bam;
use rust_htslib::bam::Read;

let bam = bam::Reader::new(&"test/test.bam").ok().expect("Error opening bam.");
let mut out = bam::Writer::with_template(&"test/test.bam", &"test/out.bam").ok().expect("Error opening bam.");

// copy reverse reads to new BAM file
for r in bam.records() {
    let record = r.ok().expect("Error reading BAM file.");
    if record.is_reverse() {
        out.write(&record).ok().expect("Error writing BAM file.");
    }
}

Pileups can be performed with

use rust_htslib::bam;
use rust_htslib::bam::Read;

let bam = bam::Reader::new(&"test/test.bam").ok().expect("Error opening bam.");

// pileup over all covered sites
for p in bam.pileup() {
    let pileup = p.ok().expect("Error reading BAM file.");
    println!("{}:{} depth {}", pileup.tid(), pileup.pos(), pileup.depth());

    for alignment in pileup.alignments() {
        match alignment.indel() {
            bam::pileup::Indel::Ins(len) => println!("Insertion of length {}", len),
            bam::pileup::Indel::Del(len) => println!("Deletion of length {}", len),
            _ => println!("Base {}", alignment.record().seq()[alignment.qpos()])
        }
    }
}

In both cases, indexed BAM files can be seeked for specific regions, constraining either the record iterator or the pileups:

use rust_htslib::bam;

let mut bam = bam::IndexedReader::new(&"test/test.bam").ok().expect("Error opening indexed BAM.");

// seek to chr1:50000-100000
let tid = bam.header.tid(b"CHROMOSOME_I").unwrap();
bam.seek(tid, 0, 20).ok().expect("Error seeking BAM file.");
// afterwards, read or pileup in this region

Modules

bam
bcf
htslib
utils