HTSlib bindings for Rust

This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.

To clone this repository, issue

git clone --recursive https://github.com/christopher-schroeder/rust-htslib.git

ensuring that the HTSlib submodule is fetched, too.

Usage

To use Rust-HTSlib in your Rust project, import the crate from your source code:

extern crate htslib;
use htslib::bam;

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

let bam = bam::Reader::new("path/to/some.bam");
let out = bam::Writer::with_template("path/to/some.bam", "reversereads.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);
    }
}

Pileups can be performed with

let bam = bam::Reader::new("path/to/some.bam");

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

let bam = bam::IndexedReader::new("path/to/some.bam");

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

Authors

• Christopher Schröder (christopher.schroeder@tu-dortmund.de)
• Johannes Köster (johannes.koester@tu-dortmund.de)

License

Licensed under the MIT license http://opensource.org/licenses/MIT. This project may not be copied, modified, or distributed except according to those terms.