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/rust-bio/rust-htslib.git
ensuring that the HTSlib submodule is fetched, too. If you only want to use the library, there is no need to clone the repository. Go on to the Usage section in this case.
- Homepage: https://github.com/rust-bio/rust-htslib
- API documentation: https://docs.rs/rust-htslib
- Continuous integration tests: https://travis-ci.org/rust-bio/rust-htslib
To use Rust-HTSlib in your Rust project, import the crate from your source code:
extern 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 regionLicensed under the MIT license http://opensource.org/licenses/MIT. This project may not be copied, modified, or distributed except according to those terms.
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