Crates.io Crates.io Crates.io Travis

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/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.

Resources

Usage

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

rust extern crate htslib; use htslib::bam;

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

```rust 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

Contributors

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.