bam is a crate that allows to read and write BAM and BGZIP files, written completely in Rust.

Why?

Having a crate written completely in Rust reduces the number of dependencies and compilation time. Additionally, it removes the need to install additional C libraries.

Errors produced by this crate are more readable and easier to catch and fix on-the-fly.

Overview

Currently, there are three readers and two writers: * bam::IndexedReader - fetches records from random genomic regions. * bam::BamReader - reads a BAM file consecutively. * bam::SamReader - reads a SAM file consecutively. * bam::BamWriter - writes a BAM file. * bam::SamWriter - writes a SAM file.

BAM readers and writers have single-thread and multi-thread modes.

You can use bgzip module to interact directly with bgzip files (BGZF).

The crate also allows to conviniently work with SAM/BAM records and their fields, such as CIGAR or tags.

Usage

The following code would load BAM file in.bam and its index in.bam.bai, take all records from 3:600001-700000 and print them on the stdout.

```rust extern crate bam;

use std::io; use bam::RecordWriter;

fn main() { let mut reader = bam::IndexedReader::frompath("in.bam").unwrap(); let output = io::BufWriter::new(io::stdout()); let mut writer = bam::SamWriter::build() .writeheader(false) .from_stream(output, reader.header().clone()).unwrap();

for record in reader.fetch(2, 600_000, 700_000).unwrap() {
    let record = record.unwrap();
    writer.write(&record).unwrap();
}

} ```

You can find more detailed usage here.

Changelog

You can find changelog here.

Future versions

Issues

Please submit issues here or send them to timofey.prodanov[at]gmail.com.