Bigtools

Bigtools is a library and associated tools for reading and writing bigwig and bigbed files.

The primary goals of the project are to be

Performant
Extensible
Modern

Performant

Bigtools uses async/await internally to allow for efficient, multi-core computation when possible. In addition, tools are optimized for minimal memory usage. See Benchmarks for more details.

Extensible

Bigtools is designed to be as modular as possible. This, in addition to the safety and reliability of Rust, allows both flexibility and correctness as a library. In addition, its extremely easy to quickly create new tools or binaries.. (TODO: mention python wrapper)

Modern

Bigtools is written in Rust and published to crates.io, so binaries can be installed with cargo install bigtools or it can be used as a library by simply including it in your cargo.toml.

Library

Example

use bigtools::bbiread::BigWigRead;

let mut reader = BigWigRead::open("test.bigWig").unwrap();
let chr1 = reader.get_interval("chr1", 0, 10000).unwrap();
for interval in chr1 {
    println!("{:?}", interval);
}

Binaries

TODO

Benchmarks

Benchmarks are included in the ./bench directory. The require python to run.

Multiple tools are compared against the comparable UCSC tools. For completeness, both single-threaded and multi-threaded (when available) benchmarks are included.

TODO: include image of benchmarks

anderspitman / bigtools