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

```rust,norun 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