{"id":18543264,"url":"https://github.com/jackh726/bigtools","last_synced_at":"2026-02-13T09:37:18.935Z","repository":{"id":161723567,"uuid":"182300329","full_name":"jackh726/bigtools","owner":"jackh726","description":"A high-performance BigWig and BigBed library in 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Bigtools \u003ca href=\"https://github.com/jackh726/bigtools\"\u003e\u003cimg align=\"right\" src=\"https://github.com/jackh726/bigtools/raw/master/assets/bigtools-logo.svg\" height=\"38\"\u003e\u003c/img\u003e\u003c/a\u003e\n\n[![License](https://img.shields.io/badge/license-MIT-green)](https://github.com/jackh726/bigtools/blob/master/LICENSE)\n[![Paper](https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtae350-blue)](https://doi.org/10.1093/bioinformatics/btae350)\n[![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.10606493.svg)](https://doi.org/10.5281/zenodo.10606493)\n\n\u003ctable\u003e\n    \u003ctr\u003e\n        \u003ctd\u003eRust, CLI\u003c/td\u003e\n        \u003ctd\u003e\n            \u003ca href=\"https://crates.io/crates/bigtools\"\u003e\n                \u003cimg src=\"https://img.shields.io/crates/v/bigtools.svg\" alt=\"crates.io\"\u003e\n            \u003c/a\u003e\n            \u003ca href=\"https://bioconda.github.io/recipes/bigtools/README.html\"\u003e\n                \u003cimg src=\"https://img.shields.io/conda/vn/bioconda/bigtools.svg?color=green\" alt=\"bigtools on Bioconda\"\u003e\n            \u003c/a\u003e\n            \u003ca href=\"https://docs.rs/bigtools\"\u003e\n                \u003cimg src=\"https://img.shields.io/docsrs/bigtools/latest?label=docs.rs\" alt=\"Rust Docs\"\u003e\n            \u003c/a\u003e\n        \u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003ePython\u003c/td\u003e\n        \u003ctd\u003e\n            \u003ca href=\"https://pypi.org/project/pybigtools/\"\u003e\n                \u003cimg src=\"https://img.shields.io/pypi/v/pybigtools?color=orange\" alt=\"PyPI\"\u003e\n            \u003c/a\u003e\n            \u003ca href=\"https://bioconda.github.io/recipes/pybigtools/README.html\"\u003e\n                \u003cimg src=\"https://img.shields.io/conda/vn/bioconda/pybigtools?color=green\" alt=\"pybigtools on Bioconda\"\u003e\n            \u003c/a\u003e\n            \u003ca href=\"https://bigtools.readthedocs.io/\"\u003e\n                \u003cimg src=\"https://img.shields.io/readthedocs/bigtools/latest?label=docs\" alt=\"Python Docs\"\u003e\n            \u003c/a\u003e\n        \u003c/td\u003e\n    \u003c/tr\u003e\n\u003c/table\u003e\n\nBigtools is a library and associated tools for reading and writing bigwig and bigbed files.\n\nThe primary goals of the project are to be\n- Performant\n- Extensible\n- Modern\n\n### Performant\n\nBigtools 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.\n\n### Extensible\n\nBigtools 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. A number of binaries are available that parallel related existing binaries from [UCSC](https://hgdownload.soe.ucsc.edu/admin/exe/), with drop-in compatibility for the most common flags.\n\n### Modern\n\nBigtools 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`.\n\n## Library\n\nTo use `bigtools` in your Rust project, add `bigtools` to your `Cargo.toml` or run:\n\n```sh\ncargo add bigtools\n```\n\nSee the `bigtools` 🦀 [Documentation](https://docs.rs/bigtools).\n\n### Example\n\n```rust,norun\nuse bigtools::bbiread::BigWigRead;\n\nlet mut reader = BigWigRead::open(\"test.bigWig\").unwrap();\nlet chr1 = reader.get_interval(\"chr1\", 0, 10000).unwrap();\nfor interval in chr1 {\n    println!(\"{:?}\", interval);\n}\n```\n\n## Binaries\n\nThe `bigtools` CLI binaries can be installed through [crates.io](https://crates.io/crates/bigtools) or [conda](https://anaconda.org/bioconda/bigtools/).\n\n```sh\ncargo install bigtools\n```\n\n```sh\nconda install -c bioconda bigtools\n```\n\nAdditionally, pre-built binaries can be downloaded through [Github releases](https://github.com/jackh726/bigtools/releases).\n\nThe following binaries are available:\n\n|binary|description|\n| ---- | ----- |\n|bigtools|Provides access to multiple subcommands, including all below|\n|bedgraphtobigwig|Writes a bigWig from a given bedGraph file|\n|bedtobigbed|Writes a bigBed from a given bed file|\n|bigbedinfo|Shows info about a provided bigBed|\n|bigbedtobed|Writes a bed from the data in a bigBed|\n|bigwigaverageoverbed|Calculate statistics over the regions of a bed file using values from a bigWig|\n|bigwiginfo|Shows info about a provided bigWig|\n|bigwigmerge|Merges multiple bigWigs, outputting to either a new bigWig or a bedGraph|\n|bigwigtobedgraph|Writes a bedGraph from the data in a bigWig|\n|bigwigvaluesoverbed|Get the per-base values from a bigWig over the regions of a bed file using values|\n\nRenaming the `bigtools` binary to any of the subcommands (case-insensitive) allows you to run that subcommand directly.\n\n## Python wrapper\n\nThe `pybigtools` package is a Python wrapper written using [`PyO3`](https://pyo3.rs/). It can be installed or used as a dependency either through [PyPI](https://pypi.org/project/pybigtools/) or [conda](https://anaconda.org/bioconda/pybigtools/).\n\n```sh\npip install pybigtools\n```\n\n```sh\nconda install -c bioconda pybigtools\n```\n\nSee the `pybigtools` 🐍 [API Documentation](https://bigtools.readthedocs.io/en/latest).\n\n## How to build from source\n\nIn order to build the bigtools binaries, you can run\n\n```\ncargo build --release\n```\n\nand the binaries can be found in `target/release/`.\n\nOtherwise, you can install the binaries from source by running\n\n```\ncargo install --path bigtools/\n```\n\nBuilding the python wheels for pybigtools requires [maturin](https://pypi.org/project/maturin/). To build the pybigtools wheel for installation (and install), you can run\n\n```\nmaturin build --release -m pybigtools/Cargo.toml\npip install target/wheels/pybigtools*.whl\n```\n\nor\n\n```\nmaturin develop --release -m pybigtools/Cargo.toml\n```\n\n## Benchmarks\n[Benchmarks]: #Benchmarks\n\nBenchmarks are included in the `./bench` directory. They require `python` to run.\n\nMultiple tools are compared against the comparable UCSC tools. For completeness, both single-threaded and multi-threaded (when available) benchmarks are included. Multiple different configuration options are benchmarked across multiple replicates, but a summar is available in the table below:\n\n\u003cimg src=\"https://github.com/jackh726/bigtools/raw/master/assets/bigtools-bench.png\"\u003e\u003c/img\u003e\u003c/a\u003e\n\n## How to cite\n\nThis repository contains contains a `CITATION.cff` file with citation information. Github allows you to get a citation in either APA or BibTeX format; this is available in \"Cite this repository\" under About.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjackh726%2Fbigtools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjackh726%2Fbigtools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjackh726%2Fbigtools/lists"}