{"id":31913430,"url":"https://github.com/alejandrogzi/packbed","last_synced_at":"2025-10-13T18:49:51.203Z","repository":{"id":257809292,"uuid":"867529522","full_name":"alejandrogzi/packbed","owner":"alejandrogzi","description":"pack a .bed into overlapping 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align=\"center\"\u003e\n  \u003ch1 align=\"center\"\u003e\n    packbed\n  \u003c/h1\u003e\n\n  \u003cp align=\"center\"\u003e\n    \u003ca href=\"https://img.shields.io/badge/version-0.0.1dev-green\" target=\"_blank\"\u003e\n      \u003cimg alt=\"Version Badge\" src=\"https://img.shields.io/badge/version-0.0.1-green\"\u003e\n    \u003c/a\u003e\n    \u003ca href=\"https://crates.io/crates/packbed\" target=\"_blank\"\u003e\n      \u003cimg alt=\"Crates.io Version\" src=\"https://img.shields.io/crates/v/packbed\"\u003e\n    \u003c/a\u003e\n    \u003ca href=\"https://github.com/alejandrogzi/packbed\" target=\"_blank\"\u003e\n      \u003cimg alt=\"GitHub License\" src=\"https://img.shields.io/github/license/alejandrogzi/packbed?color=blue\"\u003e\n    \u003c/a\u003e\n    \u003ca href=\"https://crates.io/crates/packbed\" target=\"_blank\"\u003e\n      \u003cimg alt=\"Crates.io Total Downloads\" src=\"https://img.shields.io/crates/d/packbed\"\u003e\n    \u003c/a\u003e\n  \u003c/p\u003e\n\n\n  \u003cp align=\"center\"\u003e\n    pack a .bed into overlapping components\n  \u003c/p\u003e\n\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n    \u003cimg width=700 align=\"center\" src=\"./.github/assets/img.png\"\u003e\n\u003c/p\u003e\n\n\n## Features\n- pack any number of .bed files into overlapping components through a binary, Rust library or Python module\n- write a unique overlapping-component-colorized bed file out of any number of .bed files through a binary, Rust library or Python module\n- split components into separate .bed files through a binary, Rust library or Python module\n- write serialized components to a binary file through a binary and Rust library\n- read serialized components from a binary file through a Rust library or Python module\n- write specific components each to a different .bed file through a Rust library or Python module\n\n\u003e What's new on packbed v0.0.7!\n\u003e\n\u003e - Implements a new query range algorithm to pack components\n\u003e - Reduces time by more than x25 when working with more than 1 million reads\n\n## Usage\n### Binary\n``` bash\nUsage: packbed [OPTIONS] --bed \u003cPATHS\u003e... --output \u003cPATH\u003e\n\nArguments:\n    -b, --bed \u003cPATHS\u003e...     Paths to BED12 files delimited by comma\n    -o, --output \u003cPATH\u003e      Path to output BED12 file [not required if -c flag is set]\n\nOptions:\n    -t, --threads \u003cTHREADS\u003e  Number of threads [default: 8]\n    --type \u003cTYPE\u003e   Type of output [default: bed] [possible values: bin, comp, bed]\n    --overlap_type \u003cTYPE\u003e  Type of overlap [default: exon]\n    -s, --subdirs   Flag to split components into separate BED files in subdirectories\n    --colorize      Flag to colorize components in output BED(s) file\n    -h, --help      Print help\n    --version:      Print version\n```\n\n\u003e [!TIP]\n\u003e If you want to get components in separate .bed files use:\n\u003e ```bash\n\u003e packbed -b path/to/b1.bed,path/to/b2.bed -o path/to/output --type comp\n\u003e ```\n\u003e in case you want to send each component to a different subdirectory (good to parallelize processes):\n\u003e ```bash\n\u003e packbed -b path/to/b1.bed,path/to/b2.bed -o path/to/output --type comp -s\n\u003e ```\n\u003e if you want to colorize the components but send them all to just 1.bed file [default]:\n\u003e ```bash\n\u003e packbed -b path/to/b1.bed,path/to/b2.bed -o path/to/output --colorize\n\u003e ```\n\n### Library\n``` rust\nuse packbed::packbed;\n\nfn main() {\n\n    let bed1 = PathBuf::new(\"/path/to/b1.bed\");\n    let bed2 = PathBuf::new(\"/path/to/b2.bed\");\n    let beds = vec![bed1, bed2];\n\n    let overlap_type = OverlapType::Exon;\n    let colorize = true;\n\n    let comps: HashMap\u003cString, Vec\u003cVec\u003cArc\u003cGenePred\u003e\u003e\u003e\u003e = packbed(\n        beds,\n        overlap_type,\n        colorize)\n    .unwrap();\n}\n```\n### Python\nbuild the port to install it as a pkg:\n```bash\ngit clone https://github.com/alejandrogzi/packbed.git \u0026\u0026 cd packbed/py-packbed\nhatch shell\nmaturin develop --release\n```\nuse it:\n``` python\nfrom packbed import pack\n\nbeds = [\"path/to/bed1.bed\", \"path/to/bed2.bed\"]\ncomps = pack(beds)\n```\n\n### crate: [https://crates.io/crates/packbed](https://crates.io/crates/packbed)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falejandrogzi%2Fpackbed","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falejandrogzi%2Fpackbed","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falejandrogzi%2Fpackbed/lists"}