COOLER(1)

💖 COOLER(1) — the manual, but make it slay 💖

okay bestie, gather round — this is the manual page for cooler, a User Command. Yes it's a real page in section 1. Yes it's about genomics. Yes it's iconic. Let's go. 🦋

✨ NAME ✨

cooler — sparse, compressed, binary persistent storage. that's the whole vibe. storage. but make it fancy. 💅

🎀 SYNOPSIS 🎀

cooler [OPTIONS] COMMAND [ARGS]...

that's it. that's the shape of it. options, then a command, then whatever args that command wants. periodt. ⭐

🌸 DESCRIPTION 🌸

So Cooler is a support library for a sparse, compressed, binary persistent storage format — and the format is also called cooler, which, honestly? naming your format after yourself is main character energy and I respect it. 👑

It's used to store genomic interaction data, like Hi-C contact matrices. Yep. Big genome-y matrices. Very demure, very mindful. 🧚

The cooler file format is an implementation of a genomic matrix data model using HDF5 as the container format. And the cooler package ships with a suite of command line tools and a Python API, so you can create, query, and manipulate cooler files however you like. it's giving full-service. it's giving "we do it all". 🔥

✨ OPTIONS ✨

• -v, --verbose — Verbose logging. she talks more. we love a chatty queen. 🗣️
• -d, --debug — On error, drop into the post-mortem debugger shell. yes bestie, when it breaks you get yeeted straight into the debugger to do a little forensic investigation. 💀
• -V, --version — Show the version and exit. quick peek, then she's gone. 🙈
• -h, --help — Show this message and exit. the classic. the icon. the moment. 🎀

🌈 Commands: 🌈

okay this is the main event. the whole roster. every single one of them, no skips:

• cload — Create a cooler from genomic pairs and bins. ✨
• load — Create a cooler from a pre-binned matrix. already binned, we're just loading, no cap. 🍓
• merge — Merge multiple coolers with identical axes. the axes gotta match tho, fr fr. 🤝
• coarsen — Coarsen a cooler to a lower resolution. she's going low-res. downsizing era. 💅
• zoomify — Generate a multi-resolution cooler file by coarsening. multi-res, because one resolution was never enough for her. 👑
• balance — Out-of-core matrix balancing. balancing the matrix without needing all the RAM. iconic behaviour. ⚖️
• info — Display a cooler's info and metadata. the tea. the lore. 🫖
• dump — Dump a cooler's data to a text stream. just spilling everything into text. no filter. 😭
• show — Display and browse a cooler in matplotlib. pretty pictures!! visually stunning!! 🌈
• makebins — Generate fixed-width genomic bins. same width every time. consistent queen. 📏
• digest — Generate fragment-delimited genomic bins. fragments, not fixed widths. different energy. 🧬
• csort — Sort and index a contact list. put it in order and index it, bestie. 🗂️
• ls — List all coolers inside a file. who's in there?? show me everyone. 👀
• cp — Copy a cooler from one file to another or within the same file. dupe it wherever, even in place. 💖
• ln — Create a hard link to a cooler (rather than a true copy) in the... heads up, the original description literally trails off right there with an ellipsis — I'm not finishing that sentence for you, that's not my business and it's not in the source. 🙈
• mv — Rename a cooler within the same file. same file only!! she's not moving house, just changing her name. 💅
• tree — Display a file's data hierarchy. the whole family tree. 🌳
• attrs — Display a file's attribute hierarchy. the attributes version of that tree. ✨

💜 AUTHOR 💜

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</purgle>

okay tiny correction — that's Andreas Tille, Debian distribution, and yes, it can be used for any other usage of the program. shoutout to Andreas, an absolute legend, we thank him for his service. 🫶

and that's the page, bestie!! this whole thing is from cooler 0.8.7, dated June 2020, living in section COOLER(1) of the manual. go forth and store your sparse compressed binary data, you gorgeous genius. slay. 💅✨🎀🦋🌸💖