MKARV(1)

✨ MKARV(1) ✨

okay so bestie, welcome to the mkarv page, a.k.a. the little tool that Turns ataqv results into a web app 💖 (yes the manual page literally calls it MKARV(1) up top and mkarv down here, we contain multitudes)

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🌸 NAME 🌸

mkarv — Turns ataqv results into a web app 👑

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🦋 DESCRIPTION 🦋

here's the whole invocation, exactly as it comes, no notes:

usage: mkarv [-h] [-c CONCURRENCY] [-d DESCRIPTION] [-f] [-i] [-l]
       [-m MAXIMUM_FRAGMENT_LENGTH] [-p PEAK_REFERENCE] [-r REFERENCE]
       [-t TEMPLATE_DIRECTORY] [-v] [--version] directory [metrics ...]

so the vibe is: you hand it one or more ataqv metrics files in JSON format, and it creates an instance of the ataqv result visualization tool ✨. The web application gets copied into the directory you named, and your JSON results get translated for it. Then you can literally just open the index.html file and load the resulting directory into a web browser locally, or publish it with a web server like Apache or nginx. it's giving "deploy from your bedroom" 🎀

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💅 positional arguments 💅

• directory — The path to the directory where the web app will be created. that's where the whole thing lives, bestie 🏠
• metrics — One or more ataqv metrics files in JSON format. (default: None) so if you pass nothing, it's literally nothing, no cap 🙈

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👑 options 👑

• -h, --help — show this help message and exit. the classic, the icon, the moment 🫶
• -c, --concurrency CONCURRENCY — The number of concurrent processes to use (default: 1). (default: 1) yes it says the default twice, we love a redundancy moment 💀
• -d, --description DESCRIPTION — A description for the viewer instance. (default: None) give your little viewer a little identity 🌈
• -f, --force — Overwrite the output directory if it exists. (default: False) careful bestie, this one does exactly what it says 🔥
• -i, --indent — If indent is given, JSON output will be pretty-printed and indented. (default: False) pretty JSON my beloved ✨
• -l, --less-redundant — Produce a viewer with fewer metrics (metrics that are expected to be largely redundant will not be displayed. (default: False) yep the parenthesis is unbalanced in the original, I'm not touching it, that's load-bearing 🎀
• -m, --maximum-fragment-length MAXIMUM_FRAGMENT_LENGTH — The maximum fragment length for which the distance to the reference fragment length count distribution will be measured. (default: 1000) numbers, we love her 📏
• -p, --peak-reference PEAK_REFERENCE — A reference set of peak metrics to plot. The default value is "SRR891268", the peak metrics of that sample in the ATAC-seq paper, as generated with MACS2 in our pipeline. It can be specified as "calculate", in which case these metrics will be averaged from the given metrics. It can also be the name of a JSON file, which must contain an object with two keys, "cumulative_fraction_of_hqaa" and "cumulative_fraction_of_territory", the value of each being an array of fractions of high-quality autosomal alignments (HQAA) or total peak territory, respectively. A tab- or comma-separated value file may also be given, in which each line contains two fractions, of HQAA and peak territory. All of these arrays should represent values at percentiles from 1-100. (default: SRR891268) that's a lot of lore for one flag and every single bit of it matters 💜
• -r, --reference REFERENCE — How to make the reference fragment length count distribution. The default value is "SRR891268", the fragment length distribution of that sample in the ATAC-seq paper. It can be specified as "calculate", in which case a distance will be calculated for each set of metrics from a reference distribution constructed from the rest of the given metrics. It can also be the name of a file containing a reference distribution. This file may be in JSON format, containing an object mapping fragment lengths to counts (e.g. "{0: 0, 1: 10, 2: 17}", or it may be a tab- or comma-separated value file in which each line contains a fragment length and count. It may (default: SRR891268) — and yeah, the original sentence genuinely just trails off at "It may" 😭 I'm reporting what's there, not guessing, that's the rule fr fr
• -t, --template-directory TEMPLATE_DIRECTORY — The location of the web app directory template. (default: auto) it'll figure it out itself if you let it 🧚
• -v, --verbose — Talk more. (default: False) honestly the most relatable flag on this entire page 🗣️
• --version — show program's version number and exit 👑

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reminder bestie: -f/--force overwrites the output directory if it exists. if that directory is precious to you, maybe vibe check it first 🙈

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and that's the page, mwah 💋 this was mkarv version {{VERSION}}, March 2026, same MKARV(1) energy, now with more glitter 🌟 bye bestie, go visualize some results 💖🦋🌸