RAPMAP_PSEUDOMAP(1)

💅 RAPMAP_PSEUDOMAP(1) 💅

okay so bestie, welcome to the User Commands section of the manual — this is rapmap_pseudomap, section 1, and she's here to serve.

✨ NAME ✨

rapmap_pseudomap — the rapmap module that maps reads using a k-mer-based index 🧚

🌸 SYNOPSIS 🌸

,B rapmap pseudomap [-e] [-m <positive integer>] [-t <positive integer>]
[-o <path>] [-r <path>] [-2 <path>] [-1 <path>] [-n] -i <path> [--]
[--version] [-h]

(yes the ,B is right there in the original, we don't question the ancestors 💀)

🦋 DESCRIPTION 🦋

RapMap Mapper

So here's the tea ☕ — RapMap is literally a testing ground for ideas in quasi-mapping / (lightweight / pseudo) transcriptome alignment. Which means, at this point in her journey, she is somewhat experimental. Not a red flag exactly but like… a yellow flag 🚩

The develop branch is where all the fresh new improvements and additions live, but it is not guaranteed to be stable between commits. So if you're building on develop, know that. Breaking changes to the master branch will be accompanied by a tag to the version before the breaking change — so you can always find your way back home 🫶

Currently, RapMap is a stand-alone quasi-mapper that can be used with other tools. She's also out here being used as part of Sailfish and Salmon — multi-hyphenate queen 👑

Eventually, the hope is to create and stabilize an API so that it can be used as a library from other tools. The dream ✨

🎀 OPTIONS 🎀

• -e, --endCollector — use the simpler (and faster) "end" collector instead of the more sophisticated "skipping" collector. Less complicated, more speed, she's efficient 💅
• -m, --maxNumHits <positive integer> — reads that map to more than this many loci get discarded. Too popular? Not in this house 🚫
• -t, --numThreads <positive integer> — how many threads to use. Go off, parallel processing 🌈
• -o, --output <path> — the output file. Default is stdout, so if you say nothing she just talks right at you 🗣️
• -r, --unmatedReads <path> — where the single-end reads live 🏠
• -2, --rightMates <path> — where the right paired-end reads live 👉
• -1, --leftMates <path> — where the left paired-end reads live 👈
• -n, --noOutput — don't write out any alignments at all. This exists for speed testing purposes only, so like… don't be surprised when nothing comes out 🙈
• -i, --index <path> — (required) the location of the pseudoindex. You literally cannot skip this one, it's giving main character energy and she knows it 👑
• --, --ignore_rest — ignores the rest of the labeled arguments following this flag. Everything after this? Not her problem anymore 💀
• --version — displays version information and exits. Quick lil vibe check 📋
• -h, --help — displays usage information and exits. When in doubt, ask for help bestie 🫶

💜 AUTHOR 💜

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. King behavior, we love a contributor 👏

rapmap_pseudomap 0.3.0 · September 2016

and that's the whole page bestie, no cap, go map some reads and slay 💖✨🦋