RAPMAP_QUASIMAP(1)

💖 RAPMAP_QUASIMAP(1) 💖

okay bestie, welcome to the manual page for rapmap_quasimap — it's section 1 of the manual, it's a User Command, and it is so much cooler than it sounds. grab a strawberry 🍓 and let's go.

✨ NAME ✨

rapmap_quasimap — the rapmap module that maps reads using the SA-based index. that's the whole vibe. 🦋

🌸 SYNOPSIS 🌸

rapmap quasimap [-c] [-f] [-s] [-m <positive integer>] [-t <positive
integer>] [-o <path>] [-r <path>] [-2 <path>] [-1 <path>] [-n] -i <path>
[--] [--version] [-h]

like, that's the shape of the command, fr fr. every bracket is a choice you get to make. 💅

🎀 DESCRIPTION 🎀

RapMap Mapper (SA-based) — that's the title card, periodt.

so, here's the tea ☕: RapMap is a testing ground for ideas in quasi-mapping / (lightweight / pseudo) transcriptome alignment. and because it's a testing ground, that means that, at this point, it is somewhat experimental. 😭 no cap.

the develop branch will have the latest improvements and additions, but — and this is important, bestie — it is not guaranteed to be stable between commits. breaking changes to the master branch will be accompanied by a tag to the version before the breaking change. so there's a safety net, but it's a tag safety net, not a promise. 💀

currently, RapMap is a stand-alone quasi-mapper that can be used with other tools. it is also being used as part of Sailfish and Salmon. the way that it's just out there doing its thing in multiple ecosystems?? iconic. 👑

eventually, the hope is to create and stabilize an API so that it can be used as a library from other tools. fingers crossed, bestie. 🤞✨

💅 OPTIONS 💅

okay this is the part you actually came for. one bullet per flag, no skipping, we keep ALL the details because that's the rule and we respect the rule. 🫶

• -c, --consistentHits — ensure that the hits collected are consistent (co-linear). yes, consistent. keep your hits in a straight line, bestie. 📏
• -f, --fuzzyIntersection — find paired-end mapping locations using fuzzy intersection. it's giving "close enough counts". 🦋
• -s, --strictCheck — perform extra checks to try and assure that only equally "best" mappings for a read are reported. no mid mappings allowed, only the besties. 💯
• -m, --maxNumHits <positive integer> — reads mapping to more than this many loci are discarded. bye. 🗑️
• -t, --numThreads <positive integer> — number of threads to use. more threads = more chaos in parallel, slay. ⚡
• -o, --output <path> — the output file (default: stdout). if you don't say where, it just yells into your terminal. 🗣️
• -r, --unmatedReads <path> — the location of single-end reads. single and thriving. 🙈
• -2, --rightMates <path> — the location of the right paired-end reads. yes, the literal digit 2. not a typo, it's just built different. ✌️
• -1, --leftMates <path> — the location of the left paired-end reads. the other half of the pair, we love a duo. 💞
• -n, --noOutput — don't write out any alignments (for speed testing purposes). literally just vibes, no receipts. 🏃♀️💨
• -i, --index <path> — (required) the location of the quasiindex. you cannot skip this one, bestie, it's mandatory. 🚨
• --, --ignore_rest — ignores the rest of the labeled arguments following this flag. "and that's all i'm hearing." 🤐
• --version — displays version information and exits. quick little flex, then gone. 👋
• -h, --help — displays usage information and exits. when in doubt, ask the program. 🆘

🌈 AUTHOR 🌈

this manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. shoutout to Andreas, absolute legend, we stan. 🫶✨

and that's the whole page, bestie!! 🎀 the source is rapmap_quasimap 0.3.0, dated September 2016 — vintage but still eating. 💖 mwah, go map some reads. 👑🧚