RAPMAP_QUASIINDEX(1)

💖 rapmap_quasiindex(1) — the girlies' guide to building a suffix-array index 💖

okay so bestie, welcome to section 1 of the manual, aka the part where we talk about rapmap_quasiindex, which is the rapmap module that builds a suffix array-based (SA) index. yes, SA like suffix array, not like... anything else. stay focused. ✨

✨ NAME ✨

rapmap_quasiindex — it's the rapmap module that builds a suffix array-based (SA) index. that's the whole job. it builds it. it indexes it. it's giving construction worker but make it bioinformatics. 💅

🦋 SYNOPSIS 🦋

rapmap quasiindex [-x <positive integer <= # cores>] [-p] [-n] [-k
<positive integer less than 32>] -i <path> -t <path> [--] [--version]
[-h]

no cap, that's the whole invocation. -i and -t are required, the rest are the little garnish on top. 🎀

🌸 DESCRIPTION 🌸

RapMap Indexer — that's literally the title, we're keeping it. 👑

so, tea time: RapMap is a testing ground for ideas in quasi-mapping / (lightweight / pseudo) transcriptome alignment. that means that, at this point, it is somewhat experimental. i know, i know. it's not a bug, it's a lifestyle. 😭

here's the vibe:

• The develop branch will have the latest improvements and additions, but is not guaranteed to be stable between commits. she's spontaneous. she's unpredictable. she's not stable, bestie.
• Breaking changes to the master branch will be accompanied by a tag to the version before the breaking change. so at least there's a paper trail. 🫶
• Currently, RapMap is a stand-alone quasi-mapper that can be used with other tools. it's independent! it doesn't need a man! (well, it doesn't need another tool.)
• It is also being used as part of Sailfish and Salmon. collab era. 🔥
• Eventually, the hope is to create and stabilize an API so that it can be used as a library from other tools. manifesting that for real. ⭐

💅 OPTIONS 💅

okay this is the part you actually came for. one bullet per flag, no skipping, no summarizing, we eat every single one. 🍓

• -x, --numThreads <positive integer <= #cores> — use this many threads to build the perfect hash function. so like, how much of your CPU is coming to the party. don't put a number bigger than your core count, she will not be happy about that. 🙈
• -p, --perfectHash — use a perfect hash instead of a dense hash. heads up: this somewhat slows construction, but uses less memory. classic tradeoff, pick your fighter. ⚖️
• -n, --noClip — don't clip poly-A tails from the ends of target sequences. if you say this flag, the poly-A tails stay. they're invited. they're staying for dinner. 🎀
• -k, --klen <positive integer less than 32> — the length of k-mer to index. must be a positive integer less than 32, so like... 31 max. don't get cute with it. 💀
• -i, --index <path> — (required) the location where the index should be written. required means required. no -i, no index, no service. 🚫
• -t, --transcripts <path> — (required) the transcript file to be indexed. also required. also mandatory. also cannot be skipped. we've been over this. 💖
• --, --ignore_rest — ignores the rest of the labeled arguments following this flag. it's the "and that's enough out of you" flag. ✋
• --version — displays version information and exits. short and sweet, like a lil text. 📩
• -h, --help — displays usage information and exits. when in doubt, -h it out. ✨

⚠️ lowkey important: -i <path> and -t <path> are both marked (required) in the original. if you forget either one, the vibe check fails and nothing gets indexed. you've been warned, bestie. 🌈

👑 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, doing the lord's work in the docs department. 🫶

and that's the whole page, babe. rapmap_quasiindex 0.3.0, dated September 2016 — old enough to be vintage, iconic enough to still index your transcripts. mwah. 💋

💖 periodt. 💖