RAPMAP_PSEUDOINDEX(1)

💖 RAPMAP_PSEUDOINDEX(1) 💖

okay bestie, welcome to the rapmap_pseudoindex page — it's the User Commands girlie of the rapmap manual set, and she's here to help you build a k-mer-based index. no cap. let's get into it 🦋

✨ NAME ✨

rapmap_pseudoindex — the rapmap module whose whole entire job is building a k-mer-based index. that's it. that's the vibe. 👑

🌸 SYNOPSIS 🌸

rapmap pseudoindex [-k <positive integer less than 32>] -i <path> -t
<path> [--] [--version] [-h]

lowkey just remember: -i and -t are the required besties, everything else is optional garnish ✨

🎀 DESCRIPTION 🎀

RapMap Indexer — yes, that's the title, she said what she said 💅

so like, RapMap is a whole testing ground for ideas in quasi-mapping / (lightweight / pseudo) transcriptome alignment. and by "testing ground" we mean: at this point, it is somewhat experimental. 🙈

the tea on the branches, fr fr:

• the develop branch gets all the latest improvements and additions, but 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 you always have a safe spot to go back to 🫶

currently, RapMap is a stand-alone quasi-mapper that can be used with other tools. it's also being used as part of Sailfish and Salmon. 🐟✨

and eventually?? the hope is to create and stabilize an API so it can be used as a library from other tools. manifesting that for her ngl 🌈

💅 OPTIONS 💅

• -k, --klen <positive integer less than 32> — the length of k-mer to index. yes it has to be a positive integer, yes it has to be less than 32, don't test her 🫶
• -i, --index <path> — (required) the location where the index should be written. required, bestie, don't skip it 💀
• -t, --transcripts <path> — (required) the transcript file to be indexed. also required. also don't skip it. 🍓
• --, --ignore_rest — ignores the rest of the labeled arguments following this flag. she's done listening basically ✋
• --version — displays version information and exits. quick lil peek 👀
• -h, --help — displays usage information and exits. when in doubt, ask for help, that's main character energy ⭐

🌷 AUTHOR 🌷

this manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. iconic of him honestly 👑

and that's the whole page!! 🎀 version rapmap_pseudoindex 0.3.0, dated September 2016 — yeah she's a vintage queen, an oldie but a goodie, and she still slays 💖✨ bye bestie, go build that index 🦋