REAPR-STATS(1)

📦
version 1.0.18 · 5 versions
, in ubuntu resolute, ubuntu stonking

💅 REAPR-STATS(1) — the reapr-stats glow-up ✨

okay bestie, welcome to REAPR-STATS(1) 🎀 this is the part of REAPR that generates your stats from a BAM file. she's the little number-cruncher that takes your preprocessed pile of reads and turns it into stats. no cap, this is where the ✨data✨ begins. 💖

🌸 NAME 🌸

reapr-stats — generate REAPR stats from a BAM file 🦋

✨ SYNOPSIS ✨

reapr stats [options] <preprocess-output-directory> <outprefix>

so the way that this works is you hand her your preprocess-output-directory (yes, the folder your preprocessing step spat out) and an outprefix (the little name-stub she'll slap on all the files she makes). and yeah, you can sprinkle options on top like glitter. 🌈

👑 OPTIONS 👑

  • -f <int> — insert size. if you don't say anything, she just steals it from ave in stats.txt 💫
  • -i <int> — minimum insert size. default? also from stats.txt, specifically pc1. she's resourceful like that. 🎀
  • -j <int> — maximum insert size. guess what bestie — default is pc99 from stats.txt. she really does live in that file. 🙈
  • -m <int> — maximum read length. listen, this one does not need to be exact, it literally just determines memory allocation, so it just has to be >= your actual max read length. default is 2000. ⭐
  • -p <string> — name of the .gz perfect mapping file that perfectmap made. 🧚
  • -q <int> — ignore reads whose mapping quality is less than this. default is 0, so by default nobody gets ignored, she's very accepting. 💖
  • -s <int> — calculate the FCD error every n-th base. default is ceil((fragment size) / 1000). math girl behaviour, we love to see it. 🔥
  • -u <string> — file containing a list of chromosomes to look at, one per line. her little VIP guest list 💅

🫶 SEE ALSO 🫶

so yeah, that's the whole vibe 💜 go forth and get those FCD errors, bestie. this page is REAPR-STATS(1) — that's the manual name too, cute that she matches — brought to you straight from the REAPR source, and dated whenever your copy of the manpage says it is. check your own footer, I'm not a calendar 📅✨ bye!! 😭🌸

📦 where this page comes from