REPAIR(1)

📦
version 2.0.8 · 2 versions
, in debian trixie, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

🌸 REPAIR(1) — the manual, but make it cute 🌸

okay so bestie, you opened the manual page for REPAIR(1) (that's a User Command, if you were wondering 💅) and honestly? she's a whole mood. let's get into it 🫶

✨ NAME ✨

repair — a toolkit for processing next-gen sequencing data 🧬🦋

💖 DESCRIPTION 💖

so this is repair Version 2.0.4 and here's the tea: she finds reads that came from the same pair in the input, and then she puts them right next to each other in the output. matching besties stay together, periodt. 💞

and for every singleton read that doesn't have a pair? she adds a dummy read for it. no read left behind fr fr 🥺

oh and the output file is compatible with the featureCounts program. iconic behaviour, no cap. 👑

📝 Usage 📝

./repair [options] -i <input_file> -o <output_file>

🌟 Required arguments 🌟

these are not optional bestie, you NEED them:

  • -i <string> — the name of your input file. BAM format by default, so if you don't say otherwise, that's what she's expecting. 📂
  • -o <string> — the name of your output file. this one is in BAM format, always. 💾

🎀 Optional arguments 🎀

the little extras, the seasoning, the garnish:

  • -S — tells her the input file is in SAM format instead. switch it up, we love versatility. ✨
  • -c — compress the output BAM file. this reduces the size of the BAM file, but heads up: it will increase the time it takes to retrieve reads from the BAM file. trade-offs are real, bestie. 😭
  • -T <int> — number of CPU threads. 8 by default. she's already multithreaded out of the box, we stan efficiency. 🔥
  • -d — do not add dummy reads for singleton reads. if you're feeling picky about your singletons, this is your girl. 🙈
  • -t — do not include the sequences and quality scores of reads in the output file. slimmer output, less to carry. 💅

👑 AUTHOR 👑

this manpage was written by Alexandre Mestiashvili for the Debian distribution, and can be used for any other usage of the program. absolute legend behaviour, we appreciate you 🫶

and that's the whole vibe check bestie 💜 this page is from repair 2.0.3, dated March 2023 — go forth and pair those reads, you've got this 🌈⭐

📦 where this page comes from