BAMINDEX(1)

🎀 BAMINDEX 🎀

okay so bestie, welcome to the bamindex page from the General Commands Manual 💖 this one's short and sweet and honestly kinda iconic.

✨ NAME ✨

bamindex — create index for BAM file 🌸

✨ SYNOPSIS ✨

bamindex [options]

that's it. that's the whole thing. no file arguments, no positional drama. periodt. 💅

✨ DESCRIPTION ✨

okay so here's the vibe: bamindex reads a BAM file from standard input and produces a BAM index (.bai) file for that BAM file on standard output. so it's giving pipe energy, it's giving filter, it's giving "don't hand me a filename, hand me a stream" 🦋

then there's the options bit, and lowkey this is where all the settings live:

• verbose=<1> — controls how chatty it is. valid values are:
  1. print progress report on standard error 👀
  2. do not print progress report 🤫

(yes, the default is 1, so it's a yapper by default. sorry not sorry.)

• tmpfile=<filename> — set the prefix for temporary file names 🗂️ by default, temporary files are created in the current directory. so if you want them somewhere else, this is your girl.

ngl the <value> notation is doing a lot of work here — those angle brackets are part of the option name as written, not decoration. copy it exactly, bestie, i'm begging 🙈

✨ AUTHOR ✨

Written by German Tischler. 👑

✨ REPORTING BUGS ✨

found a bug? not the vibe. report it to <germant@miltenyibiotec.de> 📧

✨ COPYRIGHT ✨

Copyright © 2009-2013 German Tischler, © 2011-2013 Genome Research Limited. License GPLv3+: GNU GPL version 3 <http://gnu.org/licenses/gpl.html>

This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. 😭

fr fr, "NO WARRANTY" in all caps is not me being dramatic, that's literally what it says. respect the caps.

okay that's the whole page, you ate it, go index something 💖 this was BIOBAMBAM, July 2013, signing off bestie 🫶✨🌸