BAMCHECKSORT(1)

💖 bamchecksort(1) — the General Commands Manual glow-up ✨

okay bestie, gather round, because we're checking the sort order of a BAM file and honestly? it's giving quality control queen 👑

✨ NAME ✨

bamchecksort — check sort order of a BAM file 🦋

🌸 SYNOPSIS 🌸

bamchecksort [options]

💅 DESCRIPTION 💅

so here's the vibe: bamchecksort reads a BAM file in through standard input and checks the sort order of the records in that file. no cap, that's the whole job. it's the vibe check your BAM never asked for but absolutely needs. 💀

and for query name sorted files? oh she's strict. like, stricter than your group chat's spoiler policy. the program strictly checks the order used by the bamsort program — meaning for lines with equal names, it requires reads marked as read 1 to appear before reads marked as read 2. read 1 first, bestie. that's the rule. 🎀

The following key=value pairs can be given:

• verbose=<1> — the chattiness setting, and here are the valid values:
  1. print progress report on standard error 📢
  0. do not print progress report 🤫

ngl, 1 is the default, so if you say nothing she will be yapping on stderr. iconic behavior, honestly. 👑

🫶 AUTHOR 🫶

Written by German Tischler. 💜

😭 REPORTING BUGS 😭

Report bugs to <germant@miltenyibiotec.de>

(please be nice, they're doing their best 🥺)

👑 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, so don't come for her if your BAM was a mess to begin with 🙈

and that's the whole page, bestie — bamchecksort(1) from the General Commands Manual, brought to you by BIOBAMBAM, October 2013 ⭐ stay sorted, stay slay 💖✨🎀