BAMBISECT(1)

💖 BAMBISECT — find the tiniest little BAM that still breaks your program 💖

okay so bestie, welcome to bambisect, a member of the General Commands Manual family, and honestly? she's a baddie. she takes your big messy BAM file and hunts down the smallest possible slice that still makes your program crash. debugging arc, but make it efficient. periodt. 🎀

✨ NAME ✨

bambisect — find reduced size BAM file on which a program fails

like, the whole vibe is: "your program exploded on this BAM? cool. let's find the minimal BAM that still explodes it so you don't have to stare at a million records." 🦋

🌸 SYNOPSIS 🌸

bambisect [options] in.bam prog

💅 DESCRIPTION 💅

So here's the tea, bestie. bambisect runs prog on in.bam. If that fails — and by fails we mean a non-zero return code, the classic "it's giving error" moment — then it starts systematically reducing the number of records by extracting intervals of records from in.bam and rerunning prog on those intervals. It keeps going until it finds an interval where prog fails, but where prog succeeds on any proper sub interval. That's the winner. That's the main character. 👑

The following key=value pairs can be given:

• level=<-1|0|1|9> — sets the compression level used when compressing BAM. The valid values are:
  • -1 — zlib/gzip default compression level
  • 0 — uncompressed
  • 1 — zlib/gzip level 1 (fast) compression
  • 9 — zlib/gzip level 9 (best) compression
• verbose=<1> — the valid values are:
  • 1 — print progress report on standard error
  • 0 — do not print progress report
• tmpfile=<filename> — prefix for temporary files. By default the temporary files are created in the current directory

ngl, that verbose default is 1, so she's gonna yap about her progress on stderr unless you tell her not to. 💬

🫶 AUTHOR 🫶

Written by German Tischler. icon behavior, honestly. 💜

😭 REPORTING BUGS 😭

Report bugs to <germant@miltenyibiotec.de>

(not me begging you to actually email instead of just yelling into the void, fr fr 🙈)

👑 COPYRIGHT 👑

Copyright © 2009-2019 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.

okay that last bit is the serious one bestie — no warranty, no cap. use it, remix it, redistribute it, but nobody's covering you if it goes sideways. 💀

and that's the whole page!! stay slay, go find that one cursed record, and remember: BIOBAMBAM, July 2019 ✨🎀🌈💖