BAMRECOMPRESS(1)

📦 version 2.0.185, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 BAMRECOMPRESS 💖

okay bestie, so this is bamrecompress from the General Commands Manual section — and yes it's literally just "recompress BAM file", that's the whole name, she's simple and she serves 🎀

✨ NAME ✨

bamrecompress — recompress BAM file. that's it. that's the girl.

🌸 SYNOPSIS 🌸

bamrecompress [options]

🦋 DESCRIPTION 🦋

so here's the vibe: bamrecompress reads a BAM file from standard input and writes it back out to standard output, but using whatever compression setting you asked for. glow-up via re-encode, basically. and the way that it's also capable of using multi threading?? she's got range, fr fr 🔥

you configure her with these key=value pairs, and honestly they're giving choose-your-own-adventure:

💅 level=<-1|0|1|9|11> 💅

sets the compression level of the output BAM file. valid values are, in order:

  • -1 — the zlib/gzip default compression level (let her cook, she knows what she's doing)
  • 0 — uncompressed. zero. nothing. raw. 💀
  • 1 — zlib/gzip level 1, which is the fast one
  • 9 — zlib/gzip level 9, which is the best one

and if libmaus has been compiled with support for igzip (see https://software.intel.com/en-us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-data) then there's one more valid value, a little bonus round:

  • 11 — igzip compression 👑

🎀 verbose=<1> 🎀

valid values:

  • 1 — print progress report on standard error
  • 0 — do not print progress report

(that <1> in the header is the default, so yes, she's chatty by default. main character energy.)

🧚 numthreads=<1> 🧚

number of threads to be used for comrpession/decompression — one by default. yes, one. she's polite.

🌈 tmpfile=<filename> 🌈

prefix for temporary files. by default the temporary files are created in the current directory, no cap.

🍓 md5=<0|1> 🍓

md5 checksum creation for output file. valid values:

  • 0 — do not compute checksum. this is the default.
  • 1 — compute checksum. but (and this is the plot twist) if the md5filename key is set, then the checksum is written to the given file. if md5filename is unset, then no checksum will be computed. so like... you asked for a checksum and got nothing. tragic but that's the rules 😭

💜 md5filename 💜

file name for md5 checksum if md5=1.

⭐ index=<0|1> ⭐

compute BAM index for output file. valid values:

  • 0 — do not compute BAM index. this is the default.
  • 1 — compute BAM index. if the indexfilename key is set, then the BAM index is written to the given file. if indexfilename is unset, then no BAM index will be computed. same energy as the md5 thing, iykyk 🙈

👑 indexfilename 👑

file name for BAM index if index=1.

🌟 AUTHOR 🌟

Written by German Tischler.

🫶 REPORTING BUGS 🫶

Report bugs to <germant@miltenyibiotec.de>

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. like, none. zero. don't come for her if it breaks 💀

and that's the whole page bestie!! this was the BIOBAMBAM joint, dated July 2013, living in section 1 of your manual — go forth and recompress responsibly 💖✨🎀

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