BAMZZTONAME(1)

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

💖 BAMZZTONAME(1) 💖

okay bestie, so this is a page from the General Commands Manual and it's literally about bamzztoname, and it's giving "let me move that rank where it belongs" energy. stay with me, it's shorter than it looks and it's honestly iconic. 🎀

✨ NAME ✨

bamzztoname — move the rank of an alignment stored as an auxiliary field to the alignment's name

🌸 SYNOPSIS 🌸

bamzztoname [options]

🦋 DESCRIPTION 🦋

okay so picture this: bamzztoname reads a BAM file from standard input, pulls out the auxiliary field for the zz tag, prepends the rank as a decimal number to the read name, erases the zz auxiliary field, and writes the whole glow-up out to standard output as a BAM file. no cap, that's the entire job. 👑

🌈 the key=value pairs you can hand it 🌈

these are the little settings you can pass in, and yes they're key=value style, we love a format.

🍓 level=<-1|0|1|9|11>

sets the compression level of the output BAM file. 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

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 extra valid value bestie:

  • 11 — igzip 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. 💅

⭐ md5=<0|1>

md5 checksum creation for the output file. valid values are:

  • 0 — do not compute checksum. this is the default.
  • 1 — compute checksum. 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.
ngl the 1 case has a little trap in it — checksum only actually happens when md5filename is set too. read it twice, bestie. 🙈

🎀 md5filename

file name for md5 checksum if md5=1.

🔥 index=<0|1>

compute BAM index for output file. valid values are:

  • 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.

🌸 indexfilename

file name for BAM index if index=1.

👑 AUTHOR 👑

Written by German Tischler. (yes, the actual author, we stan. 🫶)

💀 REPORTING BUGS 💀

found something cursed? Report bugs to <germant@miltenyibiotec.de>. be nice about it, it's giving "helpful email" not "main character meltdown". ✨

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, zero warranty, none, don't come crying. 😭

and that's the whole page, bestie!! this came from BIOBAMBAM and it's dated July 2013, and yeah, the manual section is BAMZZTONAME(1). slay, go move some ranks. 💅🌈

📦 where this page comes from