BAMAUXSORT(1)

💖 BAMAUXSORT — okay bestie, let's talk about your aux tags 💖

It's a General Commands Manual situation, and the command is bamauxsort. Buckle up, it's giving tag-sorting royalty. 👑

✨ NAME ✨

bamauxsort — filter auxiliary tags from BAM file

🌸 SYNOPSIS 🌸

bamauxsort [options]

🦋 DESCRIPTION 🦋

Okay so here's the tea, bestie: bamauxsort reads a BAM file from standard input, sorts the auxiliary fields of each alignment by tag name, and writes the resulting data to standard output as a BAM file. That's it, that's the whole vibe. ✨

The following key=value pairs can be given:

• level=<-1|0|1|9|11> — set the compression level of the output BAM file. 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

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 an additional valid value is:

• 11: igzip compression

• verbose=<1> — 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 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.
• 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.

🫶 tiny heads-up: those last two keys (md5filename and indexfilename) are written without an =, exactly like the original says. Not a typo, not me being chaotic — that's just how it's listed. Copy it as-is, bestie. 💅

💜 AUTHOR 💜

Written by German Tischler.

😭 REPORTING BUGS 😭

Report bugs 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.

no cap, that last line is doing the most — but it's fr fr real, so don't come for me. 💀

and that's the whole page, periodt. This one's from the BIOBAMBAM fam, dated July 2013 — thanks for reading, mwah! 💖🎀🦋