BAMFILTERAUX(1)

💅 BAMFILTERAUX — ok bestie, let's talk auxiliary tag glow-ups

So like… this is bamfilteraux, from the General Commands Manual section (that's section 1, iykyk). It's giving ✨ tag surgeon ✨ and honestly? obsessed.

🌸 NAME 🌸

bamfilteraux — filter auxiliary tags from BAM file

✨ SYNOPSIS ✨

bamfilteraux [options]

🦋 DESCRIPTION 🦋

Okay so here's the tea: bamfilteraux reads a BAM file from standard input, filters the list of auxiliary fields of each alignment, and writes the resulting data to standard output as a BAM file. Stream in, stream out, no drama, no cap. 💖

You can give it the following key=value pairs, and heads up: the keep and remove keys are mutually exclusive. Pick a lane bestie, you literally cannot do both.

• 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 like, 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 in the chat:

• 11 — igzip compression

• verbose=<1> — the valid values are:
  • 1 — print progress report on standard error
  • 0 — do not print progress report
• keep=<> — list of tag ids to keep. By default all are kept. If this key is set, then all the ids not in this list are discarded. 🫶
• remove=<> — list of tag ids to remove. By default none are removed. If this key is set, then all the ids not in this list are kept.
• 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.

not me pointing out that md5=1 and index=1 both need their filename buddy set or they just… do nothing 😭 read the fine print bestie, it's giving plot twist.

👑 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. (fr fr, no warranty at all, she said what she said 💀)

and that's the whole page, bestie — go filter some tags and slay ✨

this was BIOBAMBAM, July 2013, page BAMFILTERAUX(1) — mwah, take care of her 🎀💖