BAMFILTERRG(1)

✨ BAMFILTERRG 💅

okay bestie, gather round, because this one is a little tool with big main character energy 🎀 it's called bamfilterrg, and it lives in the General Commands Manual section of your terminal. she's from the biobambam crew. let's get into it.

🌸 NAME 🌸

bamfilterrg — filter read groups from a BAM file 🧬

like. that's it. that's the whole job. she filters read groups. slay.

🦋 SYNOPSIS 🦋

bamfilterrg [options]

no positional args, no drama, just vibes and options 💖

💜 DESCRIPTION 💜

so here's the tea, bestie: bamfilterrg reads a BAM file from standard input, keeps only the reads that belong to a given set of read groups, and writes those reads to standard output in BAM format. that's the whole arc. no cap. 🔥

and these are the key=value pairs you can hand her:

• readgroups=<[]> — the list of read groups you wanna keep. if you don't set it, the default is to keep all the reads (she's generous like that 🫶). multiple read groups get separated by commas.
• verbose=<1> — how chatty she is. valid values are:
  • 1: print a progress report on standard error 📢
  • 0: do not print a progress report 🤫
• level=<-1|0|1|9|11> — sets 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 👑

and if libmaus has been compiled with support for igzip (peep <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, and it's:

• 11: igzip compression 🚀

• tmpfile=<filename> — a prefix for temporary files. by default the temporary files are created in the current directory. (yes, current directory. she's keeping it local 💅)
• 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. 😭 (yes, you read that right, bestie — set md5=1 with no filename and you get nothing. no cap.)
• md5filename — file name for md5 checksum if md5=1.
• index=<0|1> — compute BAM index for the 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. 🙈 (same energy as the md5 thing, fr fr)
• indexfilename — file name for BAM index if index=1.

🌈 AUTHOR 🌈

Written by German Tischler. iconic of him, honestly 💜

🎀 REPORTING BUGS 🎀

found a bug? not the vibe. report it to <germant@miltenyibiotec.de> 📧 she'll appreciate it.

⭐ 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. 🫶

okay that's the whole page, bestie — this one shipped as part of BIOBAMBAM, dated July 2013, and it's filed under BAMFILTERRG(1). go filter those read groups, you absolute legend 👑✨ bye!!