BAMRANK(1)

🌸 NAME 🌸

Okay so real quick — you're looking at the bamrank page from the General Commands Manual (yes, the classic BAMRANK(1) situation, iykyk).

bamrank — she inserts the rank (aka the line number) of each alignment as an auxiliary field for tag zz. 💅

✨ SYNOPSIS ✨

bamrank [options]

💖 DESCRIPTION 💖

So here's the vibe: bamrank reads a BAM file from standard input, slides in a brand new auxiliary field tagged zz that holds the rank (the line number) of the respective read/alignment, and then writes all that out to standard output as a BAM file. Iconic behaviour, no notes.

And why do you care about this rank, bestie? Because it lets you restore the original order of the file after you've gone and reordered everything. You do it with this little sequence right here:

bamzztoname | bamsort SO=queryname | bam12strip

Obsessed. 🦋

The following key=value pairs can be given:

• 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 (peep https://software.intel.com/en-us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-data for the details), then there's one more 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. The 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 the output file. The 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. (We stan. 🫶)

🙈 REPORTING BUGS 🙈

Report bugs to <germant@miltenyibiotec.de> — like, please actually tell him, don't just suffer in silence. 💀

🎀 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, the "no warranty" part is not a joke — it's giving very real legal energy, so read it as written. 💜

Okay that's the whole page, bestie. This one's from BIOBAMBAM, dated July 2013, and it's the BAMRANK(1) manual page. Slay, go rank some alignments. ⭐🧚🌈