BAM12SPLIT(1)

✨ NAME ✨

bam12split — bestie, this is the little tool that takes rank pairs (the ones bamcollate2 made) and projects them into single ranks per read. We're going from duo to solo, main-character style 💅

It's from the General Commands Manual, so you know it's legit.

🦋 SYNOPSIS 🦋

bam12split [options]

🎀 DESCRIPTION 🎀

Okay so here's the tea: bam12split reads a BAM file from standard input, projects rank pairs produced by bamcollate2 to single ranks per read, and writes the resulting data as a BAM file. In through the front door, out through the back, glow-up complete ✨

The way this works is: when the name A_B_C was produced for a pair of reads by

bamcollate2 collate=2

then bam12split produces the name A_C for the first read of the pair and B_C for the second read of the pair. Like, it splits the pair name up and hands each read its own lil rank. So fair, so iconic 🫶

The following key=value pairs can be given:

• 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 (see https://software.intel.com/en-us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-data) then there's an additional valid value, and it's kind of a big deal:

• 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 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 bestie, even though you said 1. it's giving "you had one job" 😭)
• 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.
• indexfilename — file name for BAM index if index=1.

⚠️ Heads up bestie: for both md5=1 and index=1, the file only actually gets written if you also set the matching ...filename key. Set the flag, set the name, or the output just doesn't happen. No cap.

👑 AUTHOR 👑

Written by German Tischler. King behaviour 💜

🙈 REPORTING BUGS 🙈

Report bugs to <germant@miltenyibiotec.de>. Don't be shy, they wanna hear it fr fr 🐛

🌈 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. (Read that one again. There is no warranty, bestie. Protect yourself 💀)

okay and that's the whole page, you ate that 🍓 This was BIOBAMBAM, dated July 2013 — ancient, yes, but still serving looks. Go split some ranks, you've got this 🧚✨