BAMSPLITDIV(1)

✨ bamsplitdiv(1) ✨

okay so bestie, this is a page from the General Commands Manual, and it's all about bamsplitdiv 💅 buckle up, it's lowkey iconic.

🌸 NAME 🌸

bamsplitdiv — split a BAM file into a whole set of BAM files 🧚

🎀 SYNOPSIS 🎀

bamsplitdiv [options]

💖 DESCRIPTION 💖

so here's the vibe: bamsplitdiv reads a BAM file through standard input and creates a set of output BAM files holding the alignments from the input. ✨

Give it a positive natural number div and it will make div files. The alignments from the input get distributed across the output files in a round robin type scheme, like:

• entries 0, div, 2div, 3div, etc. → go to the first output file 🥇
• 1, div+1, 2div+1, 3div+1, etc. → go to the second, etc. 🥈

periodt. that's the whole distribution scheme, no cap.

The following key=value pairs can be given:

• div=<1> — number of output files 💅
• prefix=<filename> — prefix for the created files. The created files will have names ${prefix}_000000.bam, ${prefix}_000001.bam, etc. 🎀
• 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

👑 AUTHOR 👑

Written by German Tischler. 💜

😭 REPORTING BUGS 😭

Report bugs to <germant@miltenyibiotec.de> — yes bestie, fr fr, they want to hear about 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. ⚠️

and that's a wrap, my love 💖 this page came to you courtesy of BIOBAMBAM, dated October 2013 — vintage but still slaying ✨🦋🎀