BAM12STRIP(1)

💖 BAM12STRIP 💖

okay bestie, pull up a chair, we're doing bam12strip from the General Commands Manual section (that's section 1, iykyk) 🎀

✨ NAME ✨

bam12strip — the girl who removes the rank that bam12split left behind in your read names 💅

🦋 SYNOPSIS 🦋

bam12strip [options]

🌸 DESCRIPTION 🌸

okay so here's the vibe: bam12strip reads a BAM file from standard input, strips out the rank that bam12split left sitting in your read names, and writes the whole thing back out as a BAM file. that's it. that's the job. no cap. ✨

and the way it does it? it takes names shaped like A_B and turns them into B. literally just yeets the part of the name up to and including the first underscore symbol. A_B ➡️ B. iconic behaviour honestly. 🫶

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 one more valid value for you: - 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 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.

👑 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, that's the whole legal situation. free to change, free to share, but zero warranty. no take-backs, bestie. 😭

and that's the page, bestie!! 🎀 this one's brought to you by BIOBAMBAM, dated July 2013, and yeah the page name is BAM12STRIP(1) — go forth and strip those ranks, you absolute main character 🌈💖