BAMTAGCONVERSION(1)

💖 BAMTAGCONVERSION 💖

okay bestie, welcome to bamtagconversion, section 1 of the General Commands Manual — she's giving glow-up energy and she's here to fix your tags ✨

🌸 NAME 🌸

bamtagconversion — convert old tags to new ones 💅

✨ SYNOPSIS ✨

bamtagconversion [options]

🦋 DESCRIPTION 🦋

So like, bamtagconversion takes your old MS, MT and MC tags and converts them into the matching ms, mt and mc tags. Iconic, right? But wait — plot twist 🙈 — because there's already an official MC:Z tag in the SAM spec, bamtagconversion only converts MC:i tags. no cap.

She takes a BAM file as input and outputs a BAM file with the changes made. in and out, bam to bam, slay 💖

the following key=value pairs can be given:

• level=<-1|0|1|9|11> — set 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.

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 on the menu:

• 11: igzip compression.

• verbose=<0|1> — valid values are:
  • 0: do not print progress report (default).
  • 1: print progress report to standard error.
• md5=<0|1> — md5 checksum creation for the output file. this one can only be given if outputformat=bam. then 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.
• outputthreads=<[1]> — output helper threads. 🧚

👑 AUTHOR 👑

Written by Andrew Whitwham. periodt 💅

💀 REPORTING BUGS 💀

Report bugs to <aw7@sanger.ac.uk> 🫶

🌈 COPYRIGHT 🌈

Copyright © 2015 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. (yes bestie, that's the dramatic part, take it seriously 🫡)

BIOBAMBAM · June 2015 — mwah, that's the whole page, go convert those tags and be the main character of your own BAM file 💖✨🎀🦋