BAMADAPTERCLIP(1)

💖 BAMADAPTERCLIP 💖

okay bestie, gather round, because this is the little tool that does the cleanup after the main character (that's bamadapterfind) has done its thing. it's a general commands manual page, and it is genuinely iconic. no cap. 🎀

✨ NAME ✨

bamadapterclip — remove the adapters marked by bamadapterfind

🌸 SYNOPSIS 🌸

bamadapterclip [options]

🦋 DESCRIPTION 🦋

so here's the vibe. bamadapterclip reads a BAM file from standard input — and it has to be one that was produced by bamadapterfind, okay, that's the whole point, it's a two-step glow-up — then it moves the detected adapters into auxiliary fields and writes the resulting data to standard output in BAM format. slay. 💅

then, the actual clipping: bamadapterclip uses the maximum m of the tag fields as and a3 if present. it then clips m bases off the end of the query sequence and the quality string, and places those clipped-off bits into the auxiliary fields qs and qq respectively. bye-bye adapter, hello clean reads. ✨

and here's the part where you get to customise, because 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 (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, a lil bonus round:

• 11: igzip compression

• verbose=<1> — the valid values are:
  • 1: print progress report on standard error
  • 0: do not print progress report
• mod=<1048576> — print progress every mod'th read/alignment, but only if verbose is set. it's giving "tell me how it's going, but only sometimes." 👑
• tmpfile=<filename> — prefix for temporary files. by default the temporary files are created in the current directory. (yes, your current directory. she's right there. 🫶)
• 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. (😭 the way it just silently doesn't do it)
• 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.

lowkey important: if you set md5=1 or index=1 but forget the matching filename key, you get nothing. not an error, just nothing. so double check those, bestie. 🙈

👑 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, no warranty at all. 😭

and that's the whole page, babes. this one shipped as part of BIOBAMBAM, back in July 2013 — vintage but still serving. go clip some adapters. periodt. 💜✨🎀