BAMCLIPXT(1)

💖 NAME 💖

ok so bamclipXT — she puts back the query sequence fragments that bamadapterclip took out 🫶 no cap, that's literally the whole job.

✨ SYNOPSIS ✨

bamclipXT [options]

🌸 DESCRIPTION 🌸

ok bestie, listen up, because this one's actually kind of iconic. 👑

bamclipXT takes a SAM/BAM/CRAM file that's carrying the XT flag — you know, the one Picard's MarkIlluminaAdapters leaves behind — and it sets the designated base qualities to 2. That's the vibe. 💅

But here's the part that eats: the original base qualities don't just get yeeted into the void. Nope. They get copied over to a brand new aux tag named cq (short for clipped quality, iykyk 🎀). So nothing is lost, everything is preserved, we love a data-hygiene moment.

Then the resulting data gets written back out as a SAM/BAM/CRAM file. slay. ✨

🧚 the key=value pairs you can hand her 🧚

These are the little key=value combos you can pass in:

• 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
• verbose=<1> — the 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.
• md5filename — file name for md5 checksum if md5=1.

🫶 quick heads up bestie: level lists 11 as a valid value up top, but the descriptions below only spell out -1, 0, 1 and 9. Just passing along exactly what she said, no edits, no guessing, periodt.

🌈 AUTHOR 🌈

Written by German Tischler.

💀 REPORTING BUGS 💀

Report bugs to <germant@miltenyibiotec.de>

(ngl if something's broken, tell the author, not me 😭)

👑 COPYRIGHT 👑

Copyright © 2009-2019 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, read that last line again. no warranty, bestie. she's free and she's fabulous and she comes with zero promises. 💅

that's the whole page, mwah 💖 this one comes to you from BIOBAMBAM, dated July 2019, and it's page BAMCLIPXT(1) of the manual — go forth and clip responsibly, queen 🎀✨🦋