BAMCLIPREINSERT(1)

💖 NAME 💖

bamclipreinsert — bestie, this one puts back the query sequence fragments that bamadapterclip yeeted out. Like, un-yeeting. Reinsertion. Slay.

✨ SYNOPSIS ✨

bamclipreinsert [options]

🦋 DESCRIPTION 🦋

okay so here's the tea ☕ bamclipreinsert reads a BAM file from standard input, reinserts the query sequence and quality score fragments that were removed by bamadapterclip, and for mapped reads it inserts the corresponding soft clip cigar operations. then it writes the whole resulting data out to standard output as a BAM file. iconic behaviour, honestly. 💅

the following key=value pairs can be given:

🎀 the key=value pairs 🎀

• 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 extra valid value for you: - 11: igzip 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. 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.
• index=<0|1> — compute BAM index for the output file. the 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. periodt. 💜

🙈 REPORTING BUGS 🙈

report bugs to <germant@miltenyibiotec.de> — they wanna hear it, fr fr. 🫶

🌸 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. no cap, zero warranty. 😭

and that's the whole thing bestie, go forth and reinsert 🧚✨ — this page is from BIOBAMBAM, dated July 2013, and it's the bamclipreinsert manual, section 1 of the general commands manuals. 💖⭐