BAMRECALCULATECIGAR(1)

👑 BAMRECALCULATECIGAR 👑

okay bestie, so the manual name is bamrecalculatecigar — it lives in the General Commands Manual section, and it's about to fix up your CIGAR strings for you. let's go 💅

✨ NAME ✨

bamrecalculatecigar — concatenate BAM files

(yes, that's literally what it says up there in the original, and I am not the one who wrote it, so we keep it fr fr 🙈)

🎀 SYNOPSIS 🎀

bamrecalculatecigar [options]

🌸 DESCRIPTION 🌸

So here's the vibe: bamrecalculatecigar reads a SAM/BAM/CRAM file, and for every aligned read it rewrites the CIGAR string, swapping out the M operations for = and X operations. Then it writes all of that out to a SAM/BAM/CRAM file. ✨

Reads that aren't aligned? They get left alone. Not touched. Not changed. They're minding their own business, we're minding ours. 🫶

Rewriting the CIGAR strings requires a reference in FastA format, no cap. You gotta hand over the path to that FastA file using the reference key. And heads up: your alignment input file needs to be sorted by coordinate. 📍

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

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, and it's:

• 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. 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.
• inputformat=<bam> — input file format. all versions of bamsort come with support for the BAM input format. if the program in addition is linked to the io_lib package, then the following options are valid:
  • bam — BAM (see http://samtools.sourceforge.net/SAM1.pdf)
  • sam — SAM (see http://samtools.sourceforge.net/SAM1.pdf)
  • cram — CRAM (see http://www.ebi.ac.uk/ena/about/cram_toolkit)
• outputformat=<bam> — output file format. all versions of bamsort come with support for the BAM output format. if the program in addition is linked to the io_lib package, then the following options are valid:
  • bam — BAM (see http://samtools.sourceforge.net/SAM1.pdf)
  • sam — SAM (see http://samtools.sourceforge.net/SAM1.pdf)
  • cram — CRAM (see http://www.ebi.ac.uk/ena/about/cram_toolkit). this format is not advisable for data sorted by query name 🚩
• I=<[stdin]> — input filename, standard input if unset.
• O=<[stdout]> — output filename, standard output if unset.
• inputthreads=<[1]> — input helper threads, only valid for inputformat=bam.
• outputthreads=<[1]> — output helper threads, only valid for outputformat=bam.
• reference=<[]> — reference FastA file for inputformat=cram and outputformat=cram. an index file (.fai) is required. 📎

💖 AUTHOR 💖

Written by German Tischler.

😭 REPORTING BUGS 😭

Report bugs to <germant@miltenyibiotec.de>

🦋 COPYRIGHT 🦋

Copyright © 2009-2016 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.

okay that's the whole thing bestie, and lemme just say — this page came from BIOBAMBAM, dated February 2016, and honestly? iconic. periodt 💅✨🎀