BAMFIXMATEINFORMATION(1)

✨ NAME ✨

bamfixmateinformation — the little icon that fixes up mate pair info in BAM files 💅

🌸 SYNOPSIS 🌸

bamfixmateinformation [options]

🦋 DESCRIPTION 🦋

okay so picture this: you've got a BAM, a SAM or a CRAM file, and the mate pair info on your paired alignments is a whole mess. bamfixmateinformation reads it, fixes the mate pair info, and writes the result back out as BAM, SAM or CRAM. that's it, that's the job, and it ate 💅

🚨 IMPORTANT 🚨 the input file must be sorted by query name — go look at bamsort if you need that done first. don't skip this step bestie, it's not optional.

so for paired reads that have aligned mates, it goes in and modifies these fields:

• mate alignment reference sequence id
• mate alignment position on reference sequence
• mate unmapped/mate mapped to reverse strand flags
• MQ auxiliary tag denoting the mapping quality of the mapped mate
• inferred template length

periodt. those are the fields, and it fixes them. moving on 💖

👑 OPTIONS 👑

the following key=value pairs can be given, bestie. read them all, there are no skips here:

• 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 was 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 on the menu:

• 11 — igzip compression

• verbose=<1> — valid values are:
  • 1 — print progress report on standard error
  • 0 — do not print progress report
• disablevalidation=<0|1> — sets whether input validation is performed. valid values are:
  • 0 — validation is enabled (this is the default)
  • 1 — validation is disabled
• 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 the md5 checksum if md5=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. like, just don't 💀
• 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. don't forget it bestie, it will not work without it 🫶

🎀 AUTHOR 🎀

written by German Tischler. king behavior honestly 👑

🙈 REPORTING BUGS 🙈

found a bug? report it to <germant@miltenyibiotec.de>. be nice, be specific, include the receipts 💌

⭐ 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, read the license bestie 💖

and that's the whole page! this one's from the BIOBAMBAM girlies, dated December 2013 — yeah she's a little vintage but she still slays ✨🦋🌸