BAMMDNM(1)

💖 NAME 💖

bammdnm — bestie, it computes the MD and NM fields, that's the whole job, and it does it flawlessly ✨

🦋 SYNOPSIS 🦋

bammdnm [options]

🌸 DESCRIPTION 🌸

okay so here's the vibe: bammdnm reads a coordinate sorted BAM file straight from standard input, fills in the MD and NM auxiliary fields for every mapped read fragment, and then writes the whole thing out as a BAM file on standard output. that's it. that's the girl. 💅

and then you can hand it these key=value pairs, one by one, no cap:

• reference=<> — the file name of your reference, in either uncompressed or compressed FastA format. this one is REQUIRED, like fr fr, the program will literally quit if you don't give it. Uncompressed FastA is expected in general FastA file format, and you need a FastA index (a .fai file) — you can make that index while you reformat your input file using normalisefasta. Now, compressed FastA comes in two forms, bestie, pay attention 🫶. Form one is the format generated by the razip program — for that you need a razf file plus a corresponding FastA index file (.fai). Form two can be generated by normalisefasta using the setting bgzf=1 — and for that one, the index that normalisefasta optionally creates when you set the index key is required by bammdnm. That index file has to be stored as ref.fa.bgzf.idx when your compressed reference file name is ref.fa.bgzf. iykyk 💜
• 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 you get one extra valid value, lucky you:

• 11: igzip compression

• verbose=<0|1> — print a progress report while processing the file. valid values:
  • 0: do not print progress report
  • 1: print progress report (default)
• disablevalidation=<0|1> — disable input validation. valid values:
  • 0: check validity of input data (default)
  • 1: do not check validity of input data
• tmpfile=<filename> — prefix for temporary files. by default, temporary files are created in the current directory.
• md5=<0|1> — md5 checksum creation for the output file. valid values:
  • 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. valid values:
  • 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 index file if index=1.
• recompindetonly=<0|1> — only compute/recompute the MD and NM fields if the read or the reference in the relevant region contain indeterminate (non A, C, G or T) bases. valid values:
  • 0: compute/recompute all MD and NM fields. this is the default.
  • 1: only recompute if indeterminate bases are involved
• warnchange=<0|1> — warn if values for the MD and NM fields are already present but different from the newly computed ones. valid values:
  • 0: do not warn about changes. this is the default.
  • 1: print a warning message when changing previously stored values
• ioblocksize=<128k> — block size used for I/O operations

👑 AUTHOR 👑

Written by German Tischler. 💖

😭 REPORTING BUGS 😭

Report bugs to <germant@miltenyibiotec.de>

⭐ COPYRIGHT ⭐

Copyright © 2009-2014 German Tischler, © 2011-2014 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.

ok that's the whole page, you ate that bestie 🎀 this was BIOBAMBAM, March 2014, and yes this manual is literally BAMMDNM(1) 💅✨