NAME

       bammdnm - compute MD and NM fields

SYNOPSIS

       bammdnm [options]

DESCRIPTION

       bammdnm  reads  a  coordinate  sorted  BAM  file  from standard input, fills the MD and NM
       auxiliary fields for each mapped read fragment and writes the resulting data to a BAM file
       on standard output.

       The following key=value pairs can be given:

       reference=<>:  file name of the reference in uncompressed or compressed FastA format. This
       field is required, i.e. the program will quit if the key is not given.  Uncompressed FastA
       is  expected  in  general  FastA  file format. A FastA index (.fai file) is required. This
       index can be created while reformatting the input file using  normalisefasta.   Compressed
       FastA  can  be provided in two forms.  The first form is the format generated by the razip
       program. In this case a razf file and a corresponding FastA index file (.fai) is required.
       The  second  form  can be generated by normalisefasta using the setting bgzf=1.  The index
       optionally created by normalisefasta when setting the index key is required  for  bammdnm.
       The index file has to be stored as ref.fa.bgzf.idx for a compressed reference file name of
       ref.fa.bgzf.

       level=<-1|0|1|9|11>: set compression level of the output BAM file. 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

       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 an additional valid value is

       11:    igzip compression

       verbose=<0|1>: print progress report while processing the file. Valid values are

       0:     do not print progress report

       1:     print progress report (default)

       disablevalidation=<0|1>: disable input validation. Valid values are

       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 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 index file if index=1.

       recompindetonly=<0|1>: only compute/recompute MD and NM fields if the read or reference in
       the relevant region contain indeterminate (non A, C, G or T) bases. Valid values are

       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 are

       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.