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 auxilliary 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 <tischler@mpi-cbg.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.

BIOBAMBAM                                          March 2014                                         BAMMDNM(1)