NAME

       bamtagconversion - convert old tags to new ones

SYNOPSIS

       bamtagconversion [options]

DESCRIPTION

       bamtagconversion  converts the old MS, MT and MC tags into the corresponding ms, mt and mc
       tags.  As there is an official MC:Z tag in the SAM spec,  bamtagconversion  only  converts
       MC:i  tags.  bamtagconversion takes a BAM file as an input and outputs a BAM file with the
       changes made.

       The following key=value pairs can be given:

       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>: Valid values are

       0:     do not print progress report (default).

       1:     print progress report to standard error.

       md5=<0|1>: md5 checksum creation for output  file.  This  option  can  only  be  given  if
       outputformat=bam. Then 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.

       outputthreads=<[1]>: output helper threads.

AUTHOR

       Written by Andrew Whitwham.

REPORTING BUGS

       Report bugs to <aw7@sanger.ac.uk>

COPYRIGHT

       Copyright  ©  2015  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.