bamtagconversion - convert old tags to new ones

       Written by Andrew Whitwham.

       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.

BIOBAMBAM                                           June 2015                                BAMTAGCONVERSION(1)

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.

       bamtagconversion - convert old tags to new ones

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

bamtagconversion [options]