.TH BAMTAGCONVERSION 1 "June 2015" BIOBAMBAM
.SH NAME
bamtagconversion - convert old tags to new ones
.SH SYNOPSIS
.PP
.B bamtagconversion
[options]
.SH DESCRIPTION
\fBbamtagconversion\fR 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, \fBbamtagconversion\fR
only converts MC:i tags.
\fBbamtagconversion\fR takes a BAM file as an input and outputs a BAM file with
the changes made.
.PP
The following key=value pairs can be given:
.PP
.B level=<-1|0|1|9|11>:
set compression level of the output BAM file. Valid
values are
.IP -1:
zlib/gzip default compression level.
.IP 0:
uncompressed.
.IP 1:
zlib/gzip level 1 (fast) compression.
.IP 9:
zlib/gzip level 9 (best) compression.
.P
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
.IP 11:
igzip compression.
.PP
.B verbose=<0|1>:
Valid values are
.IP 0:
do not print progress report (default).
.IP 1:
print progress report to standard error.
.PP
.B md5=<0|1>:
md5 checksum creation for output file. This option can only be given if
outputformat=bam. Then valid values are
.IP 0:
do not compute checksum. This is the default.
.IP 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.
.PP
.B md5filename
file name for md5 checksum if md5=1.
.PP
.B outputthreads=<[1]>:
output helper threads.
.SH AUTHOR
Written by Andrew Whitwham.
.SH "REPORTING BUGS"
Report bugs to <aw7@sanger.ac.uk>
.SH COPYRIGHT
Copyright \(co 2015 Genome Research Limited.
License GPLv3+: GNU GPL version 3 <http://gnu.org/licenses/gpl.html>
.br
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.