BAMTAGCONVERSION

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.