.TH BAMCLIPXT 1 "July 2019" BIOBAMBAM
.SH NAME
bamclipXT - reinsert query sequence fragments removed by bamadapterclip
.SH SYNOPSIS
.PP
.B bamclipXT
[options]
.SH DESCRIPTION
bamclipXT processes a SAM/BAM/CRAM file containing the XT flag produced by Picard's MarkIlluminaAdapters
and sets the designated base qualities to 2. The original base qualities are copied to a new aux tag named cq (clipped
quality). The resulting data is then written as a SAM/BAM/CRAM file.
.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
.PP
.B verbose=<1>:
Valid values are
.IP 1:
print progress report on standard error
.IP 0:
do not print progress report
.PP
.B tmpfile=<filename>: 
prefix for temporary files. By default the temporary files are created in the current directory
.PP
.B md5=<0|1>:
md5 checksum creation for output file. 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.
.SH AUTHOR
Written by German Tischler.
.SH "REPORTING BUGS"
Report bugs to <germant@miltenyibiotec.de>
.SH COPYRIGHT
Copyright \(co 2009-2019 German Tischler, \(co 2011-2013 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.