.TH BAMADAPTERCLIP 1 "July 2013" BIOBAMBAM
.SH NAME
bamadapterclip - remove the adapters marked by bamadapterfind
.SH SYNOPSIS
.PP
.B bamadapterclip
[options]
.SH DESCRIPTION
bamadapterclip reads a BAM file from standard input which was produced by bamadapterfind, 
moves the detected adapters to auxiliary fields
writes the resulting data to standard output in BAM format
.PP
bamadapterclip uses the maximum \fIm\fR of the tag fields \fIas\fR and \fIa3\fR
if present. It then clips of \fIm\fR bases from the end of the query
sequence and quality string and places those in the auxiliary fields
\fIqs\fR and \fIqq\fR respectively.
.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=<1>:
Valid values are
.IP 1:
print progress report on standard error
.IP 0:
do not print progress report
.PP
.B mod=<1048576>:
print progress every for mod'th read/alignment if verbose is set
.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.
.PP
.B index=<0|1>:
compute BAM index for output file. Valid values are
.IP 0:
do not compute BAM index. This is the default.
.IP 1:
compute BAM index. If the indexfilename key is set, then the BAM index is
written to the given file. If indexfilename is unset, then no BAM index will be computed.
.PP
.B indexfilename
file name for BAM index if index=1.
.SH AUTHOR
Written by German Tischler.
.SH "REPORTING BUGS"
Report bugs to <germant@miltenyibiotec.de>
.SH COPYRIGHT
Copyright \(co 2009-2013 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.