NAME

       bamadapterclip - remove the adapters marked by bamadapterfind

SYNOPSIS

       bamadapterclip [options]

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

       bamadapterclip uses the maximum m of the tag fields as and a3 if present. It then clips of m  bases  from
       the  end  of  the  query  sequence  and quality string and places those in the auxiliary fields qs and qq
       respectively.

       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=<1>: Valid values are

       1:     print progress report on standard error

       0:     do not print progress report

       mod=<1048576>: print progress every for mod'th read/alignment if verbose is set

       tmpfile=<filename>: prefix for temporary files. By default the temporary files are created in the current
       directory

       md5=<0|1>: md5 checksum creation for output file. 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.

       index=<0|1>: compute BAM index for output file. Valid values are

       0:     do not compute BAM index. This is the default.

       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.

       indexfilename file name for BAM index if index=1.

AUTHOR

       Written by German Tischler.

REPORTING BUGS

       Report bugs to <germant@miltenyibiotec.de>

COPYRIGHT

       Copyright © 2009-2013 German Tischler, © 2011-2013 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                                           July 2013                                  BAMADAPTERCLIP(1)