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.