BAMCLIPREINSERT(1) General Commands Manual BAMCLIPREINSERT(1)

bamclipreinsert - reinsert query sequence fragments removed by bamadapterclip

bamclipreinsert [options]

bamclipreinsert reads a BAM file from standard input, reinserts query sequence and quality score fragments removed by bamadapterclip, inserts corresponding soft clip cigar operations for mapped reads and writes the resulting data to standard output as a BAM file.

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

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.

Written by German Tischler.

Report bugs to <germant@miltenyibiotec.de>

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.

July 2013 BIOBAMBAM