NAME

       bammaskflags - remove flags from alignments

SYNOPSIS

       bammaskflags [options]

DESCRIPTION

       bammaskflags  reads  a BAM file from standard input, performs a bit wise and with the flags field of each
       read/alignment and writes the resulting data to standard output in BAM format.

       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

       maskneg=<0> mask of flags to be removed (a bit wise and is computed between the bit  complement  of  this
       number  and  the flag field of the reads/alignments in the input BAM file). This value can be obtained by
       adding up the following values of the flags:

       PAIRED 1

       PROPER_PAIR
              2

       UNMAP  4

       MUNMAP 8

       REVERSE
              16

       MREVERSE
              32

       READ1  64

       READ2  128

       SECONDARY
              256

       QCFAIL 512

       DUP    1024

       SUPPLEMENTARY
              2048

       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.

       auxexists=[taglist]:  only  mask  records  containing any of the given aux field tags. taglist is a comma
       separated list of aux field names. Flag fields of records are only filtered  if  the  respective  records
       contain  any  of  the  aux  fields  mentioned  in this list. By default all records are filtered. If e.g.
       auxexists=AS is given, then only flag fields of records containing an AS aux field are masked.

AUTHOR

       Written by German Tischler.

REPORTING BUGS

       Report bugs to <tischler@mpi-cbg.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.