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 Intel article on igzip) 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:

       1      PAIRED (paired in sequencing)

       2      PROPER_PAIR (mapped as a proper pair)

       4      UNMAP (unmapped)

       8      MUNMAP (mate unmapped)

       16     REVERSE (mapped to the reverse strand)

       32     MREVERSE (mate mapped to the reverse strand)

       64     READ1 (first read of pair)

       128    READ2 (second read of pair)

       256    SECONDARY (secondary alignment)

       512    QCFAIL (failed quality control)

       1024   DUP (duplicate)

       2048   SUPPLEMENTARY (supplementary)

       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 <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                                    BAMMASKFLAGS(1)