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
       ⟨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:

       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.