NAME

       bamfilterflags - remove entries from BAM files matching a given set of flags

SYNOPSIS

       bamfilterflags [options]

DESCRIPTION

       bamfilterflags  reads a BAM file from standard input, discards alignments matching a given
       set of flags and writes the remaining set of alignments to a  BAM  file  on  the  standard
       output stream.

       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

       numthreads=<1>:  Number  of  additional  threads  used  for  rewriting if markthreads > 1,
       otherwise no parallelism will be employed.

       exclude=<>: Do not include reads in the output that have any of the given flags  set.  The
       flags are given separated by commas. Valid flags are:

       PAIRED:
              read was paired in sequencing

       PROPER_PAIR:
              read has been mapped as part of a proper pair

       UNMAP: read was not mapped

       MUNMAP:
              mate of read was not mapped

       REVERSE:
              read was mapped to the reverse strand

       MREVERSE:
              mate of read was mapped to the reverse strand

       READ1: read was first read of a pair during sequencing

       READ2: read was second read of a pair during sequencing

       SECONDARY:
              alignment is secondary, i.e. an alternative mapping to the primary alignment in the
              same file

       QCFAIL:
              read as marked as having failed quality control

       DUP:   read  is  marked  as  a  duplicate  of  another  read  in  the   same   file   (see
              bammarkduplicates)

       SUPPLEMENTARY:
              read is marked as supplementary alignment

       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.