.TH BAMMASKFLAGS 1 "July 2013" BIOBAMBAM
.SH NAME
bammaskflags \- remove flags from alignments
.SH SYNOPSIS
.PP
.B bammaskflags
[options]
.SH 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.
.PP
The following key=value pairs can be given:
.PP
.B level=<-1|0|1|9|11>:
set compression level of the output BAM file. Valid
values are
.IP -1:
zlib/gzip default compression level
.IP 0:
uncompressed
.IP 1:
zlib/gzip level 1 (fast) compression
.IP 9:
zlib/gzip level 9 (best) compression
.P
If libmaus has been compiled with support for igzip (see
.UR https://software.intel.com/en-us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-data
Intel article on igzip
.UE )
then an additional valid value is
.IP 11:
igzip compression
.PP
.B 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:
.TP
1
PAIRED (paired in sequencing)
.TP
2
PROPER_PAIR (mapped as a proper pair)
.TP
4
UNMAP (unmapped)
.TP
8
MUNMAP (mate unmapped)
.TP
16
REVERSE (mapped to the reverse strand)
.TP
32
MREVERSE (mate mapped to the reverse strand)
.TP
64
READ1 (first read of pair)
.TP
128
READ2 (second read of pair)
.TP
256
SECONDARY (secondary alignment)
.TP
512
QCFAIL (failed quality control)
.TP
1024
DUP (duplicate)
.TP
2048
SUPPLEMENTARY (supplementary)
.PP
.B tmpfile=<filename>: 
prefix for temporary files. By default the temporary files are created in the current directory
.PP
.B md5=<0|1>:
md5 checksum creation for output file. Valid values are
.IP 0:
do not compute checksum. This is the default.
.IP 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.
.PP
.B md5filename
file name for md5 checksum if md5=1.
.PP
.B index=<0|1>:
compute BAM index for output file. Valid values are
.IP 0:
do not compute BAM index. This is the default.
.IP 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.
.PP
.B indexfilename
file name for BAM index if index=1.
.PP
.B 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.
.SH AUTHOR
Written by German Tischler.
.SH "REPORTING BUGS"
Report bugs to <germant@miltenyibiotec.de>
.SH COPYRIGHT
Copyright \(co 2009-2013 German Tischler, \(co 2011-2013 Genome Research Limited.
License GPLv3+: GNU GPL version 3 <http://gnu.org/licenses/gpl.html>
.br
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.