NAME

       bamreset - reset BAM file to unaligned state

SYNOPSIS

       bamreset [options]

DESCRIPTION

       bamreset  reads  a  BAM file from standard input, transforms it to a pre aligned state and
       writes the resulting data to standard output as a BAM file.

       Resetting the file involves the following actions:

              Remove all SQ lines from the header.

              Set the sorting order to unknown

              Drop all non primary alignments

              Remove all auxiliary fields

              Mark all reads as unmapped and erase the mapping coordinates  and  template  length
              fields

              Move  all  reads  to  the  forward  direction  by  applying  reverse complements as
              necessary such that afterwards no reverse complement flags are set.

       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

       verbose=<1>: Valid values are

       1:     print progress report on standard error

       0:     do not print progress report

       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.

       resetheadertext  file  name for replacement SAM header. By default the header of the input
       SAM/BAM/CRAM file is filtered.

       exclude=<SECONDARY,SUPPLEMENTARY>: 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

       resetaux=<0|1>: auxilliary fields (default).

       resetsortorder=<0|1>: set sort order to unknown if resetsortorder=1 (default) and leave as
       it is in the input if resetsortorder=0.

       auxfilter=<>: comma separated list of aux tags to be kept if resetaux=0. If the key is not
       set when resetaux=0, then all tags are kept.

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.