NAME

       bamfixmateinformation - fix mate pair information in BAM files

SYNOPSIS

       bamfixmateinformation [options]

DESCRIPTION

       bamfixmateinformation  reads  a  BAM, SAM or CRAM file, fixes the mate pair information of
       paired alignments and writes the resulting file as BAM, SAM or CRAM. The input  file  must
       be  sorted  by  query  name  (see  bamsort).  bamfixmateinformation modifies the following
       fields for paired reads with aligned mates:

       -      mate alignment reference sequence id

       -      mate alignment position on reference sequence

       -      mate unmapped/mate mapped to reverse strand flags

       -      MQ auxiliary tag denoting the mapping quality of the mapped mate

       -      inferred template length

       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

       disablevalidation=<0|1>: sets whether input validation is performed. Valid values are

       0:     validation is enabled (default)

       1:     validation is disabled

       md5=<0|1>: md5 checksum creation for output  file.  This  option  can  only  be  given  if
       outputformat=bam. Then 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.

       inputformat=<bam>: input file format.  All versions of bamsort come with support  for  the
       BAM  input  format.  If  the program in addition is linked to the io_lib package, then the
       following options are valid:

       bam:   BAM (see http://samtools.sourceforge.net/SAM1.pdf)

       sam:   SAM (see http://samtools.sourceforge.net/SAM1.pdf)

       cram:  CRAM (see http://www.ebi.ac.uk/ena/about/cram_toolkit)

       outputformat=<bam>: output file format.  All versions of bamsort come with support for the
       BAM  output  format.  If the program in addition is linked to the io_lib package, then the
       following options are valid:

       bam:   BAM (see http://samtools.sourceforge.net/SAM1.pdf)

       sam:   SAM (see http://samtools.sourceforge.net/SAM1.pdf)

       cram:  CRAM  (see  http://www.ebi.ac.uk/ena/about/cram_toolkit).  This   format   is   not
              advisable for data sorted by query name.

       I=<[stdin]>: input filename, standard input if unset.

       O=<[stdout]>: output filename, standard output if unset.

       inputthreads=<[1]>: input helper threads, only valid for inputformat=bam.

       outputthreads=<[1]>: output helper threads, only valid for outputformat=bam.

       reference=<[]>:  reference FastA file for inputformat=cram and outputformat=cram. An index
       file (.fai) is required.

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.