bamfixmateinformation - fix mate pair information in BAM files

       Written by German Tischler.

       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.

BIOBAMBAM                                         December 2013                         BAMFIXMATEINFORMATION(1)

       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>:inputfileformat.   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>:outputfileformat.  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.

       bamfixmateinformation - fix mate pair information in BAM files

       Report bugs to <germant@miltenyibiotec.de>

bamfixmateinformation [options]