NAME

       bam12auxmerge - merge two BAM files

SYNOPSIS

       bam12auxmerge [options] <input.bam>

DESCRIPTION

       bam12auxmerge  merges  the  contents  of  two  BAM  files containing the same set of reads
       together and writes the resulting data as a BAM file.  It reads one of the BAM files  from
       standard input, the other one is given via its file name.

       It  is assumed that the file (A) given by file name was obtained by processing another BAM
       file by the sequence

       bamcollate2 collate=1 | bamcollate2 collate=2

       where the first run of bamcollate2 makes sure that the ends of pairs appear adjacently and
       the second run attaches rank pairs to the read names.

       The  other  file  (B) read by bam12auxmerge via standard input is assumed be a (re)aligned
       version of file (A), which is processed by

       bamsort SO=queryname

       right before being passed to bam12auxmerge.

       This preprocessing ensures that bam12auxmerge observes the reads in the same  order,  with
       the  possibility  of  file  (B)  containing  multiple  lines for each read (i.e. secondary
       alignments).

       bam12auxmerge merge the SAM headers of (A) and (B) by starting with the header for (B) and
       prepending the PG type lines from (A), thus restoring the full history of the file to (B).
       Alignments are merged by  inserting  the  auxiliary  tags  from  lines  in  (A)  into  the
       corresponding  lines in (B).  Priority is given here to (B), i.e. if a tag appears in both
       than the version in (B) will be retained.

       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 (default)

       0:     do not print progress report

       mod=<1048576>: Print progress report after processing each mod'th alignment if verbose  is
       active.

       ranksplit=<1>:  Split  rank  pairs  into  single  ranks per read/alignment. This acts like
       preprocessing the file with bam12split before handing it to bam12auxmerge.

       rankstrip=<1>: Strip ranks from reads/alignments. This acts like postprocessing  the  file
       with bam12strip after handing it to bam12auxmerge.

       clipreinsert=<1>: Reinsert clipped sequence and quality string parts while marking them as
       soft clipped. This acts like postprocessing the file with bamclipreinsert after handing it
       to bam12auxmerge.

       zztoname=<1>:  Insert rank stored in zz auxiliary field to name as a prefix and remove the
       zz auxiliary field. This acts like postprocessing the file with bamzztoname after  handing
       it to bam12auxmerge.

       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 md5filenameis 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.