NAME

       bamauxmerge - merge information in unmapped and mapped alignment files

SYNOPSIS

       bamauxmerge [options] in_unmapped in_mapped

DESCRIPTION

       bamauxmerge  reads  and  merges  two  SAM/BAM/CRAM  files  which  are expected to have the
       following properties:

       *      the first file contains only unmapped reads and it's header contains no SQ lines

       *      the second file was produced by an aligner based on the content of the first file.

       *      the order of the reads is the same in the  first  an  second  file  into  a  single
              alignment file.

       The headers of the two files are merged in the following file:

       *      the  SQ lines contained in the header of the second file are appended to the header
              of the first file to obtain the header of the output file

       *      all other header information from the second file is discarded

       The output records are constructed in the following way:

       1.     Take a record from the second file

       2.     Copy all aux fields from the corresponding record in the first file which  are  not
              already present.

       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.

       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.

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

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

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.