NAME

       bamcat - concatenate BAM files

SYNOPSIS

       bamcat [options]

DESCRIPTION

       bamcat reads a set of input BAM files, merges the headers, concatenates the alignment data
       and writes the output on standard output in BAM format. The input files can  be  specified
       via  the  I key. Any none key=value arguments given after the key=value pairs will also be
       considered as input files.

       The following key=value pairs can be given:

       I=<stdin>: name of the input file. This key can be used multiple times

       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.

       streaming=<0>:  streaming  mode inactive or active. By default streaming mode is inactive.
       Valid values are

       0:     streaming mode is inactive. Only one input file will be opened at any single  time,
              but  each input file is openend twice (once for reading the header only, the second
              time for extracting the alignment data).

       1:     streaming mode is active. All input files will be opened at the same time and  kept
              open until data processing is finished. Each input file will be opened only once.

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.