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 <tischler@mpi-cbg.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.