NAME

       bamsplit - split BAM files

SYNOPSIS

       bamsplit [options]

DESCRIPTION

       bamsplit  reads  a  BAM  file via standard input and creates a set of output files with at
       most a given number of alignments each. The concatenation of the output files  via  bamcat
       restores  the  sequence  of  alignments in the original input file. The splitting does not
       consider read pairs, i.e. the ends of pairs can end up in separate files.

       The following key=value pairs can be given:

       n=<65536>: number of alignments per output file.

       prefix=<filename> prefix  for  the  create  files.  The  created  files  will  have  names
       ${prefix}_000000.bam, ${prefix}_000001.bam, etc.

       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

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.