NAME¶

bamsplitdiv - split BAM file into a set of BAM files

SYNOPSIS¶

bamsplitdiv [options]

DESCRIPTION¶

bamsplitdiv reads a BAM file via standard input and creates a set of output BAM files containing the alignments in the input. Given a positive natural number div bamsplitdiv will create div files. The alignments in the input file will be distributed to the output files in a round robin type scheme, i.e. entries 0, div, 2div, 3div, etc. will be written to the first output file, 1,div+1,2div+1, 3div+1, etc. to the second etc.

The following key=value pairs can be given:

div=<1>: number of output files

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.