bamsplitdiv - split BAM file into a set of BAM files
bamsplitdiv [options]
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
Written by German Tischler.
Report bugs to <
[email protected]>
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.