bamsplitdiv1

Usage

Overview

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

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