bamsplit1

Usage

Overview

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