USAGE

prommapped [options] -i <file>

Required arguments:

-i <string>

An input file containing read mapping results. Both SAM or BAM formats are supported.

Optional arguments:

-o <string>

Name of output file including mapping statistics.

-f

If specified, fragments (read pairs) will be counted instead of individual reads. This option is only applicable for paired-end reads.

-p

If specified, only properly paired reads will be counted. This option is only applicable for paired-end reads.