prommapped [options] -i <file>
- -i <string>
- An input file containing read mapping results. Both SAM or BAM formats are supported.
- -o <string>
- Name of output file including mapping statistics.
- If specified, fragments (read pairs) will be counted instead of individual reads. This option is only applicable for paired-end reads.
If specified, only properly paired reads will be counted. This
option is only applicable for paired-end reads.