NAME

       propmapped - calculate the proportion of mapped reads/fragments

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.