Usage:

./removeDup [options] -i <input_file> -o <output_file>

Required arguments:

-i <string> Name of input file in SAM/BAM format.

-o <string> Name of output SAM file including filtered reads. The format is

BAM unless '-S' is specified.

Optional arguments:

-S

Generate the SAM format output.

-r <int>

Specify the duplication cutoff. All the reads mapped to a location are removed from the output if the number of reads mapped to this location is equal or higher than the cutoff. 10 by default.

-t <string> A directory storing temporary files generated by the program.