text: #include "../tools/_trimmer.h"
  
  int main (int argc, char * const argv[])
  {
  	if (argc != 7)
  	{
  		cout << "Usage: ./trim genome infile outfile max_mchs max_errs min_size" << endl;
  		cout << endl;
  		cout << "Param 1: (path) genome: full path to the reference genome FastA file" << endl;
  		cout << "Param 2: (path) infile: full path to the input file of mapped reads in .slam format" << endl;
  		cout << "Param 3: (path) outfile: full path to the output file (also .slam format)" << endl;
  		cout << "Param 4: (+int) max_mchs: read kept if CH count <= max_mchs" << endl;
  		cout << "Param 5: (+int) max_errs: read kept if mismatch count <= max_errs" << endl;
  		cout << "Param 6: (+int) min_size: read kept if read length >= min_size" << endl;
  		cout << endl;
  		cout << "Example: ./trim ./human.fa ./reads.slam ./trimmed_reads.slam 4 3 20" << endl;		
  		return 1;
  	}
  	ReadSlam::Trimmer trimmer;
  	trimmer.load(argv[1]);
  	trimmer.trim(argv[2], argv[3], atoi(argv[4]), atoi(argv[5]), atoi(argv[6]));
  
  	return 0;
  }
  
  