#include <iostream>
#include <fstream>
#include <string>
#include <stdlib.h>

using namespace std;

#include "mx_node.h"
#include "build_kmer_tree.cc"
#include "print_kmer_tree.cc"

int main(int argc, char* argv[])
{
	// Check the number of parameters
	if (argc !=4) {
		// Tell the user how to run the program
             std::cerr << "Usage: " << argv[0] << " INPUT_Kmers.txt " << "HIT_FREQ.txt_FILE " << "stgRNA_length" << std::endl;
             return 1;
       	}

	ofstream hits;
	ofstream freq;

	int bc_length = atoi(argv[3]);

	string gRNA;
	int gRNA_len;
	char curr_char;
	string curr_kmer;
	int curr_depth;
	bool end_of_gRNA;
        int curr_counter;

	mx_node* master_node = new mx_node();

	build_kmer_tree(master_node, argv[1], bc_length); 

	print_kmer_tree(master_node, argv[2]);

return 0;
}