read_genes.h

#ifndef READ_GENES_H
#define READ_GENES_H 

#include <string>
#include <fstream>

#include "bwt.h"

#define ERROR_EXIT_CODE 1

typedef struct {
    std::string id;
    std::string forward_read;
    std::string forward_read_quality;
    std::string backward_read;
    std::string backward_read_quality;
} read_block;

bool checkFileExistence(const std::string&);
void getFile(const std::string&, /*out*/ std::ifstream&);

// reafactor these
std::string reverse_complement(const std::string& s);
void print_matches(block* bl, const std::string& id, const std::string& test, BWT* bwt);
int number_of_mismatches(const std::string &s1, const std::string& s2);

std::string read_reference_gene(const std::string& filename, std::string& refName, std::vector< std::pair<int, int> >& holes);

class ReadGenes {
    private:
        std::ifstream file_1;
        std::ifstream file_2;
    public:
        ReadGenes(const std::string& filename_1, const std::string& filename_2);
        read_block* get_one_read();       
};

#endif