hash.h

#include <stdint.h>
#include "bwt.h"

//#define TABLESIZE 4087//4087
#define TABLESIZE 8193//4087
#define MAX_READ_SIZE 6020 
//extern const int TABLESIZE;
#ifndef hash_header
#define hash_header
typedef struct{
	uint64_t place; //index of 2l
	int value;
	uint64_t level;
//	uint64_t width;
	uint64_t index; //real matched index
	//char cigar[100];
	//uint64_t left; //
	//uint64_t old_left;
	uint64_t last; //last seed that updtates left
	uint64_t groupid;
	uint64_t match_start[55];//start position in read
	uint64_t match_index[55];//start position in reference
	uint64_t matched[55];
	int parts;
	int mate;
}hash_element;

typedef struct{
	int paired;
	hash_element *pair_table;
	uint64_t min_dis,max_dis;
	uint64_t len1,len2;
	int pairID;
	char ori[3];
	int strict;
} pair_opt;


void add(bwt_t *const bwt, uint64_t place,uint64_t value,uint64_t level, uint64_t index, int * best, int best_size, int * best_found, hash_element * table, 
		uint64_t read_start, uint64_t read_size, uint64_t read_index, int whole_read_size,uint64_t groupid);

void reset_hash(hash_element * table);

uint64_t uminus(uint64_t x, uint64_t y);
#endif