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#include <string>
#include <stdlib.h>
#include <sys/stat.h>
#include "htslib/bgzf.h"
#include "htslib/tbx.h"
#include "htslib/kseq.h"
#include <iostream>
#include <cstring>
#include <vector>
using namespace std;
class Tabix {
htsFile* fn;
tbx_t* tbx;
kstring_t str;
hts_itr_t* iter;
const tbx_conf_t *idxconf;
int tid, beg, end;
string firstline;
bool has_jumped;
vector<string>::iterator current_chrom;
public:
string filename;
vector<string> chroms;
Tabix(void);
Tabix(string& file);
~Tabix(void);
const kstring_t * getKstringPtr();
void getHeader(string& header);
bool setRegion(string& region);
bool getNextLine(string& line);
bool getNextLineKS();
};
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