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#ifndef _GCDBYANK_H
#define _GCDBYANK_H
#include "gcdb.h"
#include <stdio.h>
#include "GFastaFile.h"
// FastaSeq class and *charFunc() callback type
#define DEF_CDBREC_DELIM ">"
#ifdef ENABLE_COMPRESSION
#include <zlib.h>
#define GCDBZ_SBUF_LEN 8192
#define GCDBZ_LBUF_LEN 8192*2
class GCdbZFasta {
private:
char* recdelim;
char lbuf[GCDBZ_LBUF_LEN]; //larger buffer
char sbuf[GCDBZ_SBUF_LEN]; //smaller buffer
char* defline; //defline copy storage -- compression only
int defline_cap; //currently allocated length of defline
int defline_len; //currently used length of defline
z_stream zstream; // de/compression stream
FILE* zf; //compressed file
long zpos; //current position in zf
int zrecsize; // the size of the compressed record
GFastaCharHandler* chrhandler;
public:
GCdbZFasta(FILE* af, int zrsize=0, char* r_delim=DEF_CDBREC_DELIM);
~GCdbZFasta();
FILE* getZFile() { return zf; }
void decomp_start(int zrsize);
void decomp_end();
int decompress(FastaSeq& rec, int csize=0, int zfofs=-1, charFunc* seqCallBack=NULL);
// uncompress csize bytes from file zf, from optional file offset zfofs,
// and send the uncompressed stream to callbackFn
};
#endif
class GCdbYank {
char* idxfile;
//char* dbfile;
char* recdelim; //record delimiter -- typically ">"
int warnings;
bool is_compressed;
char* dbname;
char* info_dbname;
off_t db_size;
cdbInfo dbstat;
GCdbRead* cdb;
#ifdef ENABLE_COMPRESSION
GCdbZFasta* cdbz;
#endif
int fdb;
int fd;
FILE* fz; // if compressed
GFastaCharHandler* fastahandler;
#ifdef ENABLE_COMPRESSION
protected:
GCdbZFasta* openCdbz(char* p);
#endif
public:
GCdbYank(const char* fidx, const char* recsep=DEF_CDBREC_DELIM);
~GCdbYank();
int getRecord(const char* key, FastaSeq& rec, charFunc* seqCallBack=NULL);
off_t getRecordPos(const char* key, uint32* record_len=NULL);
char* getDbName() { return dbname; }
};
#endif
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