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#ifndef _BLASR_FASTA_READER_HPP_
#define _BLASR_FASTA_READER_HPP_
#include <stdint.h>
#include <string>
#include "FASTASequence.hpp"
#include "metagenome/SequenceIndexDatabase.hpp"
class FASTAReader {
protected:
GenomeLength fileSize;
int fileDes;
char* filePtr;
GenomeLength curPos;
int padding;
char endOfReadDelim;
char readStartDelim;
bool doToUpper;
unsigned char *convMat;
//
// Quick check to see how much to read.
//
void SetFileSize();
void ReadTitle(GenomeLength &p, char *&title, int &titleLength);
public:
bool computeMD5;
std::string curReadMD5;
void Init();
FASTAReader();
FASTAReader(std::string &fileName);
void SetSpacePadding(int _padding);
void SetToUpper();
//
// Synonym for Init() for consistency.
//
int Initialize(std::string &seqInName);
int Init(std::string &seqInName, int passive=0);
void AdvanceToTitleStart(GenomeLength &p, char delim='>');
void CheckValidTitleStart(GenomeLength &p, char delim='>');
GenomeLength ReadAllSequencesIntoOne(FASTASequence &seq, SequenceIndexDatabase<FASTASequence> *seqDBPtr=NULL);
void ReadTitle(GenomeLength &p, FASTASequence & seq);
int GetNext(FASTASequence &seq);
/*
Advance to the read nSeq forward.
input: nSeq, the number of sequences to skip.
output:
returns 1 if after advancing nSeq sequences, the file pointer is pointing to
a new sequence.
0 otherwise.
A return value of 0 will signal that the file is done being processed if it is
iterting over reads.
*/
int Advance(int nSeq);
int CriticalGetNext(FASTASequence &seq);
int ConcatenateNext(FASTASequence &cur);
void Close();
void ReadAllSequences(vector<FASTASequence> &sequences);
};
#endif // _BLASR_FASTA_READER_HPP_
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