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fastq_reader.h
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fastq_reader.h
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#ifndef _FASTQ_READER_H_
#define _FASTQ_READER_H_
#include <vector>
#include <string>
#include <cstdlib>
#include <fstream>
#include <boost/filesystem.hpp>
#include <boost/filesystem/fstream.hpp>
#include "kmer.h"
/* FIXME - This should be more dynamic. */
const int MAX_LINE_LEN = 1024;
const int ILLUMINA_QUAL_OFFSET = 64;
class FastQReader {
public:
FastQReader(std::vector<std::string>& fnames, k_t k);
uintmax_t total_bytes(void);
void seek(uintmax_t offset);
void set_max_byte(uintmax_t max_byte);
uintmax_t tell(void);
bool next_file();
bool read_next(qekmer_t* qekmer);
protected:
void seek_to_next_read();
k_t k;
std::vector<boost::filesystem::path> paths;
std::vector<boost::filesystem::path>::iterator curr_path;
boost::filesystem::ifstream curr_file;
uintmax_t so_far; // At the granularity of files
uintmax_t max_byte;
char read[MAX_LINE_LEN]; /* In 'base' type. */
qual_t quals[MAX_LINE_LEN];
size_t read_col; /* The column index within the current read that
the next kmer (acutal kmer; not k+2-mer)
starts from. */
size_t read_len;
};
#endif /* _FASTQ_READER_H_ */