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/*
* readfastq.h
*
*  Created on: Sep 27, 2011
*      Author: michael
*      Edited by: scarysandwich
*      Edited on: April 25, 2013
*/
 
#ifndef READFASTQ_H_
#define READFASTQ_H_
 
#include<iostream> //to open files
#include<fstream> //file stream
#include<stdio.h>
#include<stdlib.h> //to use malloc
#include<string.h>
#include<string>
#include"shortread.h"
#include<vector>
 
#include <istream>
 
 
#include <boost/iostreams/device/file.hpp>
#include <boost/iostreams/stream.hpp>
#ifdef GZIP
#include <boost/iostreams/device/file.hpp>
#include <boost/iostreams/stream.hpp>
#include <boost/iostreams/filtering_streambuf.hpp>
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/filter/gzip.hpp>
#endif
 
 
#define TIMEMEASURE
#define TIMECALC(start, end) (((end.tv_sec - start.tv_sec) * 1000000 + (end.tv_usec - start.tv_usec)) / 1000)
 
 
using namespace std;
 
class fastqfile{
 
    std::vector<string> _names;
    std::vector<char>  _seqs;
    std::vector<char>  _phred;
 
    int _filelength;
    int _SRlength;
    int _blocksize;
 
 
public:
 
    fastqfile(char *filename, int SRlength, uint32_t blocksize){
        readfastq(filename, SRlength, blocksize);
    }
 
    string      *getNames(){    return &(_names[0]);}
    char        *getSeqs(){ return &(_seqs[0]);}
    char        *getPhred(){    return &(_phred[0]);}
    uint32_t    getNumberOfSR(){ return _filelength;}
    uint32_t    getSRlegth() {return _SRlength;}
 
    string      getNameAt(uint32_t i){ return _names.at(i);}
    void        getSRAt(uint32_t i, char *ret){ strncpy(ret, &(_seqs[i]), _SRlength);}
    void        getPhredAt(uint32_t i, char *ret){strncpy(ret, &(_phred[i]), _SRlength);}
 
    void        setNumberOfSRs(uint32_t num){
        _filelength = num;
    }
 
    void readfastq(char *filename, int SRlength) {
        _filelength = 0;
        _SRlength = SRlength;
 
        size_t bytes_read, bytes_expected;
        timeval start, end;
        gettimeofday(&start, 0);
 
        FILE *fp;
        fp = fopen(filename, "r");
 
        fseek(fp, 0L, SEEK_END); //go to the end of file
        bytes_expected = ftell(fp); //get filesize
        fseek(fp, 0L, SEEK_SET); //go to the begining of the file
 
        fclose(fp);
 
        if ((_seqarray = (char *) malloc(bytes_expected/2)) == NULL) //allocate space for file
            err(EX_OSERR, "data malloc");
 
 
        string name;
        string seqtemp;
        string garbage;
        string phredtemp;
 
        boost::iostreams::stream<boost::iostreams::file_source>file(filename);
 
 
        while (std::getline(file, name)) {
            std::getline(file, seqtemp);
            std::getline(file, garbage);
            std::getline(file, phredtemp);
 
            if (seqtemp.size() != SRlength) {
                if (seqtemp.size() != 0)
                    printf("Error on read in fastq: size is invalid\n");
            } else {
                _names.push_back(name);
 
                strncpy( &(_seqarray[SRlength*_filelength]), seqtemp.c_str(), seqtemp.length()); //do not handle special letters here, do on GPU
 
                _filelength++;
            }
        }
        gettimeofday(&end, 0);
 
#ifdef TIMEMEASURE
        cerr << "FastQ block read in " << TIMECALC(start, end) << "ms" << endl;
#endif
    }
 
 
 
    void print(){
        for(int i=0; i<_seqs.size(); i++){ //three lines each record
            printf("%i-", _seqs.at(i));
        }
        printf("\n");
    }
 
};
 
#endif /* READFASTQ_H_ */