/*
* 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_ */