#include <cstdio>
#include <cstdlib>
#include <iostream>
#include <algorithm>
#include <string>
#include <fstream>
#include <map>
#include <sys/stat.h>



using namespace std;

int main(int nNumberofArgs, char* pszArgs[])
{
	
	
	system("clear");
	
	cout<<"\t\t Format_convert"<<endl;
	cout<<"\t\t --------------"<<endl;
	cout<<"This program converts Illumina/Solexa output files (Fastq)"<<endl;
	cout<<"to an output file compatible with the galign program."<<endl;
	cout<<"Output of this program is a file called 'yourname_reads.txt' located"<<endl;
	cout<<"in the 'Sequence_reads' folder in the 'galign' folder."<<endl<<endl;
	cout<<"To begin, please place the files to be converted on the Desktop."<<endl<<endl;
	
	
	string name;
	cout<<"Your first name: ";
	cin>>name;
	
	name.append("_reads.txt");
	
	string outputfile="Desktop/galign/Sequence_reads/";
	
	outputfile.append(name);
	
	int srf;
	
	cout<<"How many sequence read files do you have? ";
	cin>>srf;
	
	cout<<endl;
	
	int remove;
	
	cout<<"Often, sequence reads are inaccurate at the 3' end."<<endl;
	cout<<"How many nucleotides should be removed from each end? ";
	cin>>remove;
	
	int rr;
	string file;
	
	string *filename;
	filename=new string[100];
	
	for (int i=0;i<srf;i++){
		rr=0;
		
		while (rr==0){
			cout<<"Input file name number "<<i+1<<": ";
			cin>>file;
			filename[i]="Desktop/";
			filename[i].append(file);
			
			FILE *fp;
			fp=fopen(filename[i].c_str(),"r");
			if(fp!=NULL){
				rr=1;
			}
		}
	}
	
	int hh=0;
	string line;
	int length;
	int overlap;
	double leg;
	
	ifstream fh (filename[0].c_str());
	while(! fh.eof()){
		getline (fh, line);
		hh++;
		if (hh==2){
			length=line.length()-remove;
			if (length<26){
				cout<<"Error. Sequence reads too short for conversion (minimum 26)."<<endl;
				abort();
			}
			if (length>=26 && length<=39){
				overlap=0;
			}
			if (length>39 && length<=52){
				overlap=26;
			}
			if (length>53 && length<=78){
				leg=length;				
				overlap=int((leg/2)+0.5);
			}
			if (length>78){
				cout<<"Error. Sequence reads too long for conversion (maximum 78)."<<endl;
				abort();
			}
			
			break;
		}
	}
	
	fh.close();
	
	hh=0;
	string subfirst;
	string subsecond;
	
	ofstream f(outputfile.c_str());
		
	if (overlap==0){
		f<<length-26<<endl;
		f<<"0"<<endl;
		for (int i=0;i<srf;i++){
			ifstream fh1 (filename[i].c_str());
			cout<<"Reading"<<filename[i]<<endl;
			
			while (! fh1.eof()){
				getline (fh1, line);
				if (line.size()<1){
					break;
				}
					
				hh++;
				if (hh==4){
					hh=0;
				}
				if (hh==2){					
					subfirst=line.substr(0,length);
					transform(subfirst.begin(), subfirst.end(), subfirst.begin(), ::tolower);
					f<<subfirst<<endl;
				}
			}
			
			fh1.close();
		}
	}
	
	if (overlap>0){
		f<<overlap-26<<endl;
		f<<2*overlap-length<<endl;
		
		for (int i=0;i<srf;i++){
			ifstream fh1 (filename[i].c_str());
			cout<<"Reading "<<filename[i]<<endl;
			
			while (! fh1.eof()){
				getline (fh1, line);
				if (line.size()<1){
					break;
				}
				hh++;
				if (hh==4){
					hh=0;
				}
				if (hh==2){
					subfirst=line.substr(0,overlap);				
					transform(subfirst.begin(), subfirst.end(), subfirst.begin(), ::tolower);
					f<<subfirst<<endl;
					subsecond=line.substr(length-overlap,overlap);
					transform(subsecond.begin(), subsecond.end(), subsecond.begin(), ::tolower);
					f<<subsecond<<endl;
				}
			}
			
			fh1.close();
		}
	}
	
	f.close();
	cout<<"Done."<<endl;
	
	system("PAUSE");
	return 0; 
}