#include <iostream>
#include <fstream>
#include <string>
#include <vector>

using namespace std;

int main (int argc, char* argv[]) 
{
	string line, discard;
	if(argc < 3){
		cerr << "Usage: <bgl file> <fam file>";
		return 0;
	}
	ifstream file_bgl(argv[1]);
	ifstream file_ped(argv[2]);
	if(!file_bgl || !file_ped) { cerr << "file could not be opened" << endl; return 0; }

	// get number of individuals
	file_bgl >> discard >> discard;
	getline(file_bgl,line);
	int nr_ind = line.length()/4;
	file_bgl.seekg(0);
	string * seq = new string[nr_ind];

	// read all markers
	int snp_ctr = 0;
	while(!file_bgl.eof())
	{
		// discard meta info
		discard = "";
		file_bgl >> discard >> discard;
		if(discard == "") continue;

		// read haplotype
		for(int i=0;i<nr_ind;i++)
		{
			file_bgl >> discard;
			if(snp_ctr == 0) seq[i] = discard;
			else seq[i] += " " + discard;
			file_bgl >> discard;
			seq[i] += " " + discard;
		}
		snp_ctr++;
	}

	// print all markers
	file_bgl.close();
	for(int i=0;i<nr_ind;i++)
	{
		// print meta info
		getline(file_ped,line);
		cout << line << ' ';
		cout << seq[i] << endl;
	}
	file_ped.close();
	return 1;
}