# HG changeset patch
# User fz77
# Date 1416235244 18000
# Node ID 6a5cfb8a872f8e82391a3fd028304faea4031fa0
# Parent  2aad8f91e6f21187ef47f15a51c74ebd49b8f2ba
Uploaded

diff -r 2aad8f91e6f2 -r 6a5cfb8a872f pscan_chip/pscan_chip_g.cpp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pscan_chip/pscan_chip_g.cpp	Mon Nov 17 09:40:44 2014 -0500
@@ -0,0 +1,2908 @@
+// Pscan-ChIP 1.1
+// // Copyright (C) 2013  Federico Zambelli and Giulio Pavesi
+// //
+// // This program is free software: you can redistribute it and/or modify
+// // it under the terms of the GNU General Public License as published by
+// // the Free Software Foundation, either version 3 of the License, or
+// // (at your option) any later version.
+// //
+// // This program is distributed in the hope that it will be useful,
+// // but WITHOUT ANY WARRANTY; without even the implied warranty of
+// // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// // GNU General Public License for more details.
+// //
+// // You should have received a copy of the GNU General Public License
+// // along with this program.  If not, see <http://www.gnu.org/licenses/>.
+// //
+// // If you find Pscan-ChIP useful in your research please cite our paper:
+// //
+// // Zambelli F, Pesole G, Pavesi G. PscanChIP: Finding over-represented
+// // transcription factor-binding site motifs and their correlations in sequences from
+// // ChIP-Seq experiments. 
+// // Nucleic Acids Res. 2013 Jul;41(Web Server issue):W535-43.
+
+#include <string>
+#include <iostream>
+#include <fstream>
+#include <vector>
+#include <sstream>
+#include <math.h>
+#include <map>
+#include <cstdlib>
+#include <gsl/gsl_randist.h>
+#include <gsl/gsl_cdf.h>
+#include <string.h>
+#include <ctime>
+
+using namespace std;
+
+const double MIN_ADD_FREQ = 0.01, EPSILON = pow(10,-21), INF = pow(10,21), /*POS_VIS_THRESHOLD = pow(10,-5),*/ DIST_RATIO_THRESHOLD = 3, DIST_PV_THRESHOLD = pow(10,-5);
+const unsigned int MAX_REG_SIZE = 3000, ALPHABET_SIZE = 4, TOP_P = 1, DIST_HIT_THRESHOLD = 10;
+//const char ALPHABET[4] = {'A','C','G','T'}, RC_ALPHABET[4] = {'T','G','C','A'};
+char VI['T' + 1];
+string regfile, genome, matrixfile, additional_matrixfile, outfile, bgfile, selected, obstf, GALAXY_OUTPUT;
+unsigned int RSIZE = 150, MAX_L = 0, W_SIZE = 10, W_STEP = 5;
+bool SECOND_BEST_POS = false, SINGLE_STRAND = false, VERBOSE = false, GET_SEQUENCES = false, POSITIONAL = false, SINGLE_MATRIX = false, SPEARMAN = false, TWOBIT = false, QUIET = false; //NAIVE = false;
+ofstream fasta_out;
+double SINGLE_MATRIX_BG_AVG = 0;
+
+struct mpoint
+{
+	unsigned int x;
+	unsigned int y;
+};
+
+struct bg
+{
+	unsigned int Size;
+	double Avg, Var;
+};
+
+class sequence
+{
+	private:
+	string Chr, Name;
+	char *Seq;
+	unsigned int Start, End, E_Rank;
+	char Strand, AntiStrand;
+	bool good;
+	public:
+	sequence(string*, ifstream*, unsigned int);	
+	sequence(string*, unsigned int, string, unsigned int);
+	char strand();
+	char antistrand();
+	string chr();
+	unsigned int start();
+	unsigned int end();
+	unsigned int e_rank();
+	string name();
+	char* seq();
+	bool is_good();
+	double score();
+	int mpos();
+};
+
+class matrix
+{
+	friend void scanner(vector<matrix>*, vector<sequence>*);
+	private:
+	void normalizer();
+	void to_log();
+	void avg();
+	void max_min();
+	void rev_c();
+	double get_M_value(int, char);
+	double get_rc_M_value(int, char);
+	void calc_var(double);
+	void calc_W_param(double);
+	void welch_test(double);
+	void welch_test_bg(double);
+//	void welch_test_bg_G(double);
+	void welch_test_pos(double);
+	void z_test_pos(double);
+	unsigned int L, bg_Size, BIN_NUM;
+	double **M;
+	double **rc_M;
+	double max_score, min_score, t, dof, t_bg, dof_bg;
+	double spearman;
+	string Name, Id;
+	bool O_U, O_U_bg;
+	vector<bool> W_O_U;
+	bool good, BG;
+	bool norm_sec_step;
+	vector<double> v_score, vF_score;
+	vector<unsigned int> v_pos;
+	vector<bool> v_strand;
+	vector<vector<double> > W_R_v_score;
+	vector<double> W_R_Avg, W_R_Var, W_R_pvalue, W_R_T_pvalue;
+	double R_Avg, F_Avg, R_Var, F_Var, /*G_Avg, G_Var,*/ pvalue, W_Avg, W_Var;
+	double bg_Avg, bg_Var, pvalue_bg;
+	public:
+	matrix(vector<string>*, map<string,bg>*);
+	void display();
+	bool is_good();
+	string name();
+	string id();
+	string o_or_u();
+	string o_or_u_bg();
+	int W_o_or_u(unsigned int);
+	void scan(vector<sequence>*);
+	double scan_seq_ds(char*, bool, unsigned int, vector<double>*);
+	double scan_seq_ss(char*, bool, unsigned int, char, vector<double>*);
+	double scan_seq_ds_second_best(char*, unsigned int, unsigned int *, bool *, int);
+	double scan_seq_ss_second_best(char*, unsigned int, unsigned int *, bool *, unsigned int, bool);
+	double get_score_at(unsigned int);
+	unsigned int get_pos_at(unsigned int);
+	unsigned int length();
+	bool get_strand_at(unsigned int);
+	bool have_bg();
+	unsigned int bin_num();
+	double get_R_Avg();
+	double get_F_Avg();
+	double get_bg_Avg();
+	double get_R_Var();
+	double get_F_Var();
+	double max();
+	double min();
+	double get_pvalue();
+	double get_pvalue_bg();
+	double get_W_pvalue(unsigned int);
+	double get_W_R_Avg_at_pos(unsigned int);
+	double get_t();
+	double get_dof();
+	double get_spearman();
+	double get_W_Avg();
+	double get_W_R_T_pvalue(unsigned int);
+};
+
+void command_line_parser(int, char**);
+void acquire_regions(vector<sequence>*);
+void acquire_matrices(vector<matrix>*, map<string,bg>*, string*);
+void acquire_background(map<string,bg>*);
+void scanner(vector<matrix>*, vector<sequence>*);
+void main_output(vector<matrix>*, vector<sequence>*, unsigned int);
+void main_output_single_matrix(vector<matrix>*, vector<sequence>*);
+void distance_analysis(vector<matrix>*, vector<sequence>*, unsigned int, multimap <double, vector<matrix>::iterator>*);
+void display_help();
+
+int main(int argc, char **argv)
+{
+	srand(time(NULL));
+	
+	vector<sequence> Seq;
+	vector<matrix> Mat;
+	map<string,bg> Bg;
+	VI['A'] = 0;
+	VI['C'] = 1; 
+	VI['G'] = 2;
+	VI['T'] = 3;
+	VI['N'] = 4;
+
+	obstf.clear();
+
+	command_line_parser(argc, argv);		
+
+	if(GET_SEQUENCES)
+	{
+		string outfile = regfile;
+		outfile += ".fasta";
+		fasta_out.open(outfile.c_str(), ios::out);
+	}
+
+	if(!regfile.empty() && !matrixfile.empty())
+	{
+		if(!bgfile.empty())
+		{
+			if(!QUIET) cerr << "\nAcquiring background file... ";
+			acquire_background(&Bg);
+			if(!QUIET) cerr << "done" << endl;
+		}
+
+		if(!QUIET) cerr << "\nReading binding profiles...";
+                acquire_matrices(&Mat, &Bg, &matrixfile);
+		
+		if(!additional_matrixfile.empty())
+			acquire_matrices(&Mat, &Bg, &additional_matrixfile);
+		
+		if(Mat.empty())
+		{
+			if(!QUIET) cerr << "\nZero valid matrices acquired. Quitting..." << endl;
+			exit(1);
+		}
+	
+                if(!QUIET) cerr << "done: " << Mat.size() << " binding profiles acquired. Max matrix length = " << MAX_L << endl;
+
+		if(Mat.size() == 1)
+		{
+			if(!QUIET) cerr << "\nSwitching to single matrix mode..." << endl;
+			SINGLE_MATRIX = true;
+		}
+
+		if(!QUIET) cerr << "\nAcquiring regions...";
+		acquire_regions(&Seq);
+		if(!QUIET) cerr << "done: " << Seq.size() << " unique regions acquired." << endl;
+
+		if(Seq.size() <= 2)
+			POSITIONAL = false;
+
+		if(Seq.empty())
+		{
+			if(!QUIET) cerr << "\nZero regions to work on! Exiting..." << endl;
+			exit(1);
+		}
+
+		if(GET_SEQUENCES)
+		{
+			fasta_out.close();
+			exit(0);
+		}
+
+//		for(unsigned int i = 0; i < Mat.size(); i++)
+//			Mat[i].display();
+
+		if(!QUIET) cerr << "\nScanning...";
+		scanner(&Mat, &Seq);
+
+		if(!QUIET) cerr << "\nWriting output..." << endl;
+
+		if(!SINGLE_MATRIX)
+			main_output(&Mat, &Seq, Seq.size());
+		else
+			main_output_single_matrix(&Mat, &Seq);
+
+		if(!QUIET) cerr << "\nOutput written in file: " << outfile << endl;
+		
+	}
+	else if(GET_SEQUENCES && !regfile.empty())
+	{
+		if(!QUIET) cerr << "\nAcquiring regions...";
+                acquire_regions(&Seq);
+                if(!QUIET) cerr << "done: " << Seq.size() << " unique regions acquired." << endl;
+
+		fasta_out.close();
+                exit(0);
+	}
+	else
+		display_help();
+
+
+/*	for(unsigned int i = 0; i < Seq.size(); i++)
+	{
+		cout << ">" << i+1 << '\t' << Seq[i].name() << '\t' << Seq[i].start() << '\t' << Seq[i].end()  << '\t'
+		<< Mat[0].get_score_at(i) << '\t' << Mat[0].get_pos_at(i) << '\t' << Mat[0].get_strand_at(i) << '\t' 
+                << "Max = " << Mat[0].max() << '\t' << "Min = " << Mat[0].min()
+		<< endl << Seq[i].seq() << endl;
+		cout << ">" << i+1 << '\t' << Seq[i].name() << '\t' << "UPSTREAM" << endl << Seq[i].uf_seq() << endl;
+		cout << ">" << i+1 << '\t' << Seq[i].name() << '\t' << "DOWNSTREAM" << endl << Seq[i].df_seq() << endl;
+	}
+*/
+	
+	return 0;
+}
+
+void display_help()
+{
+	if(!QUIET) cerr << endl << "Syntax: pscan_chip -r region_file.bed -M matrixfile.wil -g genome [-pos] [-wsize window_size] [-wstep window_step] [-bg background_file] [-s region_size]" << endl << endl;
+	exit(0);
+}
+
+void main_output_single_matrix(vector<matrix> *Mat, vector<sequence> *Seq)
+{
+	outfile = regfile;
+	outfile += ".";
+	outfile += Mat->at(0).id();
+
+	string outfile2 = outfile;
+
+	outfile += ".ris";
+	outfile2 += ".all.ris";
+
+	if(!GALAXY_OUTPUT.empty())
+                outfile = GALAXY_OUTPUT;
+	
+	multimap <double, string> outmap;
+
+	ofstream out(outfile.c_str(), ios::out);
+	ofstream out2(outfile2.c_str(), ios::out);
+
+	if(!out)
+        {
+                if(!QUIET) cerr << "\nError! Can't open output file: " << outfile << " for writing..." << endl;
+                exit(1);
+        }
+
+	out << "CHR\tREG_START\tREG_END\tREG_STRAND\tABS_SITE_START\tABS_SITE_END\tREL_SITE_START\tREL_SITE_END\tSITE_STRAND\tSCORE\tSITE";
+	out2 << "CHR\tREG_START\tREG_END\tREG_STRAND\tABS_SITE_START\tABS_SITE_END\tREL_SITE_START\tREL_SITE_END\tSITE_STRAND\tSCORE\tSITE";
+
+//	if(SPEARMAN)
+//		out << "\tE_RANK";
+
+	if(SECOND_BEST_POS)
+	{
+		out << "\tSB_POS\tSB_SCORE\tSB_OLIGO\tSB_STRAND" << endl;
+		out2 << "\tSB_POS\tSB_SCORE\tSB_OLIGO\tSB_STRAND" << endl;
+	}
+	else
+	{
+		out << endl;
+		out2 << endl;
+	}
+
+	matrix *M = &Mat->at(0);
+
+/*	if(SINGLE_MATRIX_BG_AVG == 0)   //QUESTO SERVE PER QUANDO NON C'E' IL VALORE DI BACKGROUND!
+	{
+		double loc_avg = 0, loc_stdev = 0;
+
+		for(unsigned int i = 0; i < Seq->size(); i++)
+			loc_avg += M->get_score_at(i);
+
+		loc_avg /= Seq->size();	
+
+		for(unsigned int i = 0; i < Seq->size(); i++)
+			loc_stdev += pow(M->get_score_at(i) - loc_avg, 2);
+
+		loc_stdev /= (Seq->size() - 1);
+
+		loc_stdev = sqrt(loc_stdev);
+
+		SINGLE_MATRIX_BG_AVG = loc_avg - (2*loc_stdev);
+
+		if(!QUIET) cerr << "\nSMBG = " << SINGLE_MATRIX_BG_AVG;
+	}
+*/
+	char Oligo[M->length() + 1];
+
+	Oligo[M->length()] = '\0';	
+
+	for(unsigned int i = 0; i < Seq->size(); i++)
+	{
+//		if(!QUIET) cerr << endl << M->get_score_at(i) << '\t' << M->get_bg_Avg() << '\t';
+
+//		if(M->get_score_at(i) < SINGLE_MATRIX_BG_AVG)  //ONLY REPORT OCCURRENCES WITH SCORE >= BG_AVG
+//			continue;
+
+//		if(!QUIET) cerr << "passed";
+
+		ostringstream outbuf;
+
+		sequence *S = &Seq->at(i);
+
+		strncpy(Oligo, S->seq() + RSIZE/2 + (M->get_pos_at(i) - M->length()/2), M->length());
+
+		outbuf << S->chr() << '\t' << S->start() << '\t' << S->end() << '\t' << S->strand() << '\t'
+		    << S->start() + M->get_pos_at(i) - M->length()/2 << '\t' << S->start() + M->get_pos_at(i) + M->length()/2 << '\t'
+		    << (int)((M->get_pos_at(i) - M->length()/2) - RSIZE/2) << '\t' << (int)((M->get_pos_at(i) + M->length()/2 - 1) - RSIZE/2)<< '\t'; 
+
+		if(S->strand() == '+')
+		{
+			if(!M->get_strand_at(i))
+				outbuf << S->strand();
+			else
+				outbuf << S->antistrand();
+		}
+		else
+		{
+			if(!M->get_strand_at(i))
+                                outbuf << S->antistrand();
+                        else
+                                outbuf << S->strand();
+		}
+
+		outbuf << '\t' << M->get_score_at(i) << '\t' << Oligo; 
+	
+//		if(SPEARMAN)
+//			outbuf << '\t' << S->e_rank();
+
+		if(SECOND_BEST_POS)
+		{
+			if(SINGLE_STRAND)
+			{
+				bool s;
+				unsigned int P;
+				double score;
+
+				score = M->scan_seq_ss_second_best(S->seq() + (RSIZE/2), RSIZE, &P, &s,M->get_pos_at(i), S->strand());
+
+				strncpy(Oligo, S->seq() + RSIZE/2 + P, M->length());
+
+				outbuf << '\t' << P << '\t' << score << '\t' << Oligo;
+			}
+			else
+			{
+				bool s;
+                        	unsigned int P;
+                        	double score;
+
+                        	score = M->scan_seq_ds_second_best(S->seq() + (RSIZE/2), RSIZE, &P, &s, (int)M->get_pos_at(i));
+
+				strncpy(Oligo, S->seq() + RSIZE/2 + P, M->length());
+
+				outbuf << '\t' << (int)P - (int)RSIZE/2 << '\t' << score << '\t' << Oligo << '\t';
+
+				if(s)
+					outbuf << '-';
+				else 
+					outbuf << '+';
+			}
+
+			outbuf << endl;
+		}
+		else
+			outbuf << endl;
+
+		outmap.insert(make_pair(M->get_score_at(i),outbuf.str()));
+	}
+
+	multimap<double,string>::reverse_iterator mi = outmap.rbegin();
+
+//	unsigned int count = 0;
+
+	while(mi != outmap.rend())
+	{
+//		if(count >= outmap.size()/2 && outmap.size() > 1)  //SOLO LA MIGLIORE META' DELLE OCCORRENZE!!!
+//			break;
+		if(mi->first >= SINGLE_MATRIX_BG_AVG || mi == outmap.rbegin())  
+			out << mi->second;
+
+		out2 << mi->second;
+
+		mi++;
+//		count++;
+	}
+
+	out.close();
+	out2.close();
+	return;
+}
+
+void main_output(vector<matrix> *Mat, vector<sequence> *Seq, unsigned int SIZE)
+{
+	multimap <double, vector<matrix>::iterator> S_map;
+	outfile = regfile;
+	
+	outfile += ".res";
+
+	if(!GALAXY_OUTPUT.empty())
+		outfile = GALAXY_OUTPUT;
+
+	ofstream out(outfile.c_str(),ios::out);
+
+	if(!out)
+	{
+		if(!QUIET) cerr << "\nError! Can't open output file: " << outfile << " for writing..." << endl;
+		exit(1);
+	}
+
+	out << "NAME\tID\tREG_N\tL_PVALUE O/U\tG_PVALUE O/U\tR_AVG\tR_STDEV\tF_AVG\tBG_AVG";
+
+	if(SPEARMAN)
+		out << "\tSP_COR";
+
+	if(POSITIONAL)
+		out << "\tPREF_POS\tPREF_POS_PV\n";
+	else
+		out << endl;
+
+	vector<matrix>::iterator vi = Mat->begin();
+
+	while(vi != Mat->end())
+	{
+		if(S_map.find(vi->get_pvalue()) != S_map.end())  //GFI WORKAROUND
+		{
+			if(S_map.find(vi->get_pvalue())->second->get_pvalue_bg() < vi->get_pvalue_bg())
+			{
+				S_map.insert(make_pair(vi->get_pvalue() + pow(10,-240), vi));
+				vi++;
+				continue;
+			}
+			else if((S_map.find(vi->get_pvalue())->second->get_pvalue_bg() > vi->get_pvalue_bg()))
+			{
+				S_map.insert(make_pair(vi->get_pvalue() - pow(10,-240), vi));
+                                vi++;
+                                continue;
+			}
+			else
+			{
+				if(S_map.find(vi->get_pvalue())->second->get_spearman() > vi->get_spearman())
+				{
+					S_map.insert(make_pair(vi->get_pvalue() + pow(10,-240), vi));
+                                	vi++;
+                                	continue;
+				}
+				else if(S_map.find(vi->get_pvalue())->second->get_spearman() <= vi->get_spearman())
+				{
+					S_map.insert(make_pair(vi->get_pvalue() - pow(10,-240), vi));
+                                        vi++;
+                                        continue;
+				}
+			}
+			
+		}
+		else
+			S_map.insert(make_pair(vi->get_pvalue(), vi));
+
+		vi++;
+	}
+
+	multimap <double, vector<matrix>::iterator>::iterator mi = S_map.begin();
+
+	while(mi != S_map.end())
+	{
+		double pv1, pv2;
+
+		pv1 = mi->second->get_pvalue() * Mat->size();
+
+		if(pv1 > 1)
+			pv1 = 1;
+
+		pv2 = mi->second->get_pvalue_bg() * Mat->size();
+
+		if(pv2 > 1)
+			pv2 = 1;
+
+		out << mi->second->name() << '\t' << mi->second->id() << '\t' << SIZE << '\t' << pv1 << ' ' << mi->second->o_or_u() << '\t';
+
+		if(mi->second->have_bg())
+			out << pv2 << ' ' << mi->second->o_or_u_bg() << '\t';
+		else
+			out << "N/A N/A\t";
+
+		out << mi->second->get_R_Avg() << '\t' << pow(mi->second->get_R_Var(), 0.5) << '\t' << mi->second->get_F_Avg() << '\t';
+
+		if(mi->second->have_bg())
+                        out << mi->second->get_bg_Avg() << '\t';
+                else
+                        out << "N/A" << '\t';
+
+		if(SPEARMAN)
+			out << mi->second->get_spearman() << '\t';
+
+		if(POSITIONAL)
+		{
+			double min_pv = 1, min_pv_c;
+			unsigned int min_pos;
+	
+			for(unsigned int i = 0; i < mi->second->bin_num() - 1; i++)
+			{
+				if(mi->second->get_W_pvalue(i) <= min_pv) //&& mi->second->W_o_or_u(i) == 1)
+				{
+					min_pv = mi->second->get_W_pvalue(i);
+					min_pos = i;
+				}
+			}
+
+			min_pv_c = min_pv * (mi->second->bin_num() * Seq->size());
+
+			if(min_pv_c > 1)
+				min_pv_c = 1;
+
+			out << '[' << (int)(((W_STEP * min_pos) + mi->second->length()/2) - RSIZE/2) << ',' << (int)(((W_STEP * min_pos) + W_SIZE) + mi->second->length()/2  - RSIZE/2) << ']' << '\t' << min_pv_c;// << '\t' << mi->second->get_W_R_T_pvalue(min_pos) << '\t' << min_pv_c;
+		}
+
+		out << endl;
+
+		mi++;
+	}
+	
+	if(POSITIONAL)
+	{
+		out << endl << endl << "POSITIONAL ANALYSIS: W_SIZE = " << W_SIZE << " W_STEP = " << W_STEP << endl << endl;
+
+		out << "NAME\tID\t";
+
+		mi = S_map.begin();
+	
+		for(int i = -(int)(RSIZE/2); i <= (int)((RSIZE/2) - W_SIZE); i += W_STEP)
+			out << i /*<< '|' << i + (int)(W_SIZE - 1)*/  << '\t';
+
+		out << endl;
+		
+		while(mi != S_map.end())
+		{
+/*			bool gflag = false;
+
+			for(unsigned int i = 0; i < mi->second->bin_num() - 1; i++)
+				if(mi->second->get_W_pvalue(i) <= POS_VIS_THRESHOLD)
+				{
+					gflag = true;
+					break;
+				}				
+
+			if(!gflag)
+			{
+				mi++;
+				continue;	
+			}
+*/
+			out << mi->second->name() << '\t' << mi->second->id() << '\t';
+
+			for(unsigned int i = 0; i < mi->second->bin_num() - 1; i++)
+			{
+//				out << (-log(mi->second->get_W_pvalue(i))/log(10)) * mi->second->W_o_or_u(i)  << '\t';//<< " [" << mi->second->W_o_or_u(i) << "]\t";
+//
+				double bpv = mi->second->get_W_pvalue(i) * (mi->second->bin_num() * Seq->size());
+
+				if(bpv > 1)
+					bpv = 1;
+
+				out << bpv << '\t';
+			}
+
+			out << endl;
+
+			mi++;
+		}
+
+		if(!obstf.empty())
+			distance_analysis(Mat, Seq, SIZE, &S_map);
+	}
+
+	out.close();
+
+	return;
+}
+
+void distance_analysis(vector<matrix> *Mat, vector<sequence> *Seq, unsigned int SIZE, multimap <double, vector<matrix>::iterator> *S_map)
+{
+	string dist_outfile = regfile, dist2_outfile = regfile, dist3_outfile = regfile;
+
+        dist_outfile += ".dist";
+	dist2_outfile += ".exp_dist";
+	dist3_outfile += ".pv_dist";
+	
+	ofstream out(dist_outfile.c_str()), out2, out3;
+
+	if(!obstf.empty())
+	{
+		out2.open(dist2_outfile.c_str());
+		out3.open(dist3_outfile.c_str());
+
+		out2 << "TF/EXP_HITS\t";
+		out3 << "TF/PVALUE\t";
+	}
+
+	out << "TF1|TF2/HITS\t";
+
+	for(int p = -(int)(RSIZE - 1); p < (int)RSIZE; p++)
+		out << p  << '\t';
+
+	out << endl;
+
+	if(!obstf.empty())
+	{
+		for(int p = -(int)(RSIZE - 1); p < (int)RSIZE; p++)
+		{
+			out2 << p  << '\t';
+              		out3 << p << '\t';
+		}
+
+		out2 << endl;
+		out3 << endl;
+	}
+
+	multimap <double, vector<matrix>::iterator>::iterator MRI = S_map->begin();
+	unsigned int LCOUNT = 0;
+
+	while(MRI != S_map->end())
+	{
+		if((MRI->second->get_pvalue_bg() > DIST_PV_THRESHOLD || MRI->second->o_or_u_bg() == "UNDER") && 
+		   (MRI->second->get_pvalue() > DIST_PV_THRESHOLD || MRI->second->o_or_u() == "UNDER") )
+		{
+			MRI++;
+			continue;
+		}
+
+//		if(!QUIET) cerr << endl << MRI->second->name() << endl;
+
+		LCOUNT++;
+
+		map<int, double> R_dist_map;
+		
+		if(!obstf.empty() && obstf == MRI->second->id())
+		{
+			map<int, unsigned int> M_hit_distr;
+
+			for(unsigned int a = 0; a < SIZE; a++)
+			{
+				map<int, unsigned int>::iterator mi; 
+
+				if(!MRI->second->get_strand_at(a))
+					mi = M_hit_distr.find(MRI->second->get_pos_at(a));
+				else
+					mi = M_hit_distr.find(RSIZE - MRI->second->get_pos_at(a));
+			
+				if(mi == M_hit_distr.end())
+				{
+					if(!MRI->second->get_strand_at(a))
+						M_hit_distr[MRI->second->get_pos_at(a)] = 1;
+					else
+						M_hit_distr[RSIZE - MRI->second->get_pos_at(a)] = 1;
+				}
+				else
+					mi->second++;
+			}
+
+			map<int, unsigned int>::iterator mi = M_hit_distr.begin();
+
+			while(mi != M_hit_distr.end())
+			{
+				for(int b = 0; b < RSIZE; b++)
+				{
+					int dpos = mi->first - b;
+
+					map<int, double>::iterator ri = R_dist_map.find(dpos);
+				
+					if(ri == R_dist_map.end())
+						R_dist_map[dpos] = mi->second;		
+					else
+						ri->second += mi->second;
+					
+				}	
+			
+				mi++;
+			}
+
+			map<int, double>::iterator ri = R_dist_map.begin();
+			double risum = SIZE * RSIZE;
+	
+			out2 << MRI->second->name() << '\t';
+
+			while(ri != R_dist_map.end())
+			{
+				ri->second /= risum;	
+				out2 << ri->second*SIZE << '\t';
+				ri++;
+			}
+
+			out2 << endl;
+		}
+		
+//		multimap <double, vector<matrix>::iterator>::iterator MRI2 = MRI;
+		multimap <double, vector<matrix>::iterator>::iterator MRI2 = S_map->begin();
+
+		while(MRI2 != S_map->end())	
+		{
+			vector<unsigned int> hit_v((RSIZE*2) - 1, 0);
+
+			if(MRI2 == MRI)
+			{
+				vector<unsigned int> SBPOS;
+//				vector<bool> SBSTRAND;
+
+				if(SINGLE_STRAND)
+                        	{
+					for(unsigned int i = 0; i < Seq->size(); i++)
+					{
+                                		bool s;
+                                		unsigned int P;
+                                		double score;
+
+                                		score = MRI->second->scan_seq_ss_second_best(Seq->at(i).seq() + (RSIZE/2), RSIZE, &P, &s, MRI->second->get_pos_at(i), Seq->at(i).strand());
+						SBPOS.push_back(P);
+			//			SBSTRAND.push_back(s);
+					}
+
+                        	}
+                        	else
+                        	{
+					for(unsigned int i = 0; i < Seq->size(); i++)
+					{
+                                		bool s;
+                                		unsigned int P;
+                                		double score;
+
+                                		score = MRI->second->scan_seq_ds_second_best(Seq->at(i).seq() + (RSIZE/2), RSIZE, &P, &s, (int)MRI->second->get_pos_at(i));
+
+						SBPOS.push_back(P + MRI->second->length()/2);
+				//		SBSTRAND.push_back(s);
+
+                        		}
+				}
+
+				for(unsigned int k = 0; k < SIZE; k++)
+                                {
+                                        int dist;
+
+					if(!MRI->second->get_strand_at(k))
+						dist = (int)SBPOS.at(k) - (int)MRI->second->get_pos_at(k);
+					else
+						dist = ((int)(RSIZE-1) - (int)SBPOS.at(k)) - ((int)(RSIZE - 1) - (int)MRI->second->get_pos_at(k));
+
+                                        hit_v.at((RSIZE-1) + dist)++;
+                                }
+				
+			}
+			else
+			{
+				for(unsigned int k = 0; k < SIZE; k++)
+				{
+					int dist; 
+
+					if(!MRI->second->get_strand_at(k))
+						dist = (int)MRI2->second->get_pos_at(k) - (int)MRI->second->get_pos_at(k);
+					else
+						dist = ((int)(RSIZE - 1 ) - (int)MRI2->second->get_pos_at(k)) - ((int)(RSIZE - 1 ) - (int)MRI->second->get_pos_at(k));
+
+//					if(!QUIET) cerr << endl << (int)((RSIZE-1) + dist) << endl;
+
+					hit_v.at((RSIZE-1) + dist)++;
+				}	
+			}
+
+			if((!obstf.empty() && obstf == MRI->second->id()) || obstf.empty())
+				out << MRI->second->name() << "|" << MRI2->second->name() << '\t';
+
+			if(!obstf.empty() && obstf == MRI->second->id())
+				out3 << MRI->second->name() << "|" << MRI2->second->name() << '\t';
+
+			for(unsigned int p = 0; p < (RSIZE*2) - 1; p++)
+			{
+				if((!obstf.empty() && obstf == MRI->second->id()) || obstf.empty())
+					out << hit_v[p] << '\t';
+		
+				if(!obstf.empty() && obstf == MRI->second->id())
+				{
+					map<int, double>::iterator ri = R_dist_map.find(p - (RSIZE - 1));					
+
+					if(hit_v[p] >= DIST_HIT_THRESHOLD && hit_v[p]/(ri->second * SIZE) >= DIST_RATIO_THRESHOLD)
+					{
+						double pv = gsl_cdf_binomial_Q(hit_v[p], ri->second, SIZE);
+
+						if(pv <= DIST_PV_THRESHOLD)
+							out3 << pv << '\t';
+						else
+							out3 << "NA" << '\t';
+					}
+					else
+						out3 << "NA" << '\t';
+				}
+			}
+
+			if((!obstf.empty() && obstf == MRI->second->id()) || obstf.empty())
+				out << endl;
+
+			if(!obstf.empty() && obstf == MRI->second->id())
+				out3 << endl;
+
+			MRI2++;
+		}
+
+		MRI++;
+	}	
+
+	out.close();
+
+	if(!obstf.empty())
+	{
+		out2.close();
+		out3.close();
+	}
+
+	if(!LCOUNT)
+	{
+		remove(dist_outfile.c_str());
+
+		if(!obstf.empty())
+		{
+			remove(dist2_outfile.c_str());
+			remove(dist3_outfile.c_str());
+		}	
+	}
+
+	if(!QUIET) cerr << "\nDistance analysis written in file: " << dist_outfile << endl;
+
+	return;
+}
+
+void scanner(vector<matrix> *Mat, vector<sequence> *Seq)
+{
+	for(unsigned int i = 0; i < Mat->size(); i++)
+	{
+		if(VERBOSE)
+		{
+			if(!QUIET) cerr << "\nScanning sequences for "
+		     	<< Mat->at(i).name() << " (" << Mat->at(i).id() << ")"<< endl;
+		}
+
+		Mat->at(i).scan(Seq);	
+		Mat->at(i).calc_var((double)Seq->size());
+
+		if(POSITIONAL)
+			Mat->at(i).calc_W_param((double)Seq->size());
+
+		if(VERBOSE)
+		{
+			if(!QUIET) cerr << "\nRegions avg = " << Mat->at(i).R_Avg << '\t' << "Flanks avg = " << Mat->at(i).F_Avg << '\t' 
+                	<< "Regions devstd = " << pow(Mat->at(i).R_Var,0.5) << '\t' << "Flanks devstd = " << pow(Mat->at(i).F_Var,0.5);
+			if(!QUIET) cerr << "\nDoing Welch's t test... ";
+		}
+
+		Mat->at(i).welch_test((double)Seq->size());
+	
+		if(Mat->at(i).have_bg())
+			Mat->at(i).welch_test_bg((double)Seq->size());
+
+		if(POSITIONAL)
+		{
+//			Mat->at(i).welch_test_pos((double)Seq->size());
+			Mat->at(i).z_test_pos((double)Seq->size());
+		}
+
+		if(VERBOSE)
+		{
+			if(!QUIET) cerr << "done. Pvalue = " << Mat->at(i).get_pvalue() << ' ' << Mat->at(i).o_or_u() << endl;
+			if(!QUIET) cerr << endl;
+		}
+	}
+
+	return;
+}
+
+void acquire_matrices(vector<matrix> *Mat, map<string,bg> *Bg, string *matfile)
+{
+	ifstream in(matfile->c_str());
+	string line;
+
+	if(!in)
+	{
+                if(!QUIET) cerr << "Can't find " << *matfile << endl;
+                exit(1);
+	}
+
+	while(getline(in,line))
+	{
+		if(line.empty())
+			continue;
+
+		vector<string> mbuf;
+		mbuf.push_back(line);
+
+		for(unsigned int i = 0; i < ALPHABET_SIZE; i++)
+		{
+			getline(in,line);
+
+			if(!line.empty())
+				mbuf.push_back(line);
+		}
+
+		if(mbuf.size() == ALPHABET_SIZE + 1)
+			Mat->push_back(matrix(&mbuf,Bg));
+	}
+
+	in.close();
+
+	vector<matrix>::iterator vi = Mat->begin();
+
+	while(vi != Mat->end())
+	{
+		if(!vi->is_good())
+		{
+			vi = Mat->erase(vi);
+			continue;
+		}
+
+		vi++;
+	}
+
+	return;
+}
+
+void acquire_background(map<string, bg> *Bg)
+{
+	ifstream in(bgfile.c_str());
+
+	if(!in)
+	{
+		if(!QUIET) cerr << "\nWarning: background file " << bgfile << " not found..." << endl;
+		return;
+	}
+
+	string line;
+
+	getline(in,line);
+
+	while(getline(in, line))
+	{
+		istringstream str(line);
+		string id, trash;
+		bg nbg;
+
+		str >> trash >> id >> nbg.Size >> trash >> trash >> trash >> trash >> nbg.Avg >> nbg.Var;
+		
+		nbg.Var = pow(nbg.Var,2);
+
+		Bg->insert(make_pair(id,nbg));
+	}
+
+	in.close();
+	return;
+}
+
+void acquire_regions(vector<sequence> *Seq)
+{
+	ifstream in(regfile.c_str());
+//	map<string, vector<string> > Regs;
+	map<string, map<unsigned int, string> > Regs; //PREVENT REG DUPLICATES
+	map<string, map<unsigned int, unsigned int > > M_RANK;
+
+	if(!in)
+	{
+		if(!QUIET) cerr << "Can't find " << regfile << endl;		
+		exit(1);
+	}
+
+	string line;
+
+	unsigned int r_count = 0;
+
+	while(getline(in,line))
+	{
+		if(line.empty())
+			continue;
+
+		if(line[0] == '#')
+			continue;
+	
+		for(unsigned int i = 0; i < 3; i++)
+                	line[i] = tolower(line[i]);
+
+		for(unsigned int i = 3; i < line.size(); i++)
+			line[i] = toupper(line[i]);
+
+		istringstream str(line);
+		string chr;
+		unsigned int start, end, mp;
+
+		str >> chr >> start >> end;
+
+//		Regs[chr].push_back(line);
+		mp = start + ((end - start)/2);
+
+		if(mp > (RSIZE + RSIZE/2) + 1)
+		{
+			Regs[chr][mp] = line;
+
+//			if(!QUIET) cerr << endl << line;
+
+			if(M_RANK.find(chr) != M_RANK.end())    //PREVENT REGIONS PRESENT MORE THAN ONCE TO DO TOO MUCH MESS WITH SPEARMAN CORRELATION 
+				if(M_RANK[chr].find(mp) != M_RANK[chr].end())
+					continue;
+
+			M_RANK[chr][mp] = r_count;	
+			r_count++;
+		}
+		else
+			if(!QUIET) cerr << "\nSkipping region: too close to chromosome start..." << endl << line << endl;
+	}
+
+	in.close();	
+
+	map<string, map<unsigned int, string> >::iterator mi = Regs.begin();
+
+	if(!TWOBIT)
+	{
+		while(mi != Regs.end())
+		{
+			string file = genome;
+        		file += "/";
+        		file += mi->first;
+        		file += ".raw";
+	
+			in.open(file.c_str());
+
+			if(!in)
+			{
+				if(!QUIET) cerr << "\nCan't find " << file << ". Skipping chromosome:\n" << mi->first << endl;
+
+				if(SPEARMAN)
+				{
+					if(!QUIET) cerr << "\nSpearman correlation disabled..." << endl;
+					SPEARMAN = false;
+				}
+
+				mi++;
+				in.close();
+				continue;
+			}
+
+			map<unsigned int, string>::iterator si = mi->second.begin();
+
+			while(si != mi->second.end())
+			{
+				Seq->push_back(sequence(&si->second, &in, M_RANK[mi->first][si->first]));
+				si++;
+			}
+
+			in.close();
+			mi++;
+		}
+	}
+	else
+	{
+		ostringstream str;
+		ofstream outfile;
+		str << ".pchip." << rand() << ".tmp";
+		string tmp1 = str.str();
+		outfile.open(tmp1.c_str(), ios::out);
+		vector<string> k1;
+		vector<unsigned int> k2;
+
+		while(mi != Regs.end())
+		{
+			map<unsigned int, string>::iterator si = mi->second.begin();
+
+			while(si != mi->second.end())
+			{
+				unsigned int Start, End;
+
+				Start = si->first - RSIZE;
+        			End = si->first + RSIZE + 1 + MAX_L;
+
+				outfile << mi->first << '\t' << Start << '\t' << End << '\t' << "." << endl;
+	
+				k1.push_back(mi->first);
+				k2.push_back(si->first);
+
+				si++;
+			}
+						
+			mi++;
+		}
+
+		string cline = "twoBitToFa -bedPos -bed=";
+		cline += str.str();
+		str << ".fa";		
+		cline += " ";
+		cline += genome;
+/*		cline += "/";
+		cline += genome;
+		cline += ".2bit "; */
+		cline += " ";
+		cline += str.str();
+	
+//		if(!QUIET) cerr << endl << "TwoBit command line:\n" << cline << endl;
+		
+		if(system(cline.c_str()) != 0)
+		{
+			if(!QUIET) cerr << endl << "twoBitToFa returned non 0 error code... aborting pscan_chip run!\n" << endl;
+			exit(1);
+		} 
+		else
+		{
+			ifstream in(str.str().c_str());
+			string seq;
+			seq.clear();
+
+			if(!in)
+			{
+				if(!QUIET) cerr << endl << "Can't access twoBitToFa output file! Aborting pscan_chip run!\n" << endl;
+				exit(1);
+			}
+
+			unsigned int scount = 0;
+
+			while(getline(in,line))
+			{
+				if(line.empty())
+					continue;
+
+				if(line[0] == '>')	
+				{	
+					if(seq.empty())
+						continue;
+					else
+					{
+						Seq->push_back(sequence(&seq, M_RANK[k1.at(scount)][k2.at(scount)], k1.at(scount), k2.at(scount)));
+						seq.clear();
+						scount++;
+						continue;
+					}
+				}
+				else
+					seq += line;
+			}
+
+			Seq->push_back(sequence(&seq, M_RANK[k1.at(scount)][k2.at(scount)], k1.at(scount), k2.at(scount)));  //LAST SEQUENCE!
+
+			in.close();
+			remove(str.str().c_str());
+			remove(tmp1.c_str());
+		}
+
+//		exit(1);
+	}
+
+	vector<sequence>::iterator vi = Seq->begin();
+
+	while(vi != Seq->end())
+        {
+                if(!vi->is_good())
+                {
+                       	vi = Seq->erase(vi);
+                        continue;
+                }
+
+                vi++;
+        }
+
+	return;
+}
+
+void command_line_parser(int argc, char **argv)
+{
+        if(argc == 1)
+                return;
+
+        for(int i = 1; i < argc; i++)
+        {
+                string buf = argv[i];
+
+                if(buf == "-r")
+                {
+                        if(i < argc - 1)
+                                regfile = argv[++i];
+                        continue;
+                }
+
+		if(buf == "-g")
+                {
+                        if(i < argc - 1)
+                                genome = argv[++i];
+                        continue;
+                }
+
+		if(buf == "-s")
+                {
+                        if(i < argc - 1)
+                                RSIZE = atoi(argv[++i]);
+                        continue;
+                }
+		if(buf == "-bgavg")
+		{
+			if(i < argc - 1)	
+				SINGLE_MATRIX_BG_AVG = atof(argv[++i]);
+			continue;
+		}
+		if(buf == "-M")
+                {
+                        if(i < argc - 1)
+                                matrixfile = argv[++i];
+                        continue;
+                }
+		if(buf == "-MADD")
+		{
+			if(i < argc - 1)
+				additional_matrixfile = argv[++i];
+			continue;
+		}
+		if(buf == "-m")
+		{
+			if(i < argc - 1)
+                                selected = argv[++i];
+                        continue;
+		}
+
+		if(buf == "-bg")
+                {
+                        if(i < argc - 1)
+                               bgfile = argv[++i];
+                        continue;
+                }
+		if(buf == "-go")
+		{
+			if(i < argc - 1)
+				GALAXY_OUTPUT = argv[++i];
+			continue;
+		}
+		if(buf == "-obs")
+		{
+			if(i < argc - 1)
+                               obstf = argv[++i];
+
+                        continue;
+		}
+		if(buf == "-ss")
+                {
+                        SINGLE_STRAND = true;
+                        continue;
+                }
+		if(buf == "-2bit")
+		{
+			TWOBIT = true;
+			continue;
+		}	
+		if(buf == "-quiet")
+		{
+			QUIET = true;
+			continue;
+		}
+		if(buf == "-sbp")
+		{
+			SECOND_BEST_POS = true;
+			continue;
+		}
+		if(buf == "-fasta")
+                {
+                        GET_SEQUENCES = true;
+                        continue;
+                }
+		if(buf == "-pos")
+                {
+                        POSITIONAL = true;
+                        continue;
+                }
+		if(buf == "-spear")
+		{
+			SPEARMAN = true;
+			continue;
+		}
+		if(buf == "-wsize")
+                {
+                        if(i < argc - 1)
+                                W_SIZE = atoi(argv[++i]);
+
+			W_STEP = W_SIZE / 2;
+                        continue;
+                }
+/*		if(buf == "-wstep")
+                {
+                        if(i < argc - 1)
+                                W_STEP = atoi(argv[++i]);
+                        continue;
+                }
+
+		if(buf == "-fast")
+                {
+                        FAST_SCAN = true;
+                        continue;
+                }*/
+/*		if(buf == "-naive")
+                {
+                        NAIVE = true;
+                        continue;
+                }
+*/		
+		if(buf == "-v")
+                {
+                        VERBOSE = true;
+                        continue;
+                }
+		else
+		{
+			if(!QUIET) cerr << "\nUnknown option: " << buf << endl;
+			exit(1);
+		}
+
+              /*  if(buf == "-Q")
+                {
+                        if(i < argc - 1)
+                                idfile = argv[++i];
+                        continue;
+                }
+                if(buf == "-ql")
+                {
+                        if(i < argc - 1)
+                                q_idlist = argv[++i];
+                        continue;
+                }
+                if(buf == "-imgm")
+                {
+                        if(i < argc - 1)
+                                bg_for_img = argv[++i];
+                        continue;
+                }
+                if(buf == "-magic")
+                {
+                        if(i < argc - 1)
+                                magic = argv[++i];
+                        continue;
+                }*/
+	}
+
+	if(RSIZE > MAX_REG_SIZE)
+	{
+		if(!QUIET) cerr << "\nRegion size exceeds " << MAX_REG_SIZE << "..." << endl;
+		exit(1);
+	}
+
+	if(RSIZE % W_SIZE != 0 || W_SIZE % 2 != 0 || RSIZE / W_SIZE < 5)
+	{
+		if(!QUIET) cerr << "\nWindow size must be even and both an exact divisor of region size and at least five times smaller of it: positional analysis disabled." << endl;
+		POSITIONAL = false;
+	}
+
+	return;
+}
+
+//SEQUENCE CLASS BEGIN
+
+sequence::sequence(string *seq, unsigned int R, string chr, unsigned int mp)   //CONSTRUCTOR FOR 2BIT INPUT
+{
+	Chr = chr;
+	Strand = '+';
+	AntiStrand = '-';
+	E_Rank = R;
+	good = true;
+
+	Start = mp - RSIZE/2;
+        End = (mp + RSIZE/2) - 1;
+
+	for(unsigned int i = 0; i < seq->size(); i++)
+		seq->at(i) = toupper(seq->at(i));
+
+	Seq = new char[(RSIZE*2) + 1 + MAX_L];
+
+//	if(!QUIET) cerr << "\nseq.size = " << seq->size() << endl;	
+//	if(!QUIET) cerr << "\narray.size = " << (RSIZE*2) + 1 + MAX_L << endl;
+
+	strcpy(Seq, seq->c_str());
+
+	if(seq->size() != RSIZE*2 + MAX_L + 1)
+	{
+		good = false;
+		return;
+	}
+
+	if(GET_SEQUENCES)
+                fasta_out << ">" << Chr << '\t' << Start + 1 << '\t' << End + 1 << endl << seq->substr(RSIZE/2, RSIZE) << endl;
+
+	return;
+}
+
+sequence::sequence(string *line, ifstream *in, unsigned int R)
+{
+	istringstream str(*line);
+	string trash;
+	int buf_s, buf_e, mp;
+	good = true;
+
+	E_Rank = R;
+
+	str >> Chr >> buf_s >> buf_e >> Name >> trash >> Strand;
+
+	if(Strand == 'R')
+		Strand = '-';
+
+	if(Strand != '+' && Strand != '-')
+		Strand = '+';
+
+	if(Strand == '+')
+		AntiStrand = '-';
+	else
+		AntiStrand = '+';
+
+	mp = buf_s + ((buf_e -  buf_s)/2);
+
+	Start = mp - RSIZE/2;
+	End = (mp + RSIZE/2) - 1;
+
+//	Seq = new char[RSIZE + 1];
+//	UF_Seq = new char[(RSIZE/2) + 1 + MAX_L/2];
+//	DF_Seq = new char[(RSIZE/2) + 1 + MAX_L/2];
+
+	Seq = new char[(RSIZE*2) + 1 + MAX_L];
+
+	in->seekg((Start) - RSIZE/2);
+
+	in->get(Seq, (RSIZE*2 + 1) + MAX_L);
+
+	if(in->gcount() != RSIZE*2 + MAX_L)
+	{
+		good = false;
+		return;
+	}
+
+	if(GET_SEQUENCES)
+	{
+		char *out_seq;
+		out_seq = new char[RSIZE + 1];
+
+		in->seekg(Start);
+		in->get(out_seq, (RSIZE + 1));
+
+		fasta_out << ">" << Chr << '\t' << Start + 1 << '\t' << End + 1 << '\t' << "---" << '\t' << buf_s << '\t' << buf_e << '\t' << endl << out_seq << endl;
+
+		delete[] out_seq;
+	}
+
+	/*in->seekg(((Start - 1) - RSIZE/2) - (MAX_L/2));
+
+	in->get(UF_Seq, RSIZE/2 + 1 + MAX_L /2);
+
+	if(in->gcount() != RSIZE/2 + (MAX_L/2))
+	{
+		good = false;
+		return;
+	}
+	
+	in->get(Seq, RSIZE + 1);
+
+	if(in->gcount() != RSIZE)
+        {       
+                good = false;
+                return;
+        }
+
+	in->get(DF_Seq, RSIZE/2 + 1 + (MAX_L/2));
+
+	if(in->gcount() != RSIZE/2 + (MAX_L/2))
+                good = false;
+*/
+
+	return;
+}
+
+unsigned int sequence::e_rank()
+{
+	return E_Rank;
+}
+
+string sequence::chr()
+{
+	return Chr;
+}
+
+/*string* sequence::seq()
+{
+	return &Seq;
+}*/
+
+char* sequence::seq()
+{
+	return Seq;
+}
+
+char sequence::strand()
+{
+	return Strand;
+}
+
+char sequence::antistrand()
+{
+	return AntiStrand;
+}
+
+/*char* sequence::uf_seq()
+{
+        return UF_Seq;
+}
+
+char* sequence::df_seq()
+{
+        return DF_Seq;
+}
+*/
+string sequence::name()
+{
+	return Name;
+}
+
+unsigned int sequence::start()
+{
+	return Start;
+}
+
+unsigned int sequence::end()
+{
+	return End;
+}
+
+bool sequence::is_good()
+{
+	return good;
+}
+
+// SEQUENCE CLASS END
+
+// MATRIX CLASS BEGIN
+
+matrix::matrix(vector<string>* mbuf, map<string, bg> *Bg)
+{
+	string buf;
+	istringstream bstr(mbuf->at(1)), nstr(mbuf->at(0));		
+	L = 0;
+	R_Avg = 0; 
+	F_Avg = 0;
+	R_Var = 0;
+	F_Var = 0;
+	bg_Avg = 0;
+	bg_Var = 0;
+
+	BIN_NUM = RSIZE / W_STEP;
+
+	W_R_Avg.resize(BIN_NUM, 0);
+	W_R_Var.resize(BIN_NUM, 0);
+	W_R_pvalue.resize(BIN_NUM, 0);
+	W_R_T_pvalue.resize(BIN_NUM,0);
+	spearman = 42;
+	
+	O_U = false;
+	O_U_bg = false;
+	W_O_U.resize(BIN_NUM, 0);
+
+	BG = false;
+	good = true;
+	norm_sec_step = false;
+	
+	while(bstr >> buf)
+		L++;	
+
+	if(L > RSIZE/2)
+	{
+		good = false;
+		return;
+	}
+
+	if(L > MAX_L)
+		MAX_L = L;
+
+	if(!mbuf->at(0).empty())
+	{
+		if(mbuf->at(0).at(0) != '>')
+		{
+			good = false;
+			return;
+		}
+	}
+	else
+	{
+		good = false;
+		return;
+	}
+
+//	Name = mbuf->at(0).substr(1);
+	nstr >> Id >> Name;
+
+	Id = Id.substr(1);
+
+	if(!selected.empty())
+	{
+//		cerr << endl << selected << '\t' << Id << '\t' << Name << endl;
+
+		if(selected != Id && selected != Name)
+		{
+			good = false;
+			return;
+		}
+	}
+
+	if(!Bg->empty())
+	{
+		map<string,bg>::iterator mi = Bg->find(Id);
+
+		if(mi == Bg->end())
+			mi = Bg->find(Name);
+	
+		if(mi != Bg->end())
+		{
+			bg_Avg = mi->second.Avg;
+			bg_Var = mi->second.Var;	
+			bg_Size = mi->second.Size;
+			BG = true;
+		}
+		else
+			if(!QUIET) cerr << "\nWarning: no background for matrix: " << Id << endl;
+	}
+
+	M = new double*[L];
+        rc_M = new double*[L];
+
+	for(unsigned int i = 1; i < ALPHABET_SIZE + 1; i++)
+	{
+		istringstream str(mbuf->at(i));
+
+		unsigned int count = 0;
+
+		while(str >> buf)
+		{
+			if(i == 1)	
+			{
+				M[count] = new double[ALPHABET_SIZE + 1];
+                		rc_M[count] = new double[ALPHABET_SIZE + 1];
+			}
+			
+			M[count][i-1] = atof(buf.c_str());
+			count++;
+
+			if(count > L)
+			{
+				good = false;
+				return;
+			}
+		}
+
+		if(count != L)
+		{
+			good = false;
+                        return;
+		}
+	}
+
+	normalizer();
+	to_log();
+	rev_c();
+	avg();
+	max_min();
+//	set_top_pos();	
+
+	if(min_score == max_score)
+		good = false;
+
+	return;
+}
+
+void matrix::display()
+{
+	if(!QUIET) cerr << "\n>" << Name << '\t' << good << endl;
+
+	for(unsigned int i = 0; i < ALPHABET_SIZE; i++)
+	{
+		for(unsigned int j = 0; j < L; j++)
+			if(!QUIET) cerr << M[j][i] << '\t';
+
+		if(!QUIET) cerr << endl;
+	}
+
+	if(!QUIET) cerr << endl;
+
+//	for(unsigned int i = 0; i < TOP_P; i++)
+//		if(!QUIET) cerr << "TOP[" << i+1 << "] = " << top_pos[i] + 1 << "-" << top_char[i] << '\t';
+
+	if(!QUIET) cerr << "\n\n>" << Name << '\t' << good << '\t' << "RC" << endl;
+
+        for(unsigned int i = 0; i < ALPHABET_SIZE; i++)
+        {
+                for(unsigned int j = 0; j < L; j++)
+                        if(!QUIET) cerr << rc_M[j][i] << '\t';
+
+                if(!QUIET) cerr << endl;
+        }
+
+	if(!QUIET) cerr << endl;
+
+//	 for(unsigned int i = 0; i < TOP_P; i++)
+  //              if(!QUIET) cerr << "TOP[" << i+1 << "] = " << rc_top_pos[i] + 1 << "-" << rc_top_char[i] << '\t';
+
+	if(!QUIET) cerr << endl;
+
+	return;
+}
+
+bool matrix::is_good()
+{
+	return good;
+}
+
+
+void matrix::normalizer()
+{
+        double *sums = new double[L];
+
+        for(int x = 0; x < L; x++)
+        {
+       		sums[x] = 0;
+
+                for(int y = 0; y < ALPHABET_SIZE; y++)
+                        sums[x] += M[x][y];
+        }
+
+        for(int x = 0; x < L; x++)
+                for(int y = 0; y < ALPHABET_SIZE; y++)
+                        M[x][y] /= sums[x];
+
+        delete[] sums;
+
+        if(!norm_sec_step)
+        {
+                for(int x = 0; x < L; x++)
+                        for(int y = 0; y < ALPHABET_SIZE; y++)
+                                M[x][y] += MIN_ADD_FREQ;
+
+                norm_sec_step = true;
+
+                normalizer();
+        }
+
+        return;
+	
+}
+
+void matrix::to_log()
+{
+	for(int x = 0; x < L; x++)
+                for(int y = 0; y < ALPHABET_SIZE; y++)
+                        M[x][y] = log(M[x][y]);
+
+	return;
+}
+
+void matrix::avg()
+{
+//	mat_avg = new double[L];
+
+        for(int x = 0; x < L; x++)
+        {
+                double buf = 0;
+
+                for(int y = 0; y < ALPHABET_SIZE; y++)
+                        buf += M[x][y];
+
+               // mat_avg[x] = buf/ALPHABET_SIZE;
+               M[x][ALPHABET_SIZE] = buf/ALPHABET_SIZE;
+	       rc_M[(L-1) -x][ALPHABET_SIZE] = buf/ALPHABET_SIZE;
+        }
+
+        return;
+}
+
+void matrix::max_min()
+{
+	double min, max;
+
+        max_score = 0;
+        min_score = 0;
+
+        for(int x = 0; x < L; x++)
+        {
+                min = M[x][0];
+		max = M[x][0];
+
+                for(int y = 1; y < ALPHABET_SIZE; y++)
+                {
+                        if(M[x][y] < min)
+                                min = M[x][y];
+
+			if(M[x][y] > max)
+                                max = M[x][y];
+                }
+
+                min_score += min;
+		max_score += max;
+        }
+
+        return;
+}
+
+void matrix::rev_c()
+{
+	for(unsigned int x = 0; x < L; x++)	
+		for(unsigned int y = 0; y < ALPHABET_SIZE; y++)
+			rc_M[(L - 1) - x][(ALPHABET_SIZE - 1) - y] = M[x][y];
+
+	return;
+}
+
+void matrix::scan(vector<sequence> *Seq)
+{
+	v_score.reserve(Seq->size());
+	vF_score.reserve(Seq->size());
+	v_pos.reserve(Seq->size());
+	v_strand.reserve(Seq->size());
+
+	if(POSITIONAL)
+		W_R_v_score.reserve(Seq->size());
+
+	unsigned int progress;
+	
+	if(!SINGLE_STRAND)
+	{
+		for(unsigned int i = 0; i < Seq->size(); i++)
+		{
+			if(VERBOSE)
+			{		
+				progress = (unsigned int)(((double)(i+1)/(double)Seq->size()) * 100);
+				
+				if(!(progress%5))
+					if(!QUIET) cerr << progress << '%';
+			}
+
+			double max_flank_u, max_flank_d;
+			vector<double> W_buf(BIN_NUM, 0);
+
+			{
+				double r_score;
+
+				max_flank_u = scan_seq_ds(Seq->at(i).seq() , true, RSIZE/2, &W_buf);
+				r_score = scan_seq_ds(Seq->at(i).seq() + (RSIZE/2) , false, RSIZE, &W_buf);
+				max_flank_d = scan_seq_ds(Seq->at(i).seq() + ((RSIZE/2)*3) , true, RSIZE/2, &W_buf);
+
+				R_Avg += r_score;
+
+			/*	if(r_score < max_flank_u || r_score < max_flank_d)
+				{
+					if(max_flank_u > max_flank_d)
+						G_Avg += max_flank_u;
+					else
+						G_Avg += max_flank_d;
+				}
+				else
+					G_Avg += r_score;*/
+
+				if(POSITIONAL)
+				{
+				//	for(unsigned int i = 0; i < BIN_NUM; i++)
+				//		W_R_Avg[i] += W_buf[i];
+
+					W_R_v_score.push_back(W_buf);
+				}
+
+			}
+
+			if(max_flank_u > max_flank_d)
+			{
+				F_Avg += max_flank_u;
+				vF_score.push_back(max_flank_u);
+			}
+			else
+			{
+				F_Avg += max_flank_d;
+				vF_score.push_back(max_flank_d);
+			}
+
+
+			if(VERBOSE)	
+				if(!(progress%5))
+					if(!QUIET) cerr << (char)13; 
+		}
+	}
+	else
+	{
+		for(unsigned int i = 0; i < Seq->size(); i++)
+                {
+
+			if(VERBOSE)
+				if(!QUIET) cerr << (unsigned int)(((double)(i+1)/(double)Seq->size()) * 100) << '%';			
+
+                        double max_flank_u, max_flank_d;
+			vector<double> W_buf(BIN_NUM, 0);
+
+			{
+
+				double r_score;
+
+                        	max_flank_u = scan_seq_ss(Seq->at(i).seq() , true, RSIZE/2, Seq->at(i).strand(), &W_buf);
+                        	r_score += scan_seq_ss(Seq->at(i).seq() + (RSIZE/2) , false, RSIZE, Seq->at(i).strand(), &W_buf);
+                        	max_flank_d = scan_seq_ss(Seq->at(i).seq() + ((RSIZE/2)*3), true, RSIZE/2, Seq->at(i).strand(), &W_buf);
+
+				R_Avg += r_score;
+
+			/*	if(r_score < max_flank_u || r_score < max_flank_d)
+                                {
+                                        if(max_flank_u > max_flank_d)
+                                                G_Avg += max_flank_u;
+                                        else
+                                                G_Avg += max_flank_d;
+                                }
+                                else    
+                                        G_Avg += r_score;*/
+
+				if(POSITIONAL)
+				{
+				//	for(unsigned int i = 0; i < BIN_NUM; i++)
+                                //        	W_R_Avg[i] += W_buf[i];
+				
+					W_R_v_score.push_back(W_buf);
+				}
+			}
+
+                        if(max_flank_u > max_flank_d)
+			{
+                                F_Avg += max_flank_u;
+				vF_score.push_back(max_flank_u);
+			}
+                        else
+			{
+                                F_Avg += max_flank_d;
+				vF_score.push_back(max_flank_d);
+			}
+
+			if(VERBOSE)
+				if(!QUIET) cerr << (char)13; 
+                }
+	}
+
+	R_Avg /= Seq->size();
+	F_Avg /= Seq->size();
+//	G_Avg /= Seq->size();
+
+//	for(unsigned int i = 0; i < BIN_NUM; i++)
+//		W_R_Avg[i] /= Seq->size();
+
+	if(SPEARMAN)
+	{
+		multimap<double, unsigned int> SRM;
+
+		for(unsigned int i = 0; i < v_score.size(); i++)
+			SRM.insert(make_pair(v_score[i], i));
+
+		multimap<double, unsigned int>::reverse_iterator mmi = SRM.rbegin();
+		int sr = 0;
+		double d = 0;
+
+		while(mmi != SRM.rend())
+		{
+//			if(!QUIET) cerr << endl << mmi->first << '\t' << sr << '\t' << Seq->at(mmi->second).e_rank() << '\t' << this->name();
+
+			d += pow((sr - (int)Seq->at(mmi->second).e_rank()), 2);
+			sr++;
+			mmi++;
+		}
+
+		d *= 6;
+
+//		if(!QUIET) cerr << endl << "d = " << d << "\tden = " << (Seq->size() * (pow(Seq->size(), 2) - 1)) << '\t' << "ssize = " << Seq->size();
+
+		d /= (Seq->size() * (pow(Seq->size(), 2) - 1));
+
+		spearman = 1 - d;
+	}	
+
+	return;
+}
+
+void matrix::calc_var(double S)
+{
+	for(unsigned int i = 0; i < S; i++)
+	{
+		R_Var += pow(v_score[i] - R_Avg,2);
+		F_Var += pow(vF_score[i] - F_Avg,2);
+
+/*		if(v_score[i] >= vF_score[i])
+			 G_Var += pow(v_score[i] - G_Avg,2);
+		else
+			 G_Var += pow(vF_score[i] - G_Avg,2);*/
+	}
+
+	if(S > 1)
+	{
+		R_Var /= (S - 1);
+		F_Var /= (S - 1);
+//		G_Var /= (S - 1);
+	}
+
+	if(R_Var == 0)
+		R_Var += EPSILON;
+
+	if(F_Var == 0)
+		F_Var += EPSILON;
+
+//	if(G_Var == 0)
+//		G_Var += EPSILON;
+
+	return;
+} 
+
+void matrix::calc_W_param(double S)
+{
+	if(S > 1)
+		S = S/2;   //SOLO PER LA PRIMA META' DELLE SEQUENZE!!!
+
+	W_Avg = 0;
+	W_Var = 0;
+
+	multimap<double, unsigned int> score_seq_map;
+
+	for(unsigned int i = 0; i < v_score.size(); i++)
+		score_seq_map.insert(make_pair(v_score.at(i), i));
+
+	multimap<double, unsigned int>::reverse_iterator mi = score_seq_map.rbegin();
+
+	for(unsigned int i = 0; i < S; i++)
+	{
+		for(unsigned int j = 0; j < BIN_NUM; j++)
+			W_R_Avg[j] += W_R_v_score[mi->second][j];
+
+//		if(!QUIET) cerr << Name << '\t' << mi->first << endl;
+
+		mi++;
+	}
+
+	for(unsigned int j = 0; j < BIN_NUM; j++)
+		W_R_Avg[j] /= S;	
+
+	mi = score_seq_map.rbegin();
+
+	for(unsigned int i = 0; i < S; i++)
+	{
+		for(unsigned int j = 0; j < BIN_NUM; j++)
+			W_R_Var[j] += pow(W_R_v_score[mi->second][j] - W_R_Avg[j],2);
+
+		mi++;
+	}
+
+/*	for(unsigned int i = 0; i < S; i++)
+		for(unsigned int j = 0; j < BIN_NUM; j++)
+               		W_R_Var[j] += pow(W_R_v_score[i][j] - W_R_Avg[j],2);*/
+
+	if(S > 1)
+	{
+		for(unsigned int j = 0; j < BIN_NUM; j++)
+			W_R_Var[j] /= (S - 1);
+	}
+
+	for(unsigned int j = 0; j < BIN_NUM; j++)
+		if(W_R_Var[j] == 0)
+			W_R_Var[j] += EPSILON;
+
+	for(unsigned int j = 0; j < BIN_NUM - 1; j++)  //THE LAST BIN IS WASTED SINCE IT IS AN HALF BIN 
+		W_Avg += W_R_Avg[j];
+
+	W_Avg /= (BIN_NUM - 1);
+
+	for(unsigned int j = 0; j < BIN_NUM - 1; j++)
+		W_Var += pow(W_R_Avg[j] - W_Avg, 2);
+
+	W_Var /= (BIN_NUM - 2);
+
+	return;
+}
+
+void matrix::welch_test(double S)
+{
+	t = R_Avg - F_Avg;
+
+	if(t == 0)
+		t = EPSILON;
+
+	t /= pow((R_Var/S) + (F_Var/S),0.5);
+
+	dof = pow((R_Var/S) + (F_Var/S),2);	
+
+	dof /= (pow(R_Var,2)/((pow(S,2)) * (S-1))) + (pow(F_Var,2)/((pow(S,2)) * (S-1)));
+
+	if(t > 0)
+		pvalue = gsl_cdf_tdist_Q(t,dof);
+	else
+	{
+		pvalue = gsl_cdf_tdist_P(t,dof);
+		O_U = true;
+	}
+
+	return;
+}
+
+void matrix::z_test_pos(double S)
+{
+//	if(!QUIET) cerr << endl << Name;
+	
+	for(unsigned int i = 0; i < BIN_NUM; i++)
+	{
+		double se = sqrt(W_R_Var.at(i)), z;
+		se /= sqrt(S/2);
+
+		z = W_R_Avg.at(i) - W_Avg;
+		z /=se;
+
+		if(z >= 0)
+			W_O_U.at(i) = true;	
+
+		W_R_pvalue.at(i) = gsl_cdf_ugaussian_Q(z);
+	
+//		if(!QUIET) cerr << endl << "W_R_Avg.at(i) " << W_R_Avg.at(i) << '\t' <<  W_Avg << '\t' <<  W_R_pvalue.at(i) << endl;
+		
+	}	
+		
+	return;
+}
+
+void matrix::welch_test_pos(double S)
+{
+	if(S > 1)
+		S = S/2;  //SOLO LA PRIMA META' DELLE SEQUENZE!!!
+
+//	if(!QUIET) cerr << "\nRAVG = " << W_Avg << endl;
+	for(unsigned int i = 0; i < BIN_NUM; i++)
+	{
+		double T, DOF;
+
+        	T = W_R_Avg.at(i) - W_Avg;
+
+//		if(!QUIET) cerr << W_R_Avg.at(i) << '\t';
+
+	//	if(!QUIET) cerr << endl << Name << endl << "T = " << T << '\t' << W_R_Avg.at(i) << '\t' << W_Avg;
+
+        	if(T == 0)
+                	T = EPSILON;
+
+        	T /= pow((W_R_Var.at(i)/S) + (W_Var/S),0.5);
+
+        	DOF = pow((W_R_Var.at(i)/S) + (W_Var/S),2);
+
+        	DOF /= (pow(W_R_Var.at(i),2)/((pow(S,2)) * (S-1))) + (pow(W_Var,2)/((pow(S,2)) * (S-1)));
+
+        	if(T > 0)
+                	W_R_T_pvalue.at(i) = gsl_cdf_tdist_Q(T,DOF);
+        	else
+        	{
+                	W_R_T_pvalue.at(i) = gsl_cdf_tdist_P(T,DOF);
+                	W_O_U.at(i) = true;
+        	}
+
+	//	if(!QUIET) cerr << "\tPV= " << W_R_pvalue.at(i);
+
+	}
+
+//	if(!QUIET) cerr << endl;
+
+        return;
+}
+
+void matrix::welch_test_bg(double S1)
+{
+	double S2 = bg_Size;
+
+//	if(!QUIET) cerr << Name << '\t' << R_Avg << '\t' << bg_Avg << '\t' << R_Var << '\t' << bg_Var << '\t' << S1 << '\t' << S2 << endl;
+
+        t_bg = R_Avg - bg_Avg;
+
+        if(t_bg == 0)
+                t_bg = EPSILON;
+
+        t_bg /= pow((R_Var/S1) + (bg_Var/S2),0.5);
+
+        dof_bg = pow((R_Var/S1) + (bg_Var/S2),2);
+
+        dof_bg /= (pow(R_Var,2)/((pow(S1,2)) * (S1-1))) + (pow(bg_Var,2)/((pow(S2,2)) * (S2-1)));
+
+        if(t_bg > 0)
+                pvalue_bg = gsl_cdf_tdist_Q(t_bg,dof_bg);
+        else
+        {
+                pvalue_bg = gsl_cdf_tdist_P(t_bg,dof_bg);
+                O_U_bg = true;
+        }
+
+        return;
+}
+
+/*void matrix::welch_test_bg_G(double S1)
+{
+	double S2 = bg_Size;
+
+//	if(!QUIET) cerr << Name << '\t' << R_Avg << '\t' << bg_Avg << '\t' << R_Var << '\t' << bg_Var << '\t' << S1 << '\t' << S2 << endl;
+
+        t_bg = G_Avg - bg_Avg;
+
+        if(t_bg == 0)
+                t_bg = EPSILON;
+
+        t_bg /= pow((G_Var/S1) + (bg_Var/S2),0.5);
+
+        dof_bg = pow((G_Var/S1) + (bg_Var/S2),2);
+
+        dof_bg /= (pow(G_Var,2)/((pow(S1,2)) * (S1-1))) + (pow(bg_Var,2)/((pow(S2,2)) * (S2-1)));
+
+        if(t_bg > 0)
+                pvalue_bg = gsl_cdf_tdist_Q(t_bg,dof_bg);
+        else
+        {
+                pvalue_bg = gsl_cdf_tdist_P(t_bg,dof_bg);
+                O_U_bg = true;
+        }
+
+        return;
+}*/
+
+double matrix::scan_seq_ds(char *S, bool flank, unsigned int l, vector<double> *W_buf)
+{
+	unsigned int pos = 0, max_pos = 0;
+        double seq_score;
+        bool strand = false;
+
+	l -= L/2;
+
+	while(pos < l)
+        {
+
+        	double pos_score[2] = {0,0};
+
+        	for(unsigned int j = 0; j < L; j++)
+        	{
+        		pos_score[0] += get_M_value(j, S[pos+j]);
+                	pos_score[1] += get_rc_M_value(j, S[pos+j]);
+        	}
+
+        	if(seq_score < pos_score[0] || !pos)
+        	{
+        		seq_score = pos_score[0];
+        		max_pos = pos;
+                	strand = false;
+        	}
+        	if(seq_score < pos_score[1])
+        	{
+        		seq_score = pos_score[1];
+                	max_pos = pos;
+                	strand = true;
+        	}
+
+		if(!flank && POSITIONAL)
+		{
+			unsigned int vpos = pos / W_STEP;
+			
+			if(W_buf->at(vpos) < pos_score[0] || !(pos % W_STEP))
+				W_buf->at(vpos) = pos_score[0];
+			
+			if(W_buf->at(vpos) < pos_score[1])
+                                W_buf->at(vpos) = pos_score[1];
+
+			if(vpos)
+			{
+				if(W_buf->at(vpos - 1) < pos_score[0])
+                                	W_buf->at(vpos - 1) = pos_score[0];
+
+                        	if(W_buf->at(vpos - 1) < pos_score[1])
+                                	W_buf->at(vpos - 1) = pos_score[1];
+			}
+		}
+
+        	pos++;
+        }
+
+        seq_score = 1 + (seq_score - max_score)/(max_score - min_score);
+
+	if(!flank && POSITIONAL)
+	{
+//		if(!QUIET) cerr << endl << Name << endl;
+
+		unsigned int binm = 0;
+
+		for(unsigned int i = 0; i < BIN_NUM; i++)
+		{
+			if(W_buf->at(i) != 0)
+				W_buf->at(i) = 1 + (W_buf->at(i) - max_score)/(max_score - min_score);
+			else 
+				binm++;
+		}
+
+		BIN_NUM -= binm;
+	}
+
+	if(!flank)
+	{
+        	v_score.push_back(seq_score);
+        	v_pos.push_back(max_pos + L/2);
+        	v_strand.push_back(strand);
+	}
+
+	return seq_score;
+}
+
+double matrix::scan_seq_ss_second_best(char *S, unsigned int l, unsigned int *P, bool *s, unsigned int POS, bool seq_strand)
+{
+	unsigned int pos = 0, max_pos = 0;
+        double seq_score = min_score;
+        bool strand = false;
+
+	while(pos < l)
+        {
+		if(pos == POS)
+		{
+			pos++;
+			continue;
+		}
+
+        	double pos_score[2] = {0,0};
+
+		if(seq_strand == '+')
+		{
+        		for(unsigned int j = 0; j < L; j++)
+        			pos_score[0] += get_M_value(j, S[pos+j]);
+		}
+		else
+		{
+			for(unsigned int j = 0; j < L; j++)
+				pos_score[0] += get_rc_M_value(j, S[pos+j]);
+        	}
+
+        	if(seq_score < pos_score[0])
+        	{
+        		seq_score = pos_score[0];
+        		max_pos = pos;
+                	strand = false;
+        	}
+
+
+        	pos++;
+        }
+
+        seq_score = 1 + (seq_score - max_score)/(max_score - min_score);
+
+	*P = max_pos;
+        *s = strand;
+
+	return seq_score;
+}
+
+double matrix::scan_seq_ds_second_best(char *S, unsigned int l, unsigned int *P, bool *s, int POS)
+{
+	int pos = 0, max_pos = 0, count = 0;
+        double seq_score;
+        bool strand = false;
+
+	POS -= L/2;
+	l -= L/2;
+
+	while(pos < l)
+        {
+//		if(pos == POS)
+		if(pos >= (POS - L) && pos <= (POS + L))
+		{
+			pos++;
+			continue;
+		}
+	
+        	double pos_score[2] = {0,0};
+
+        	for(unsigned int j = 0; j < L; j++)
+        	{
+        		pos_score[0] += get_M_value(j, S[pos+j]);
+                	pos_score[1] += get_rc_M_value(j, S[pos+j]);
+        	}
+
+        	if(seq_score < pos_score[0] || !count)
+        	{
+        		seq_score = pos_score[0];
+        		max_pos = pos;
+                	strand = false;
+        	}
+        	if(seq_score < pos_score[1])
+        	{
+        		seq_score = pos_score[1];
+                	max_pos = pos;
+                	strand = true;
+        	}
+
+        	pos++;
+		count++;
+        }
+
+        seq_score = 1 + (seq_score - max_score)/(max_score - min_score);
+
+	*P = max_pos ;//+ L/2;
+	*s = strand;
+
+	return seq_score;
+}
+
+
+
+/*double matrix::scan_seq_ds_quick(char *S, bool flank, unsigned int l)
+{
+	unsigned int pos = 0, max_pos = 0;
+        double seq_score = min_score;
+        bool strand = false;
+
+	while(pos < l)
+        {
+        	double pos_score[2] = {0,0};
+
+		for(unsigned int j = 0; j < L; j++)
+		{
+			pos_score[0] += get_M_value(p_pos[j], S[pos+p_pos[j]]);
+
+			if((pos_score[0] + p_max[j+1]) <= seq_score)
+			{
+				pos_score[0] = min_score;
+				break;
+			}
+			
+		}
+
+		for(unsigned int j = 0; j < L; j++)
+		{
+			pos_score[1] += get_rc_M_value(rc_p_pos[j], S[pos+rc_p_pos[j]]);		
+
+			if((pos_score[1] + p_max[j+1]) <= seq_score)
+			{
+				pos_score[1] = min_score;
+				break;
+			}
+		}
+
+        	if(seq_score < pos_score[0])
+        	{
+        		seq_score = pos_score[0];
+        		max_pos = pos;
+                	strand = false;
+        	}
+        	if(seq_score < pos_score[1])
+        	{
+        		seq_score = pos_score[1];
+                	max_pos = pos;
+                	strand = true;
+        	}
+
+        	pos++;
+        }
+
+        seq_score = 1 + (seq_score - max_score)/(max_score - min_score);
+
+	if(!flank)
+	{
+        	v_score.push_back(seq_score);
+        	v_pos.push_back(max_pos);
+        	v_strand.push_back(strand);
+	}
+
+
+	return seq_score;
+}
+*/
+double matrix::scan_seq_ss(char *S, bool flank, unsigned int l, char seq_strand, vector<double> *W_buf)
+{
+	unsigned int pos = 0, max_pos = 0;
+        double seq_score = min_score;
+        bool strand = false;
+
+	while(pos < l)
+        {
+        	double pos_score[2] = {0,0};
+
+		if(seq_strand == '+')
+		{
+        		for(unsigned int j = 0; j < L; j++)
+        			pos_score[0] += get_M_value(j, S[pos+j]);
+		}
+		else
+		{
+			for(unsigned int j = 0; j < L; j++)
+				pos_score[0] += get_rc_M_value(j, S[pos+j]);
+        	}
+
+        	if(seq_score < pos_score[0])
+        	{
+        		seq_score = pos_score[0];
+        		max_pos = pos;
+                	strand = false;
+        	}
+
+		if(!flank && POSITIONAL)
+                {
+                        unsigned int vpos = pos / W_STEP;
+
+                        if(W_buf->at(vpos) < pos_score[0])
+                                W_buf->at(vpos) = pos_score[0];
+
+                        if(vpos)
+                        {
+                                if(W_buf->at(vpos - 1) < pos_score[0])
+                                        W_buf->at(vpos - 1) = pos_score[0];
+                        }
+                }
+
+        	pos++;
+        }
+
+        seq_score = 1 + (seq_score - max_score)/(max_score - min_score);
+
+	if(POSITIONAL && !flank)
+		for(unsigned int i = 0; i < W_buf->size(); i++)
+                	W_buf->at(i) = 1 + (W_buf->at(i) - max_score)/(max_score - min_score);
+
+	if(!flank)
+	{
+        	v_score.push_back(seq_score);
+        	v_pos.push_back(max_pos);
+        	v_strand.push_back(strand);
+	}
+
+	return seq_score;
+}
+
+/* double matrix::scan_seq_ss_quick(char *S, bool flank, unsigned int l, char seq_strand)
+{
+	unsigned int pos = 0, max_pos = 0;
+        double seq_score = min_score;
+        bool strand = false;
+
+	while(pos < l)
+        {
+        	double pos_score[2] = {0,0};
+
+		if(seq_strand == '+')
+		{
+        		for(unsigned int j = 0; j < L; j++)
+			{
+       				pos_score[0] += get_M_value(p_pos[j], S[pos+p_pos[j]]);
+					
+				if((pos_score[0] + p_max[j+1]) <= seq_score)
+				{
+					pos_score[0] = min_score;
+					break;
+				}
+						
+
+			}
+		}
+		else
+		{
+			for(unsigned int j = 0; j < L; j++)
+			{
+				pos_score[0] += get_rc_M_value(rc_p_pos[j], S[pos+rc_p_pos[j]]);
+	
+				if((pos_score[0] + p_max[j+1]) <= seq_score)
+                                {
+                                	pos_score[0] = min_score;
+					break;
+                                }
+	
+			}
+        	}
+
+        	if(seq_score < pos_score[0])
+        	{
+        		seq_score = pos_score[0];
+        		max_pos = pos;
+                	strand = false;
+        	}
+
+        	pos++;
+        }
+
+        seq_score = 1 + (seq_score - max_score)/(max_score - min_score);
+
+	if(!flank)
+	{
+        	v_score.push_back(seq_score);
+        	v_pos.push_back(max_pos);
+        	v_strand.push_back(strand);
+	}
+
+	return seq_score;
+}*/
+
+double matrix::get_M_value(int pos, char C)
+{
+	return M[pos][VI[C]];
+}
+
+double matrix::get_rc_M_value(int pos, char C)
+{
+	return rc_M[pos][VI[C]];
+}
+
+/*
+void matrix::set_top_pos()
+{
+	multimap<double, mpoint> Tmap;
+	vector<double> p_max_buf, rc_p_max_buf;
+
+	for(unsigned int x = 0; x < L; x++)
+	{
+		for(unsigned int y = 0; y < ALPHABET_SIZE; y++)
+		{
+			mpoint p;
+		
+			p.x = x;
+			p.y = y;
+	
+			Tmap.insert(make_pair(M[x][y],p));
+
+			if(!y)
+			{
+				p_max_buf.push_back(M[x][y]);
+				rc_p_max_buf.push_back(rc_M[x][y]);
+			}
+			else
+			{
+				if(M[x][y] > p_max_buf.back())
+					p_max_buf[p_max_buf.size() - 1] = M[x][y];
+
+				if(rc_M[x][y] > rc_p_max_buf.back())
+					rc_p_max_buf[rc_p_max_buf.size() - 1] = rc_M[x][y];
+			}
+
+		}
+		
+	//	if(!QUIET) cerr << endl << p_max_buf.back();
+	}
+
+	multimap<double, mpoint>::reverse_iterator ri = Tmap.rbegin();
+
+	for(unsigned int i = 0; i < TOP_P; i++)
+	{
+		top_pos[i] = ri->second.x;	
+		top_char[i] = ALPHABET[ri->second.y];
+
+		rc_top_pos[i] = (L - 1) - ri->second.x;
+		rc_top_char[i] = RC_ALPHABET[ri->second.y];
+
+		ri++;
+	}
+
+//	if(!QUIET) cerr << endl << name() << '\t' << max_score << '\t' << min_score << endl;
+
+	while(p_max.size() != p_max_buf.size())
+	{
+		double buf = -INF;
+		unsigned int pos;
+
+		for(unsigned int i = 0; i < p_max_buf.size(); i++)
+			if(p_max_buf.at(i) > buf)
+			{
+				pos = i;
+				buf = p_max_buf.at(i);
+			}
+
+		p_pos.push_back(pos);
+		rc_p_pos.push_back((L - 1) - pos);
+		
+		p_max.push_back(buf);
+	
+		p_max_buf[pos] = -INF;
+	}
+
+	for(unsigned int i = 0; i < L; i++)
+	{
+		//if(!QUIET) cerr << p_max[i] << "//"<< '\t';
+
+		for(unsigned int j = i + 1; j < L; j++)		
+			p_max[i] += p_max[j];
+
+	//	for(unsigned int j = i + 1; j < L; j++)
+          //              rc_p_max[i] += rc_p_max[j];
+	
+	//	if(!QUIET) cerr << p_max[i] << "(" << p_pos[i] << ")" << rc_p_max[i] << '\t';
+	}
+
+	p_max.push_back(0); //WE NEED A 0 AT THE END OF THE VECTOR!
+//	rc_p_max.push_back(0);
+
+//	if(!QUIET) cerr << endl;
+
+	return;
+}
+*/
+double matrix::get_score_at(unsigned int a)
+{
+	return v_score.at(a);
+}
+unsigned int matrix::get_pos_at(unsigned int a)
+{
+	return v_pos.at(a);
+}
+bool matrix::get_strand_at(unsigned int a)
+{
+	return v_strand.at(a);
+}
+
+double matrix::max()
+{
+	return max_score;
+}
+
+double matrix::min()
+{
+	return min_score;
+}
+
+string matrix::name()
+{
+	if(!Name.empty())
+		return Name;
+	else
+		return Id;
+}
+
+string matrix::id()
+{
+	return Id;
+}
+
+double matrix::get_pvalue()
+{
+	return pvalue;
+}
+
+double matrix::get_pvalue_bg()
+{
+        return pvalue_bg;
+}
+
+double matrix::get_W_pvalue(unsigned int pos)
+{
+	return W_R_pvalue.at(pos); 
+}
+
+double matrix::get_W_R_Avg_at_pos(unsigned int pos)
+{
+	return W_R_Avg.at(pos);
+}
+
+string matrix::o_or_u()
+{
+	if(O_U)
+		return "UNDER";
+	else
+		return "OVER";
+}
+
+string matrix::o_or_u_bg()
+{
+        if(O_U_bg)
+                return "UNDER";
+        else
+                return "OVER";
+}
+
+int matrix::W_o_or_u(unsigned int pos)
+{
+	if(W_O_U[pos])
+		return -1;
+	else
+		return 1;
+}
+
+double matrix::get_R_Avg()
+{
+	return R_Avg;
+}
+double matrix::get_F_Avg()
+{
+        return F_Avg;
+}
+double matrix::get_R_Var()
+{
+	return R_Var;
+}
+double matrix::get_F_Var()
+{
+	return F_Var;
+}
+double matrix::get_bg_Avg()
+{
+	return bg_Avg;
+}
+
+double matrix::get_t()
+{
+	return t;
+}
+
+double matrix::get_dof()
+{
+	return dof;
+}
+
+bool matrix::have_bg()
+{
+	return BG;
+}
+
+unsigned int matrix::bin_num()
+{
+	return BIN_NUM;
+}
+
+unsigned int matrix::length()
+{
+	return L;
+}
+
+double matrix::get_spearman()
+{
+	double s = spearman;
+
+	s *= 10000;
+
+	if(s > 0)
+		s = floor(s);
+	else if(s < 0)
+		s = ceil(s);
+		
+	s /= 10000;	
+
+	return s;
+}
+
+double matrix::get_W_Avg()
+{
+	return W_Avg;
+}
+
+double matrix::get_W_R_T_pvalue(unsigned int i)
+{
+	return W_R_T_pvalue.at(i);
+}
+// MATRIX CLASS END