/*****************************************************************************
 *   discoSnp++: discovering polymorphism from raw unassembled NGS reads
 *   A tool from the GATB (Genome Assembly Tool Box)
 *   Copyright (C) 2014  INRIA
 *   Authors: P.Peterlongo, E.Drezen
 *
 *  This program is free software: you can redistribute it and/or modify
 *  it under the terms of the GNU Affero 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 Affero General Public License for more details.
 *
 *  You should have received a copy of the GNU Affero General Public License
 *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 *****************************************************************************/

/*
 * outputs.h
 *
 *  Created on: 27 oct. 2010
 *      Author: ppeterlo
 */

#ifndef OUTPUTS_H_
#define OUTPUTS_H_

#include <iomanip>
#include <fragment_index.h>
#include <fragment_info.h>
#include <commons.h>
#include <string.h>
#include <iostream>
//#include <tree.h>
#include <stdlib.h>
#include <limits.h>
#include <math.h>
#include <assert.h>
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define ABS(a) (((a) < 0) ? -(a) : (a))

void print_results_2_paths_per_event(ofstream &coherent_out, ofstream & uncoherent_out,  FragmentIndex &index, GlobalValues & gv);
#endif /* OUTPUTS_H_ */
