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//Copyright inria / irisa (2013)
//
//
//raluca.uricaru@gmail.com
//pierre.peterlongo@inria.fr
//
//This software is a computer program whose purpose is to call SNPs from NGS reads.
//
//This software is governed by the CeCILL license under French law and
//abiding by the rules of distribution of free software. You can use,
//modify and/ or redistribute the software under the terms of the CeCILL
//license as circulated by CEA, CNRS and INRIA at the following URL
//"http://www.cecill.info".
//
//As a counterpart to the access to the source code and rights to copy,
//modify and redistribute granted by the license, users are provided only
//with a limited warranty and the software's author, the holder of the
//economic rights, and the successive licensors have only limited
//liability.
//
//In this respect, the user's attention is drawn to the risks associated
//with loading, using, modifying and/or developing or reproducing the
//software by the user in light of its specific status of free software,
//that may mean that it is complicated to manipulate, and that also
//therefore means that it is reserved for developers and experienced
//professionals having in-depth computer knowledge. Users are therefore
//encouraged to load and test the software's suitability as regards their
//requirements in conditions enabling the security of their systems and/or
//data to be ensured and, more generally, to use and operate it in the
//same conditions as regards security.
//
//The fact that you are presently reading this means that you have had
//knowledge of the CeCILL license and that you accept its terms.
#ifndef ITERATIVE_EXTENSION_H
#define ITERATIVE_EXTENSION_H
#include <assert.h>
#include <utility> // std::pair, std::get
#ifdef MINIA_IS_IN_PARENT_FOLDER
#include "../minia/Utils.h"
#include "../minia/Terminator.h"
#include "../minia/Traversal.h"
#include "../minia/Kmer.h"
#include "../minia/Bank.h"
#include "../minia/Debloom.h"
#else
#include "minia/Utils.h"
#include "minia/Terminator.h"
#include "minia/Traversal.h"
#include "minia/Kmer.h"
#include "minia/Bank.h"
#include "minia/Debloom.h"
#endif
extern int64_t genome_size;
extern Bloom * bloo1;
extern BinaryBank * SolidKmers;
extern BranchingTerminator * terminator;
//Raluca
extern AssocPairedSet *pairedBranchingKmers ;
typedef enum {
LARGEUR,
PROFONDEUR,
NB_PARCOURS
} parcours_t;
class IterativeExtensions {
public:
IterativeExtensions();
static void construct_linear_seqs(string L,string R, int max_depth, string output_file, int verb, int max_nodes, parcours_t search_mode = PROFONDEUR, bool swf = false );
static void construct_linear_seqs(string L, int max_depth, string output_file);
static void construct_linear_seqs_paired(string L,string R, int max_depth, string output_file , int verb, int max_nodes);
static void construct_linear_seqs_paired(string L, int max_depth, string output_file);
// controls behavior of construct_linear_seqs
enum Traversal_type { SimplePaths, Monument };
enum When_to_stop_extending { After_first_contig, Until_max_depth };
static Traversal_type traversal_type; // initialized in .cpp
static When_to_stop_extending when_to_stop_extending;
static bool dont_output_first_nucleotide;
// extra function added by pierre
static pair<char *, int> extend_a_snp(string L, int max_depth);
};
#endif
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