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/* ***************************************************************************
*
* KisSplice
* de-novo calling alternative splicing events from RNA-seq data.
*
* ***************************************************************************
*
* Copyright INRIA
* contributors : Vincent Lacroix
* Pierre Peterlongo
* Gustavo Sacomoto
* Vincent Miele
* Alice Julien-Laferriere
* David Parsons
*
* pierre.peterlongo@inria.fr
* vincent.lacroix@univ-lyon1.fr
*
* This software is a computer program whose purpose is to detect alternative
* splicing events from RNA-seq data.
*
* 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.
*/
#include <list>
#include <string>
#include <utility>
#include "NGraph.h"
#include "Utils.h"
#ifndef CYCLE_COMPRESSION_H
#define CYCLE_COMPRESSION_H
// Auxiliary functions
string merge_sequences( const string seq1, const string seq2);
void output_sequences( string seq1, string seq2, FILE * snp_log_file, const int bccid, const int cycleNumconst, int contextL, const int contextR, const int kValue);
bool is_same_node(const idx_dir u, const idx_dir v);
idx_dir reverse_dir(idx_dir node);
#endif /* CYCLE_COMPRESSION_H */
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