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/*
Ray
Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
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, version 3 of the License.
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 have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#ifndef _OpenAssemblerChooser
#define _OpenAssemblerChooser
#include "Chooser.h" // for IMPOSSIBLE_CHOICE
#include "NovaEngine.h"
/**
* de Bruijn heuristic to choose extension direction in a graph, described in paper
*
* Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies.
* Sébastien Boisvert, François Laviolette, and Jacques Corbeil.
* Journal of Computational Biology (Mary Ann Liebert, Inc. publishers).
* November 2010, 17(11): 1519-1533.
* doi:10.1089/cmb.2009.0238
* http://dx.doi.org/doi:10.1089/cmb.2009.0238
* \author Sébastien Boisvert
*/
class OpenAssemblerChooser{
NovaEngine m_novaEngine;
double m_singleEndMultiplicator;
double m_pairedEndMultiplicator;
void updateMultiplicators();
int getWinner(vector<set<int> >*battleVictories,int choices);
/**
* choose where to go based on coverage
*/
void chooseWithCoverage(ExtensionData*ed,int minCoverage,vector<set<int> >*battleVictories);
public:
int choose(ExtensionData*m_ed,Chooser*m_c,int m_minimumCoverage,
Parameters*parameters);
void constructor();
};
#endif
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