/*****************************************************************************

* GATB : Genome Assembly Tool Box

* Copyright (C) 2014 INRIA

* Authors: R.Chikhi, G.Rizk, 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/>.

*****************************************************************************/

#ifndef _GATB_TOOLS_MINIA_HPP_

#define _GATB_TOOLS_MINIA_HPP_

/********************************************************************************/

#include <gatb/gatb_core.hpp>

#include <gatb/debruijn/impl/GraphUnitigs.hpp>

#include <string>

/********************************************************************************/

/**

*/

class Minia : public gatb::core::tools::misc::impl::Tool

{

public:

/** Constructor. */

Minia ();

/** \copydoc Tool::execute. */

void execute ();

/** */

template <typename Graph_type, typename Node, typename Edge, size_t span>

std::string assemble (/*const*/ Graph_type& graph);

u_int64_t nbContigs ;

unsigned int k;

private:

/** */

template <typename Graph_type, typename Node, typename Edge, size_t span>

void assembleFrom (Node startingNode, Graph_type& graph, IBank *outputBank);

bool keepIsolatedTigs;

u_int64_t nbSmallContigs ;

u_int64_t totalNt ;

u_int64_t maxContigLen ;

};

/********************************************************************************/

#endif /* _GATB_TOOLS_MINIA_HPP_ */