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65 lines (50 loc) · 2.04 KB
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/*****************************************************************************
* 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_ */