/*
Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)

    This file is part of Velvet.

    Velvet 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; either version 2 of the License, or
    (at your option) any later version.

    Velvet 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 should have received a copy of the GNU General Public License
    along with Velvet; if not, write to the Free Software
    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA

*/
#ifndef _CORRECTEDGRAPH_H_
#define _CORRECTEDGRAPH_H_

void clipTips(Graph * graph);

void clipTipsHard(Graph * graph, boolean conserveLong);

void correctGraph(Graph * graph, ShortLength * sequenceLengths, Category * sequenceCategories, boolean conserveLong, boolean * dubious);

// Clumsy and dirty patch
boolean *removeLowCoverageNodesAndDenounceDubiousReadsConserveLong(Graph * graph,
						       double minCov,
						       ReadSet * reads,
						       boolean export,
						       Coordinate minLength,
						       char *filename);

// Black arts:
void setMaxReadLength(int value);
void setMaxGaps(int value);
void setMaxDivergence(double value);
void setEdgeMultiplicityCutoff(double value);
#endif