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correctedGraph.h
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correctedGraph.h
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/*
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