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/*
* segemehl - a read aligner
* Copyright (C) 2008-2017 Steve Hoffmann and Christian Otto
*
* 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, 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef IUPAC_H
#define IUPAC_H
/**
* iupac.h
* declarations for IUPAC nucleotide code
*
* @author Christian Otto
* @email christian@bioinf.uni-leipzig.de
* @company Bioinformatics, University of Leipzig
* @date Fri Jul 23 15:03:08 CEST 2010
*/
/*
* SVN
* Revision of last commit: $Rev: 144 $
* Author: $Author: steve $
* Date: $Date: 2010-09-02 05:58:04 -0400 (Thu, 02 Sep 2010) $
* Id: $Id: iupac.h 144 2010-09-02 09:58:04Z steve $
* Url: $URL: http://www2.bioinf.uni-leipzig.de/svn5/segemehl/libs/iupac.h $
*/
#include "basic-types.h"
void initIUPAC(Uint maxqryamb, Uint maxseqamb);
BOOL isallowedIUPAC();
BOOL matchIUPAC(char qrych, char seqch);
BOOL couldMatchIUPAC(char qrych);
Uint countAmbChars(char *seq, Uint len);
Uint countNonMatchingChars(char *seq, Uint len);
double minshannonentropy(char *seq, Uint len);
#endif /* IUPAC_H */
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