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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/>.
*/
/*
*
* bitvectoralg.h
*
*
* @author Steve Hoffmann, steve@bioinf.uni-leipzig.de
* @company Bioinformatics, University of Leipzig
* @date 05/26/2008 12:26:03 PM CEST
*
*/
#include "basic-types.h"
#include "alignment.h"
#include "bitVector.h"
PairSint myersbitvector( void *space,
char *query,
Uint qlen,
char *subject,
Uint slen,
char *alphabet,
Uint asize,
Uint *enctab,
Uint k,
bitvector *peq);
bitvector*
myersbitmatrix( void *space,
char *query,
Uint qlen,
char *subject,
Uint slen,
char *alphabet,
Uint asize,
Uint *enctab,
Uint k,
bitvector *peq,
PairSint *res,
bitvector *D,
Uint dim);
bitvector*
myersblockbitmatrix(
void *space,
char *query,
Uint qlen,
char *subject,
Uint slen,
char *alphabet,
Uint asize,
Uint *enctab,
Uint k,
bitvector *peq,
PairSint *res,
bitvector *D,
Uint dim);
bitvector*
getpeq(void *space,
char *query,
Uint qlen,
char *alphabet,
Uint asize,
Uint *enctab);
Uint*
encodetab(char *alphabet, Uint asize) ;
char*
getstringalphabet (void *space, char *string, Uint len, Uint *asize);
Alignment*
bitvectorbacktrack(Alignment *al, bitvector *D, Uint dim, Uint k,
Uint l,
char *subject, Uint *enctab, bitvector *peq); //patch
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