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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/>.
*/
/*
*
* queryalign.h
*
*
* @author Steve Hoffmann, steve@bioinf.uni-leipzig.de
* @company Bioinformatics, University of Leipzig
* @date 29.07.2013 17:57:49 CEST
*
*/
#ifndef QUERYALIGN_H
#define QUERYALIGN_H
#include "mapfrag.h"
#include "multicharseq.h"
mapseedlist_t*
bl_getGoodSeeds (matchstem_t **items, unsigned m, unsigned n, karlin_t *stats,
segemehl_t *nfo);
mappingset_t*
bl_seedAlign(Suffixarray *s, mappingset_t* set, MultiCharSeq *mseq,
char **seqs, char **qual, Uint len, char* qname, mapseedlist_t *l,
segemehl_t *nfo, Uint *enctab, bitvector* D, char ismate);
#endif
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