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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 SEQCLIP_H
#define SEQCLIP_H
/*
*
* seqclip.h
*
*
* @author Steve Hoffmann, steve@bioinf.uni-leipzig.de
* @company Bioinformatics, University of Leipzig
* @date 24.04.2010 22:32:24 CEST
*
*/
#include <stdio.h>
#include <stdlib.h>
#include "biofiles.h"
#include "basic-types.h"
Uint
bl_seqclipPolyA(void *space, char *sequence, Uint len, char* clp, Uint clen);
Uint
bl_seqclipSoft3Prime(void *space, char *sequence, Uint len,
char *toClip, Uint clipsize, Uint minclipacc, Uint pAlen);
Uint
bl_seqclipSoft5Prime(void *space, char *s, Uint len,
char *C, Uint clen, Uint minclipscr);
Uint
bl_seqclipHard3Prime(Uint len, Uint clipsize);
char*
bl_seqclipHard5Prime(char *s, Uint len, Uint clen);
char*
bl_seqclipFind3Prime (void *space, fasta_t *set, Uint samplesize, Uint fs, int ws);
#endif
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