1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
|
/*
* 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/>.
*/
/*
*
* matealign.h
*
*
* @author Steve Hoffmann, steve@bioinf.uni-leipzig.de
* @company Bioinformatics, University of Leipzig
* @date 29.07.2013 18:07:27 CEST
*
*/
mappingset_t* bl_greedypairMappingSets(mappingset_t *l, mappingset_t *r);
unsigned int bl_myersMCSA(MultiCharSeqAlignment *mcsa, MultiCharSeq *mseq,
unsigned int *enctab, bitvector *peq, bitvector *D, unsigned int maxE);
mappingset_t *
bl_matealign(mappingset_t *l, MultiCharSeq *mseq, char **seqs, char **quals, char *qname, unsigned int m,
unsigned int *enctab, bitvector *D, unsigned int maxL, char ismate, Suffixarray *s, segemehl_t *nfo);
mappingset_t *
bl_pairMateMapping (mappingset_t *l, mappingset_t *r, unsigned int insertsize);
unsigned int
bl_localMCSA(MultiCharSeqAlignment *mcsa, MultiCharSeq *mseq, int* scores, int indel, int minscore);
|
