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
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
|
/*
* 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 KDCHAIN_H
#define KDCHAIN_M
/*
*
* kdchain.h
* declarations and marcors for kd chaining
*
* @author Steve Hoffmann, steve@bioinf.uni-leipzig.de
* @company Bioinformatics, University of Leipzig
* @date 03/11/2008 06:40:32 PM CET
*
* SVN
* Revision of last commit: $Rev: 72 $
* Author: $Author: steve $
* Date: $Date: 2008-10-28 18:14:42 +0100 (Tue, 28 Oct 2008) $
*
* Id: $Id: kdchain.h 72 2008-10-28 17:14:42Z steve $
* Url: $URL: http://www.bioinf.uni-leipzig.de/svn/segemehl/segemehl/branches/esa/trunk/libs/kdchain.h $
*/
#include "manout.h"
#include "container.h"
#include "sufarray.h"
#include "kdseed.h"
#define FSTART_S(a) ((a)->p)
#define FEND_S(a) (int)((a)->p+(a)->mat+(a)->mis+(a)->del-1)
#define RINTERVALSIZE 100
#define FSTART_Q(a) ((a)->i)
#define FEND_Q(a) (int)((a)->i+(a)->mat+(a)->mis+(a)->ins-1)
#define FASSIGN(d, s) d->i = s->i;\
d->p = s->p;\
d->scr = s->scr;\
d->mat = s->mat;\
d->mis = s->mis;\
d->ins = s->ins;\
d->del = s->del
typedef struct {
Uint size;
Uint bestscr;
Uint bestscrpos;
gmatch_t* chains;
} gchains_t;
typedef struct {
Uint start;
Uint end;
Uint x;
unsigned char strand;
Uint branchno;
Uint substart;
Uint subidx;
int score;
double evalue;
branch_t *branch;
char pass;
} branchfragment_t;
typedef struct {
Uint nooffragments;
Uint start;
Uint end;
int score;
branchfragment_t **f; //**f
} branchChain_t;
void joinFragments(gmatch_t*, gmatch_t*, gmatch_t*, int err);
gmatch_t* greedyfchain(void *space, gmatch_t* F, Uint n, Uint *scr,
Uint *pos, Uint *m);
void wrapChains(void *space, branchChain_t *chains, Uint noofchains);
branchChain_t * branchChain(void *space, Suffixarray *arr, matchstem_t **stems,
char **seqs, Uint len, karlin_t *stats, Uint *noofchains,
branchfragment_t **, Uint maxocc, double maxevalue, double minentropy);
void showChains(branchChain_t *chains, Uint noofchains, Suffixarray *arr,
FILE *dev, char *, Uint);
int cmp_chainscores(const void *a, const void *b);
extern void reportfchain(void *space, gchains_t *pi, gmatch_t *e);
void branch2match(Suffixarray *s, Container *C, branch_t* b,
Uint noofbranches);
extern void reportchaincoords(gmatch_t *dest, gmatch_t *a, gmatch_t *b,
int ovq, int dmis, int dins, int ddel);
Container* findfchains(void *space, Suffixarray *s, matchstem_t* M,
Uint m, Uint t, unsigned char strict, int sigmatch, double lambda,
double H, double K, double maxevalue);
extern int misfrag (gmatch_t *a, gmatch_t *b);
extern int delfrag (gmatch_t *a, gmatch_t *b);
extern int insfrag (gmatch_t *a, gmatch_t *b);
extern void joinfrag(gmatch_t *dest, gmatch_t *a, gmatch_t *b);
int chainscore(branchChain_t *chain, branchfragment_t *f);
Lint chainovl(branchChain_t *chain, branchfragment_t *f);
void chain(branchChain_t *chain, branchfragment_t *f);
branchChain_t* condenseChain (branchChain_t * chains, Uint noofchains, MultiCharSeq *seq, Suffixarray *arr);
branchfragment_t** fixinfragments (void *space, branchChain_t *chains, Uint noofchains, Suffixarray *arr, char **seqs, Uint len, Uint *nooffragments);
void wrapFixinFragments (void *space, branchfragment_t **f, Uint nooffragments);
int cmp_chainlocality (const void *a, const void *b);
#endif
|
