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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 KDSEEDS_H
#define KDSEEDS_H
/*
*
* kdseed.h
* gettin k-diff seeds
*
* @author Steve Hoffmann, steve@bioinf.uni-leipzig.de
* @company Bioinformatics, University of Leipzig
* @date 04/13/2008 12:05:48 AM CEST
*
* SVN
* Revision of last commit: $Rev: 77 $
* Author: $Author: steve $
* Date: $Date: 2008-11-17 13:16:59 +0100 (Mon, 17 Nov 2008) $
*
* Id: $Id: kdseed.h 77 2008-11-17 12:16:59Z steve $
* Url: $URL: http://www.bioinf.uni-leipzig.de/svn/segemehl/segemehl/branches/esa/trunk/libs/kdseed.h $
*/
#include "basic-types.h"
#include "vstack.h"
#include "sufarray.h"
#include "karlin.h"
#define KMSTOREBRANCH(B,P)\
B[P].mat = m-data.mis;\
B[P].q = m-data.mis;\
B[P].mis = data.mis;\
B[P].ins = 0;\
B[P].del = 0;\
B[P].l = data.l;\
B[P].r = data.r;\
B[P].u = data.u;\
B[P].v = data.v
typedef struct branch_s {
Uint mis;
Uint mat;
Uint q;
Uint ins;
Uint del;
Uint l;
Uint r;
Uint u;
Uint v;
} branch_t;
typedef struct matchstem_s {
branch_t *branches;
Uint noofbranches;
} matchstem_t;
typedef struct {
Uint sptr;
Uint qptr;
Uint l;
Uint kcnt;
Uint mat;
Uint mis;
Uint ins;
Uint del;
PairUint child;
PairUint parent;
} kdiffm_t;
typedef struct {
Uint l;
Uint r;
Uint u;
Uint v;
Uint p;
Uint mis;
} kmis_t;
extern int kdscore(branch_t *b);
extern void
dumpkdseeds(Suffixarray *s, matchstem_t *M, Uint m, char strand, Uint T);
double
kd_getBranchEvalue(matchstem_t *stem, Uint i, Uint q, Uint m, Uint n,
karlin_t *stats);
int
kd_getBranchScore(matchstem_t *M, Uint i, Uint q);
extern int
kd_matchlcp(void *space,
Suffixarray *s, char *p, unsigned int m,
kdiffm_t *data, unsigned int cursufpos,
unsigned int lcplen, unsigned int seedlen, VStack *vstack,
unsigned int maxdiff, int sext, int pmis, int xoff, matchstem_t *b);
extern void
pushkdbranches ( void *space,
Suffixarray *s,
VStack *vstack,
char *p,
Uint m,
Uint kp,
kdiffm_t *data,
PairUint pr);
extern void
pushkdlcp ( void *space,
VStack *vstack,
char *p,
Uint m,
Uint kp,
kdiffm_t *data);
extern void
kdbest ( void *space,
Suffixarray *s,
char *seqs[],
Uint m,
Uint sext,
Uint pmis,
Uint xoff,
Uint kp,
matchstem_t *a[],
matchstem_t *b0[]);
extern matchstem_t **
kdbest2 ( void *space,
Suffixarray *s,
char *seqs[],
Uint m,
Uint sext,
Uint pmis,
Uint xoff,
Uint kp,
matchstem_t *a[],
matchstem_t *b0[]);
extern matchstem_t*
kdseeds ( void *space,
Suffixarray *s,
char *p,
Uint m,
Uint jump,
Uint sext,
Uint pmis,
Uint xoff,
Uint kp,
matchstem_t *b0, char nosuflinks);
extern matchstem_t*
kd_match ( void *space,
Suffixarray *s,
char *p,
Uint m,
Uint sext,
Uint pmis,
Uint xoff,
Uint maxdiff,
Uint iprime,
Uint jprime,
Uint kprime,
Uint lprime,
Uint sptr,
Uint qptr );
extern void
matchstemModifyBranch(void *space,
matchstem_t *a, Uint k,
Uint mat, Uint q,
Uint mis, Uint ins, Uint del,
Uint l, Uint r, Uint u, Uint v);
extern void
matchstemAddBranch(void *space,
matchstem_t *a,
Uint mat, Uint q,
Uint mis, Uint ins, Uint del,
Uint l, Uint r, Uint u, Uint v);
extern void
kd_updatebranches(matchstem_t* b, kdiffm_t *data, unsigned int seedlen);
void matchstemDestruct(void *space, matchstem_t *M);
branch_t* kmis (void *space, Suffixarray *s, char *P, Uint m, Uint k, Uint *noofmatches);
void kdcompare(TripleSint *a, branch_t *b, Uint m);
void
bl_kdMatchstemDestruct(void *space, matchstem_t* stem, Uint len);
branch_t *
copyBranch(void *space, branch_t *a);
#endif
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