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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 SPLITALIGN_H
#define SPLITALIGN_H
#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>
#include <inttypes.h>
#include "basic-types.h"
#include "bitvectoralg.h"
#include "karlin.h"
#include "mapfrag.h"
/*
*
* splitalign.h
* splitaligns
*
* @author Steve Hoffmann, steve@bioinf.uni-leipzig.de
* @company Bioinformatics, University of Leipzig
* @date 07/23/14 14:36:19 CEST
*
*/
/*
typedef struct split_s {
Uint subidx;
char strand;
Uint start;
Uint end;
uint16_t i;
uint16_t j;
} split_t;
*/
typedef struct{
//the coords of the read
uint64_t uoff;
uint64_t ulen;
//the coords of the reference
uint64_t voff;
uint64_t vlen;
//the alignment
char *cigar;
} split_t;
typedef struct{
char *u;
uint64_t ulen;
uint64_t upos;
uint64_t vpos;
Uint vidx;
char rc;
//trans alignments pointing to here
uint64_t vdonpos;
Uint vdonidx;
char vdonrc;
//the linear splits of this alignment
Uint noofsplits;
split_t *splits;
//trans alignments pointing out
uint64_t vaccpos;
Uint vaccidx;
char vaccrc;
} splitalignment_t;
typedef struct spliceevent_s {
uint64_t vdonpos;
Uint vdonidx;
char vdonrc;
char donerr; //in percent NOT YET USED!
char donins; //trailing insertions max:254 NOT YET USED!
uint64_t vaccpos;
Uint vaccidx;
char vaccrc;
char accerr; //in percent NOT YET USED!
char accins; //trailing insertions max:254 NOT YET USED!
} spliceevent_t;
typedef struct spliceevents_s {
Uint noofevents;
spliceevent_t *event;
} spliceevents_t;
typedef struct spliceventmapelem_s{
unsigned char type;
uint8_t site;
spliceevent_t *ptr;
} spliceeventmapelem_t;
typedef struct spliceeventmap_s{
Uint size;
spliceeventmapelem_t *map;
}spliceeventmap_t;
mappingset_t* bl_splitAlign(void *space, Suffixarray *arr, MultiCharSeq *seq, mappingset_t *set,
char *querydesc, matchstem_t **stems, char **seqs, char **quals, Uint len,
karlin_t *stats, Uint *enctab, bitvector *D, unsigned char ismate, segemehl_t *nfo);
char* bl_cigarSplitAlignment(char *cigar, uint64_t **, uint64_t **, Uint *nsplits);
splitalignment_t * bl_cigarGetSplitAlignment(
char* u, uint64_t ulen, uint64_t upos,
uint64_t vpos, Uint idx, char rc, uint64_t vdonpos, Uint vdonidx, char donrc,
uint64_t vaccpos, Uint vaccidx, char accrc, char *cigar) ;
spliceevents_t* bl_splitAlignmentGetSpliceEvents (splitalignment_t *aln);
void bl_dumpSpliceEvents (spliceevents_t *events);
void bl_destructSplitAlignment (splitalignment_t *aln);
void bl_destructSpliceEvents (spliceevents_t *events);
void se_kdHMMsplit (char **seqs, char **quals, Uint qrylen, char *qrydesc, MultiCharSeq *mseq,
mappingset_t *set, Uint minlen, Uint minscore);
void bl_fixSplitAlignBrendel (Suffixarray *arr, mappingset_t *set, MultiCharSeq *mseq, char *qrydesc,
char **seqs, char **quals, Uint qrylen, char ismate, segemehl_t *nfo);
char bl_crosscorrection(Suffixarray *arr, mappingset_t *set, MultiCharSeq *mseq,
char *qrydesc, char **seqs, char **quals, Uint qrylen, Uint matelen, Uint checkedist, char ismate, segemehl_t *nfo);
void
se_kdAlignEvalSplitAlign (MultiCharSeq *seq, MultiCharSeqAlignment *a,
mappingset_t* set, Uint *totalcover, int *totalscore,
unsigned char *trans, int *scores, int indel, unsigned int noofaligns,
char ismate, char **seqs, char **quals, segemehl_t *nfo);
MultiCharSeqAlignment*
se_AlignSplitMap (Uint *mystarts, Uint *myends, uint64_t *mypos, char *myrc, Uint nooffrags, MultiCharSeq *seq, char *querydesc,
char **seqs, char **quals, Uint qrylen, int *scores, int indel, int transition);
mappingset_t*
bl_fixSplitAlignHoffmann (Suffixarray *arr, mappingset_t *set, MultiCharSeq *mseq, char *qrydesc,
char **seqs, char **quals, Uint qrylen, char ismate, segemehl_t *nfo);
#endif
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