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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 MAPFRAG_H
#define MAPFRAG_H
/*
*
* mapfrag.h
*
*
* @author Steve Hoffmann, steve@bioinf.uni-leipzig.de
* @company Bioinformatics, University of Leipzig
* @date 10.12.2012 10:25:35 CET
*
*/
#include <string.h>
#include <limits.h>
#include "basic-types.h"
#include "locus.h"
#include "multicharseq.h"
#include "sufarray.h"
#include "kdseed.h"
#include "biofiles.h"
#include "segemehl.h"
typedef struct mapseed_s {
uint64_t u;
char rc; //strand TODO
double evalue;
double score;
unsigned int len;
unsigned int mat;
unsigned int mis;
unsigned int ins;
unsigned int del;
unsigned int edist;
unsigned int l;
unsigned int r;
char good;
char maxinterval;
char maxevalue;
locus_t *locus;
/*these variables are not always set*/
uint64_t seedlen;
uint64_t refidx;
uint64_t refpos;
char *refname;
} mapseed_t;
typedef struct mapseedlist_s {
unsigned int n;
mapseed_t *l;
} mapseedlist_t;
typedef struct mapfrag_s {
mapseed_t *seed;
char *seq;
char *qual;
MultiCharSeqAlignment *mcsa;
unsigned int lclip;
unsigned int rclip;
unsigned int mat;
unsigned int mis;
unsigned int ins;
unsigned int del;
unsigned int lmat;
unsigned char mate;
unsigned char mapq;
int leftgap;
int rightgap;
unsigned char nextnoncollinear;
unsigned char prevnoncollinear;
unsigned char issplit;
double mapq_dbl;
} mapfrag_t;
typedef struct mapping_s {
char *seq;
char *qual;
Uint seqlen;
Uint lclip;
Uint rclip;
int scr;
unsigned int n;
unsigned int P;
unsigned int Q;
char consecutive;
char matestatus;
mapfrag_t *f;
double mapqual;
double sigma;
double maxqual;
} mapping_t;
typedef struct mappingset_s {
unsigned int n;
mapping_t* elem;
} mappingset_t;
void bl_removeMapping (mapping_t *l);
void bl_removeMappingSet (mappingset_t *s);
void bl_removeUnpairedMapping(mappingset_t *s);
char bl_mappingsetHasPaired (mappingset_t *s);
long long int bl_distMapping(mapping_t *l, mapping_t *r);
mapping_t* bl_concatMapping(mapping_t* l, mapping_t *r);
void bl_initMappingSet(mappingset_t *set);
void bl_addMapping (mappingset_t *s, mapping_t *l);
Uint bl_addMapFrag(mapping_t *l, MultiCharSeqAlignment *mcsa,
mapseed_t *seed, unsigned char mate, unsigned char issplit) ;
mapseedlist_t*
bl_addMapSeedBranch (mapseedlist_t *s, branch_t *b, unsigned int u, unsigned int strand,
double maxE, unsigned int maxM, double SPM, karlin_t *stats);
unsigned int
bl_mappingsetHasPos (mappingset_t *s, unsigned int pos);
void bl_removeSuboptimalMapping (mappingset_t *s, int *scores, int indel);
char* bl_getMapFragQryDesc (mapfrag_t *f);
char* bl_getMapFragQry (mapfrag_t *f);
char* bl_getMapFragQual (mapfrag_t *f);
unsigned char bl_getMapFragStrand (mapfrag_t *f);
unsigned int bl_getMapFragV(mapfrag_t *f);
unsigned int bl_getMapFragU(mapfrag_t *f);
unsigned int bl_getMapFragP(mapfrag_t *f);
unsigned int bl_getMapFragQ(mapfrag_t *f);
char* bl_getMapFragRefDesc(mapfrag_t *f);
Alignment* bl_getMapFragAlignment (mapfrag_t *f);
unsigned int bl_getMappingEdist (mapping_t *l);
unsigned int bl_getMapFragEdist(mapfrag_t *f);
mapseedlist_t* bl_initMapSeedList (mapseedlist_t *l);
void bl_removeMappingSet (mappingset_t *s);
void bl_wrapSeedList (mapseedlist_t *l);
void bl_initMapping(mapping_t *l, char*, char*, Uint, Uint);
MultiCharSeqAlignment * bl_copyMCSA(MultiCharSeqAlignment *dest, MultiCharSeqAlignment *src);
char bl_isPairedMapping (mapping_t *l);
char bl_isQueryMapping (mapping_t *l);
char bl_isMateMapping (mapping_t *l);
char bl_hasMateMapping (mappingset_t *s);
char bl_hasQueryMapping (mappingset_t *s);
unsigned int bl_getMapFragChrIdx(mapfrag_t *f);
unsigned int bl_getMapFragSplit (mapfrag_t *f);
unsigned char bl_getMapFragIsMate (mapfrag_t *f);
MultiCharSeqAlignment* bl_getMapFragMCSA(mapfrag_t *f);
Uint bl_getMateStartIdx (mapping_t *l);
Uint bl_getQueryStartIdx (mapping_t *l);
mapseed_t *bl_getMapSeedListBest (mapseedlist_t *l);
locus_t * bl_getMapSeedLocus (mapseed_t *seed, Uint j, MultiCharSeq *mseq, Suffixarray *s);
void bl_getMapSeedAdditionalInformation(mapseed_t *seed, Suffixarray *s, MultiCharSeq *mseq);
void bl_addMapFragPartialEdist (mapfrag_t *frag, Uint edist);
unsigned int bl_getMapFragGetUlen (mapfrag_t *f);
uint64_t bl_getMapFragSubstart (mapfrag_t *f);
void bl_removeBadMappings (mappingset_t *s, Uint querylen, Uint matelen, Uint acc);
void bl_removeBadMates (mappingset_t *s, Uint querylen, Uint matelen, Uint acc);
void bl_countMultipleMappings (mappingset_t *s, Uint *nqueries, Uint *nmates);
unsigned int bl_getMappingEdistQM (mapping_t *l, Uint *qedist, Uint *medist);
void bl_setMapFragMapQual (mapfrag_t *f, double mapqual);
double bl_getMapFragMapQual (mapfrag_t *f);
unsigned int bl_getMapFragLongestMatch(mapfrag_t *f);
mapfrag_t* bl_getMapFrags (mapping_t *m, Uint *size);
mapping_t* bl_getMappings(mappingset_t *s, Uint *size);
unsigned int bl_getMapFragScore (mapfrag_t *f, int *scores, int indel);
void bl_removeMappingQM (mapping_t *l, char ismate);
Uint bl_getNextMapFragU (mapfrag_t *f, mapping_t *m, char ismate, Uint *lgap, Uint *rgap);
int bl_getMappingScore (mapping_t *l, int * scores, int indel);
mappingset_t* bl_copyMappingSet(mappingset_t *s);
locuslist_t* bl_getMappingLocusList(mapping_t *mapping, MultiCharSeq* mseq, char ismate);
char bl_isSplitMappingQM (mapping_t *mapping, char ismate);
char bl_getMappingStrandQM (mapping_t *mapping, char ismate);
char bl_isCollinearMapping(mapping_t *m, char ismate);
mapfrag_t* bl_getMapFragsQM (mapping_t *m, Uint *size, char ismate);
unsigned int bl_getMapFragLeft(mapfrag_t *f);
unsigned int bl_getMapFragRight(mapfrag_t *f);
int bl_getMappingScoreQM (mapping_t *l, int *scores, int indel, int *qscore, int *mscore);
int bl_getMappingFragNoQM (mapping_t *l, Uint *qno, Uint *mno);
char bl_hasQueryMappingMaxEdist (mappingset_t *s, Uint maxedist);
char bl_hasMateMappingMaxEdist (mappingset_t *s, Uint maxedist);
Uint bl_getMappingRange(mapping_t *m);
char bl_getMappingIsConsecutive(mapping_t *m);
void bl_dumpMappingSet (FILE *dev, mappingset_t *set);
int bl_getMappingMaxScore(mappingset_t *s, int *scores, int indel);
void bl_removeBadMatesEdistQM (mappingset_t *s, Uint maxedist, Uint ismate);
mappingset_t* bl_sortMappingSetByScore (mappingset_t *set, int* scores, int indel);
void bl_removeBadMatesAcc (mappingset_t *s, Uint querylen, Uint matelen, Uint acc);
int bl_getMappingMaxScoreQM(mappingset_t *s, int *scores, int indel, char ismate);
void bl_removeSuboptimalMappingQM (mappingset_t *s, int *scores, int indel, char ismate);
void bl_mergeMappings (mappingset_t *set);
void bl_removeBadMatesCov (mappingset_t *s, Uint querylen, Uint matelen, Uint mc);
void bl_concatMappingSet (mappingset_t *dest, mappingset_t*source);
char bl_hasMappingPairedMaxEdist (mappingset_t *s, Uint maxedist);
mappingset_t* bl_mappingsetRemoveDuplicates(mappingset_t *set, Uint maxdist);
void bl_dumpMapping (FILE *dev, mapping_t *m);
mapping_t* bl_copyMapping (mapping_t* dest, mapping_t* source);
char bl_hasMultipleQueryMappings (mappingset_t *s);
char bl_hasMultipleMateMappings (mappingset_t *s);
char bl_hasMultiplePairedMappings (mappingset_t *s);
char bl_isCircularMappingQM (mapping_t *m, char ismate);
void bl_dumpSpliceJunctions(mapping_t *m, char ismate, MultiCharSeq *mseq, char *basename, char *name, segemehl_t *nfo);
char bl_mappingGetType (mapping_t *m, char ismate);
Uint bl_getMappingMinFragDist (mapping_t *l);
char bl_getMapFragIsChimeric(mapfrag_t *f);
char bl_getMappingIsChimericQM (mapping_t *m, char ismate);
void bl_removeBadMatesScr (mappingset_t *s, Uint querylen, Uint matelen, int *scores, int indel, int minscr, int minmatescr);
char bl_mappingHasPairedEndOrientation(mapping_t *mapping);
#endif
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