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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 LOCUS_H
#define LOCUS_H
/*
*
* locus.h
* a genomic locus given a reference
*
* @author Steve Hoffmann, steve@bioinf.uni-leipzig.de
* @company Bioinformatics, University of Leipzig
* @date 09.12.2012 14:16:18 CET
*
*/
#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>
#include <inttypes.h>
#include <string.h>
#include "basic-types.h"
#include "charsequence.h"
#include "multicharseq.h"
#include "memory.h"
#include "stringutils.h"
#include "alignment.h"
#include "nw.h"
#include "sw.h"
typedef struct locus_s {
unsigned int idx;
uint64_t pos;
uint64_t len;
uint64_t chrstart;
uint64_t chrend;
char strand;
char *name;
uint8_t score;
Uint readstart;
Uint readend;
Uint edist;
} locus_t;
typedef struct locuslist_s {
unsigned int noofloci;
locus_t *loci;
} locuslist_t;
typedef struct multilocus_s {
unsigned int idx;
uint64_t pos;
uint64_t len;
char strand;
uint64_t chrstart;
uint64_t chrend;
char *name;
uint8_t score;
Uint readstart;
Uint edist;
Uint noofloci;
locus_t *loci;
} multilocus_t;
typedef struct multilocuslist_s {
Uint noofmultiloci;
multilocus_t *loci;
} multilocuslist_t;
uint64_t bl_getLocusChromPos ( locus_t *loc);
uint64_t bl_getLocusChromEndPos ( locus_t *loc);
char* bl_getLocusChromDesc (MultiCharSeq *mseq, locus_t *loc);
locus_t* bl_initLocus (locus_t* loc, MultiCharSeq *mseq, uint64_t pos,
unsigned char strand, uint64_t length, uint64_t loff) ;
uint64_t bl_getLocusChromIdx (locus_t *loc);
locus_t* bl_getLocusFromMultiCharSeqAlignment(MultiCharSeqAlignment *mcsa, MultiCharSeq *mseq, locus_t *loc);
void bl_addLocusToLocuslist(locuslist_t *l, locus_t *loc);
locuslist_t* bl_initLocuslist(locuslist_t *list);
int bl_cmpLocusLen(const void *a, const void *b);
locuslist_t * bl_sortLocuslistByLength (locuslist_t *list);
locuslist_t* bl_mergeLocibyDistance (locuslist_t *list, uint64_t d);
void wrapLocuslist(locuslist_t *list);
char* bl_getLocusSeq (MultiCharSeq *mseq, locus_t *loc);
unsigned int bl_getLocusLen(locus_t *loc);
unsigned int bl_getLocusLenOffset(MultiCharSeq *mseq, locus_t *loc, Uint loff, Uint roff);
char* bl_getLocusSeqOffset (MultiCharSeq *mseq, locus_t *loc, Uint off);
unsigned char bl_getLocusStrand (locus_t *loc);
uint64_t bl_getLocusChromPosOffset (locus_t *loc, Uint off);
char* bl_getLocusListSequence (MultiCharSeq *mseq, locuslist_t *list, Uint loff, Uint roff, Uint *seqlen);//Uint *start, Uint **splitpos);
locuslist_t* bl_getLocusList (MultiCharSeqAlignment *a, MultiCharSeq *mseq, unsigned int noofaligns);
int bl_cmpLocusPos(const void *a, const void *b);
void bl_locusListAddOffset ( MultiCharSeq *mseq, locuslist_t *list, Uint loff, Uint roff);
Alignment* bl_getLocusListExpandedAlignment(Alignment *al, locuslist_t *list);
char bl_getLocusListCheck(locuslist_t *list, Uint maxdist);
Alignment** expandAlignmentDisjoint(Alignment *al, locuslist_t* list, MultiCharSeq *mseq);
Alignment* bl_locusListAlign(MultiCharSeq *mseq, locuslist_t *list, char *qry, Uint qrylen, int* scores, int indel);
locuslist_t* bl_mergeLocibyDistanceNoStrand (locuslist_t *list, uint64_t d);
int bl_cmpLocusPosNoStrand(const void *a, const void *b);
void bl_showLocusList(FILE *, locuslist_t *list);
uint64_t* bl_locusListGetStartPos (locuslist_t *list);
uint64_t* bl_locusListGetEndPos (locuslist_t *list);
char* bl_locusListStrand (locuslist_t *list);
Uint* bl_locusListGetReadStart (locuslist_t *list);
Uint* bl_locusListGetReadEnd (locuslist_t *list);
char bl_locusListIsConsecutive (locuslist_t *list);
uint64_t bl_getLocusEndPos (locus_t *loc);
multilocus_t* bl_createMultiLocusFromLocusList (locuslist_t *list, Uint *noofmultiloci);
void bl_wrapMultiLocus (multilocus_t *m);
void bl_dumpMultiLocusSingle (FILE *dev, multilocus_t *m, MultiCharSeq *mseq, char *name);
void bl_dumpMultiLocusJoint (FILE *dev, multilocus_t *m, MultiCharSeq *mseq, char *name);
multilocus_t* bl_invertMultiLocus (multilocus_t *m);
void bl_setMultiLocusScore (multilocus_t *m, uint8_t score);
void bl_setMultiLocusName (multilocus_t *m, char *name);
locuslist_t* bl_mergeLocusList (locuslist_t *a, locuslist_t *b);
char* bl_printMultiLocusJoint (multilocus_t *m, MultiCharSeq *mseq, char *name);
char* bl_printMultiLocusSingle (multilocus_t *m, MultiCharSeq *mseq, char *name);
#endif
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