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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 _ANNOTATION_
#define _ANNOTATION_
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "stringutils.h"
#include "basic-types.h"
#include "charsequence.h"
#include "gzidx.h"
typedef struct {
int64_t dir5prime;
int64_t dir3prime;
int64_t left;
int64_t right;
int8_t select;
} annotationoffs_t;
typedef struct {
unsigned char type;
Uint trackid;
/*
*
* chromname is gff seqname
*
*/
char *chromname;
Uint chromnamelen;
/*
* BED und GFF: 1-offset
* for personalSNP: start with 0-offset
* end base is not part of the feature ie. if
* end = 100 last feature base is 99. see below.
*
*/
uint64_t start;
uint64_t end;
/*
* GFF: name is the feature key
* BED: name is the name of the acutal feature
* for personalSNP track name is alleles A,C,T,G separated by '/'.
* Leading '-' is indel: insertion if start-end=0
*
* */
char *name;
Uint namelen;
double score;
unsigned char strand;
/*GFF fields*/
unsigned char frame;
char *source;
Uint sourcelen;
Uint noofattributes;
char **attributes;
Uint *attributelen;
/*BED fields*/
uint64_t thickStart;
uint64_t thickEnd;
Uint *itemRgb;
Uint blockCount;
uint64_t* blockSizes;
uint64_t* blockStarts;
Uint noofovl;
Uint firstovl;
Uint level;
/*extension*/
char **blockRefseqs;
char *blockStrands;
/*SNPitem*/
Uint alleleCount;//number of alleles in name
Uint *alleleFreq;//from comma separated list of number of observed alleles - if unkowns 0
Uint *alleleScores;//from a comma separated list - if unkown 0
} annotationitem_t;
typedef struct {
uint64_t noofchr;
char **chrname;
Uint *chrnamelen;
Uint sz;
uint64_t *noofbins;
uint64_t **last; //stores the last interval strictly left of indexed interval [i*sz,i+1*sz];
} annotationindex_t;
typedef struct {
uint64_t init;
char sorted;
char *trackname;
Uint tracknamelen;
char *description;
Uint descriptionlen;
Uint noofitems;
annotationitem_t *items;
char *filename;
Uint filenamelen;
} annotationtrack_t;
typedef struct {
uint64_t init;
char sorted;
Uint nooftracks;
char **trackname;
Uint *tracknamelen;
char **description;
Uint *descriptionlen;
char **filename;
Uint *filenamelen;
Uint noofitems;
annotationitem_t *items;
} annotationmultitrack_t;
void bl_annotationtrackDestruct (void *space, annotationtrack_t *track);
Uint bl_annotationtrackGetStats (void *space, annotationtrack_t *track);
void bl_annotationitemInit (annotationitem_t *item, unsigned char type);
void bl_annotationtrackInit (annotationtrack_t *track);
void bl_annotationitemDestruct (void *space, annotationitem_t *item);
Uint bl_annotationitem_cmp_track (Uint item, void *track, void *elem, void *nfo);
int bl_annotationitem_nostrand_cmp (void const *a, void const *b);
int bl_annotationitem_cmp (void const *a, void const *b);
void bl_annotationtrackDestruct (void *space, annotationtrack_t *track);
void bl_annotationtrackAssignTrackLevel(annotationtrack_t *track);
annotationmultitrack_t* bl_annotationtrackJoin(void *space, annotationmultitrack_t *dest, annotationtrack_t *src);
annotationitem_t* bl_annotationitemCopy(annotationitem_t *dest, annotationitem_t *src);
void bl_annotationmultitrackInit (annotationmultitrack_t *track);
Uint bl_annotationitem_cmp_multitrack (Uint item, void *track, void *elem, void *nfo);
void bl_annotationtrackSetItems(annotationtrack_t* track, annotationitem_t* items, Uint n);
annotationindex_t* bl_annotationIndex(annotationtrack_t *t);
void bl_annotationtrackDumpIndex(annotationindex_t *idx,annotationtrack_t *track);
void bl_annotationmultitrackDestruct (void *space, annotationmultitrack_t *track);
void bl_annotationitemApplyOffset(annotationitem_t *item, int64_t off3, int64_t off5, int64_t left, int64_t right, int8_t select);
void bl_annotationitemDump(FILE *dev, annotationitem_t *item);
void bl_annotationmultitrackApplyOffset(annotationmultitrack_t *mtrack, annotationoffs_t *off);
#endif
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