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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 SAMOUT_H
#define SAMOUT_H
#include "multicharseq.h"
#include "mapfrag.h"
#include "segemehl.h"
#include "biofiles.h"
#include "samheader.h"
/*
*
* samout.h
* samout
*
* @author Steve Hoffmann, steve@bioinf.uni-leipzig.de
* @company Bioinformatics, University of Leipzig
* @date 21.03.2012 08:41:55 CET
*
*/
typedef struct samtag_s {
char *tag;
char *key;
char *type;
char *val;
} samtag_t;
typedef struct samrec_s {
char *qname;
unsigned flag;
char *rname;
uint64_t pos;
uint8_t mapq;
char *cigar;
char *rnext;
uint64_t pnext;
int64_t tlen;
char *seq;
char *qual;
Uint nooftags;
samtag_t *tags;
} samrec_t;
typedef struct samlist_s {
unsigned int noofrecs;
samrec_t *recs;
} samlist_t;
/*
typedef struct mapfragment_s {
char *id;
Uint subject;
unsigned char rc;
Uint i;
Uint j;
Uint p;
Uint q;
int scr;
int mat;
int mis;
int ins;
int del;
int edist;
Alignment *al;
double evalue;
char *seq;
char *qual;
char *rname;
char issplit;
char usenextfieldforsplits;
Uint fragno;
Uint previdx;
Uint prevpos;
char prevflags;
Uint nextidx;
Uint nextpos;
char nextflags;
unsigned char skip;
} mapfrag_t;
typedef struct {
Uint nooffrags;
mapfrag_t *frags;
} mapfraglist_t;*/
samlist_t *bl_samgetSamList (fasta_t *reads, Uint id, mapping_t *l, MultiCharSeq *mseq, char ismultiple, Uint noofqueries, Uint noofmates, Uint queryid, Uint mateid, char unmappedtornext, segemehl_t *nfo);
void bl_samprintSamrec (FILE *dev, samrec_t* r, char lf);
char* bl_samprintSamrec2Buffer (samrec_t* r, char lf);
void bl_samprintSamlist (samlist_t *l, mapping_t *f, segemehl_t*);
void bl_samdestructSamList (samlist_t *list);
mappingset_t* bl_sammappingJoinFrags (mappingset_t *s, segemehl_t *nfo);
void bl_samprintEmptyAlign (char *desc, char* seq, char* qual, char hasPaired, char isQuery, char nomatemapped, char *nextchr, int64_t nextrpos, char nextrc, char ismultiple, char ischimeric, mapseed_t *seed, segemehl_t *nfo);
samrec_t * bl_samline2rec(char *line, Uint len, samheader_t *head);
void bl_samDestruct(samrec_t *samrec);
samtag_t* bl_samgetTag (samrec_t *rec, char* key);
#endif
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