1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
|
/*
* 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 SAMHEADER_H
#define SAMHEADER_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 samheader_s{
char *version;
char **rnames;
uint64_t *rlens;
uint64_t nrnames;
char **rgroups;
char **rgroupsinfo;
Uint nrgroups;
char *cmd;
} samheader_t;
samheader_t* bl_samreadHeader(char* filename);
//unsigned char gzip, struct access *index,)
void bl_samaddReadGroup (samheader_t *head, char *id, char *info);
void bl_saminitHeader (samheader_t *head);
void bl_samdumpHeader (samheader_t *head);
void bl_samdestructHeader (samheader_t *head);
char* bl_samHeader (void *space, segemehl_t *info, Uint binno);
char* bl_samwriteHeader(samheader_t *hdr, Uint binno, char order, char sep, char lf) ;
samheader_t* bl_samparseHeaderLine (samheader_t *head, char *line);
void bl_samaddReferenceSequence (samheader_t *head, char *name, uint64_t len);
#endif
|
