forked from samtools/htslib
/
hfile_internal.h
139 lines (104 loc) · 5.5 KB
/
hfile_internal.h
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
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
/* hfile_internal.h -- internal parts of low-level input/output streams.
Copyright (C) 2013-2015 Genome Research Ltd.
Author: John Marshall <jm18@sanger.ac.uk>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */
#ifndef HFILE_INTERNAL_H
#define HFILE_INTERNAL_H
#include "htslib/hfile.h"
#ifdef __cplusplus
extern "C" {
#endif
struct hFILE_backend {
/* As per read(2), returning the number of bytes read (possibly 0) or
negative (and setting errno) on errors. Front-end code will call this
repeatedly if necessary to attempt to get the desired byte count. */
ssize_t (*read)(hFILE *fp, void *buffer, size_t nbytes) HTS_RESULT_USED;
/* As per write(2), returning the number of bytes written or negative (and
setting errno) on errors. Front-end code will call this repeatedly if
necessary until the desired block is written or an error occurs. */
ssize_t (*write)(hFILE *fp, const void *buffer, size_t nbytes)
HTS_RESULT_USED;
/* As per lseek(2), returning the resulting offset within the stream or
negative (and setting errno) on errors. */
off_t (*seek)(hFILE *fp, off_t offset, int whence) HTS_RESULT_USED;
/* Performs low-level flushing, if any, e.g., fsync(2); for writing streams
only. Returns 0 for success or negative (and sets errno) on errors. */
int (*flush)(hFILE *fp) HTS_RESULT_USED;
/* Closes the underlying stream (for output streams, the buffer will
already have been flushed), returning 0 for success or negative (and
setting errno) on errors, as per close(2). */
int (*close)(hFILE *fp) HTS_RESULT_USED;
};
/* May be called by hopen_*() functions to decode a fopen()-style mode into
open(2)-style flags. */
int hfile_oflags(const char *mode);
/* Must be called by hopen_*() functions to allocate the hFILE struct and set
up its base. Capacity is a suggested buffer size (e.g., via fstat(2))
or 0 for a default-sized buffer. */
hFILE *hfile_init(size_t struct_size, const char *mode, size_t capacity);
/* May be called by hopen_*() functions to undo the effects of hfile_init()
in the event opening the stream subsequently fails. (This is safe to use
even if fp is NULL. This takes care to preserve errno.) */
void hfile_destroy(hFILE *fp);
struct hFILE_scheme_handler {
/* Opens a stream when dispatched by hopen(); should call hfile_init()
to malloc a struct "derived" from hFILE and initialise it appropriately,
including setting base.backend to its own backend vector. */
hFILE *(*open)(const char *filename, const char *mode) HTS_RESULT_USED;
/* Returns whether the URL denotes remote storage when dispatched by
hisremote(). For simple cases, use one of hfile_always_*() below. */
int (*isremote)(const char *filename) HTS_RESULT_USED;
/* The name of the plugin or other code providing this handler. */
const char *provider;
/* If multiple handlers are registered for the same scheme, the one with
the highest priority is used; range is 0 (lowest) to 100 (highest). */
int priority;
};
/* May be used as an isremote() function in simple cases. */
extern int hfile_always_local (const char *fname);
extern int hfile_always_remote(const char *fname);
/* Should be called by plugins for each URL scheme they wish to handle. */
void hfile_add_scheme_handler(const char *scheme,
const struct hFILE_scheme_handler *handler);
struct hFILE_plugin {
/* On entry, HTSlib's plugin API version (currently 1). */
int api_version;
/* On entry, the plugin's handle as returned by dlopen() etc. */
void *obj;
/* The plugin should fill this in with its (human-readable) name. */
const char *name;
/* The plugin may wish to fill in a function to be called on closing. */
void (*destroy)(void);
};
#ifdef ENABLE_PLUGINS
#define PLUGIN_GLOBAL(identifier,suffix) identifier
/* Plugins must define an entry point with this signature. */
extern int hfile_plugin_init(struct hFILE_plugin *self);
#else
#define PLUGIN_GLOBAL(identifier,suffix) identifier##suffix
/* Only plugins distributed within the HTSlib source that might be built
even with --disable-plugins need to use PLUGIN_GLOBAL and be listed here;
others can simply define hfile_plugin_init(). */
extern int hfile_plugin_init_irods(struct hFILE_plugin *self);
extern int hfile_plugin_init_libcurl(struct hFILE_plugin *self);
#endif
/* This one is never built as a separate plugin. */
extern int hfile_plugin_init_net(struct hFILE_plugin *self);
#ifdef __cplusplus
}
#endif
#endif