1 /* hfile.h -- buffered low-level input/output streams.
2
3 Copyright (C) 2013-2015 Genome Research Ltd.
4
5 Author: John Marshall <jm18@sanger.ac.uk>
6
7 Permission is hereby granted, free of charge, to any person obtaining a copy
8 of this software and associated documentation files (the "Software"), to deal
9 in the Software without restriction, including without limitation the rights
10 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
11 copies of the Software, and to permit persons to whom the Software is
12 furnished to do so, subject to the following conditions:
13
14 The above copyright notice and this permission notice shall be included in
15 all copies or substantial portions of the Software.
16
17 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
18 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
19 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
20 THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
21 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
22 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
23 DEALINGS IN THE SOFTWARE. */
24
25 #ifndef HTSLIB_HFILE_H
26 #define HTSLIB_HFILE_H
27
28 #include <string.h>
29
30 #include <sys/types.h>
31
32 #include "hts_defs.h"
33
34 // #ifdef __cplusplus
35 // extern "C" {
36 // #endif
37
38 /* These fields are declared here solely for the benefit of the inline functions
39 below. They may change in future releases. User code should not use them
40 directly; you should imagine that hFILE is an opaque incomplete type. */
41 struct hFILE_backend;
42 typedef struct hFILE {
43 char *buffer, *begin, *end, *limit;
44 const struct hFILE_backend *backend;
45 off_t offset;
46 int at_eof:1;
47 int has_errno;
48 } hFILE;
49
50 /*!
51 @abstract Open the named file or URL as a stream
52 @return An hFILE pointer, or NULL (with errno set) if an error occurred.
53 */
54 hFILE *hopen(const char *filename, const char *mode) HTS_RESULT_USED;
55
56 /*!
57 @abstract Associate a stream with an existing open file descriptor
58 @return An hFILE pointer, or NULL (with errno set) if an error occurred.
59 @notes For socket descriptors (on Windows), mode should contain 's'.
60 */
61 hFILE *hdopen(int fd, const char *mode) HTS_RESULT_USED;
62
63 /*!
64 @abstract Report whether the file name or URL denotes remote storage
65 @return 0 if local, 1 if remote.
66 @notes "Remote" means involving e.g. explicit network access, with the
67 implication that callers may wish to cache such files' contents locally.
68 */
69 // int hisremote(const char *filename) HTS_RESULT_USED;
70
71 /*!
72 @abstract Flush (for output streams) and close the stream
73 @return 0 if successful, or EOF (with errno set) if an error occurred.
74 */
75 int hclose(hFILE *fp) HTS_RESULT_USED;
76
77 /*!
78 @abstract Close the stream, without flushing or propagating errors
79 @notes For use while cleaning up after an error only. Preserves errno.
80 */
81 void hclose_abruptly(hFILE *fp);
82
83 /*!
84 @abstract Return the stream's error indicator
85 @return Non-zero (in fact, an errno value) if an error has occurred.
86 @notes This would be called herror() and return true/false to parallel
87 ferror(3), but a networking-related herror(3) function already exists. */
herrno(hFILE * fp)88 static inline int herrno(hFILE *fp)
89 {
90 return fp->has_errno;
91 }
92
93 /*!
94 @abstract Clear the stream's error indicator
95 */
hclearerr(hFILE * fp)96 static inline void hclearerr(hFILE *fp)
97 {
98 fp->has_errno = 0;
99 }
100
101 /*!
102 @abstract Reposition the read/write stream offset
103 @return The resulting offset within the stream (as per lseek(2)),
104 or negative if an error occurred.
105 */
106 off_t hseek(hFILE *fp, off_t offset, int whence) HTS_RESULT_USED;
107
108 /*!
109 @abstract Report the current stream offset
110 @return The offset within the stream, starting from zero.
111 */
htell(hFILE * fp)112 static inline off_t htell(hFILE *fp)
113 {
114 return fp->offset + (fp->begin - fp->buffer);
115 }
116
117 /*!
118 @abstract Read one character from the stream
119 @return The character read, or EOF on end-of-file or error
120 */
hgetc(hFILE * fp)121 static inline int hgetc(hFILE *fp)
122 {
123 extern int hgetc2(hFILE *);
124 return (fp->end > fp->begin)? (unsigned char) *(fp->begin++) : hgetc2(fp);
125 }
126
127 /*!
128 @abstract Peek at characters to be read without removing them from buffers
129 @param fp The file stream
130 @param buffer The buffer to which the peeked bytes will be written
131 @param nbytes The number of bytes to peek at; limited by the size of the
132 internal buffer, which could be as small as 4K.
133 @return The number of bytes peeked, which may be less than nbytes if EOF
134 is encountered; or negative, if there was an I/O error.
135 @notes The characters peeked at remain in the stream's internal buffer,
136 and will be returned by later hread() etc calls.
137 */
138 ssize_t hpeek(hFILE *fp, void *buffer, size_t nbytes) HTS_RESULT_USED;
139
140 /*!
141 @abstract Read a block of characters from the file
142 @return The number of bytes read, or negative if an error occurred.
143 @notes The full nbytes requested will be returned, except as limited
144 by EOF or I/O errors.
145 */
146 static inline ssize_t HTS_RESULT_USED
hread(hFILE * fp,void * buffer,size_t nbytes)147 hread(hFILE *fp, void *buffer, size_t nbytes)
148 {
149 extern ssize_t hread2(hFILE *, void *, size_t, size_t);
150
151 size_t n = fp->end - fp->begin;
152 if (n > nbytes) n = nbytes;
153 memcpy(buffer, fp->begin, n);
154 fp->begin += n;
155 return (n == nbytes)? (ssize_t) n : hread2(fp, buffer, nbytes, n);
156 }
157
158 /*!
159 @abstract Write a character to the stream
160 @return The character written, or EOF if an error occurred.
161 */
hputc(int c,hFILE * fp)162 static inline int hputc(int c, hFILE *fp)
163 {
164 extern int hputc2(int, hFILE *);
165 if (fp->begin < fp->limit) *(fp->begin++) = c;
166 else c = hputc2(c, fp);
167 return c;
168 }
169
170 /*!
171 @abstract Write a string to the stream
172 @return 0 if successful, or EOF if an error occurred.
173 */
hputs(const char * text,hFILE * fp)174 static inline int hputs(const char *text, hFILE *fp)
175 {
176 extern int hputs2(const char *, size_t, size_t, hFILE *);
177
178 size_t nbytes = strlen(text), n = fp->limit - fp->begin;
179 if (n > nbytes) n = nbytes;
180 memcpy(fp->begin, text, n);
181 fp->begin += n;
182 return (n == nbytes)? 0 : hputs2(text, nbytes, n, fp);
183 }
184
185 /*!
186 @abstract Write a block of characters to the file
187 @return Either nbytes, or negative if an error occurred.
188 @notes In the absence of I/O errors, the full nbytes will be written.
189 */
190 static inline ssize_t HTS_RESULT_USED
hwrite(hFILE * fp,const void * buffer,size_t nbytes)191 hwrite(hFILE *fp, const void *buffer, size_t nbytes)
192 {
193 extern ssize_t hwrite2(hFILE *, const void *, size_t, size_t);
194
195 size_t n = fp->limit - fp->begin;
196 if (n > nbytes) n = nbytes;
197 memcpy(fp->begin, buffer, n);
198 fp->begin += n;
199 return (n==nbytes)? (ssize_t) n : hwrite2(fp, buffer, nbytes, n);
200 }
201
202 /*!
203 @abstract For writing streams, flush buffered output to the underlying stream
204 @return 0 if successful, or EOF if an error occurred.
205 */
206 int hflush(hFILE *fp) HTS_RESULT_USED;
207
208 // #ifdef __cplusplus
209 // }
210 // #endif
211
212 #endif
213