/usr/include/htslib/hfile.h is in libhts-dev 1.2.1-2ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 | /* hfile.h -- buffered 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 HTSLIB_HFILE_H
#define HTSLIB_HFILE_H
#include <string.h>
#include <sys/types.h>
#include "hts_defs.h"
#ifdef __cplusplus
extern "C" {
#endif
/* These fields are declared here solely for the benefit of the inline functions
below. They may change in future releases. User code should not use them
directly; you should imagine that hFILE is an opaque incomplete type. */
struct hFILE_backend;
typedef struct hFILE {
char *buffer, *begin, *end, *limit;
const struct hFILE_backend *backend;
off_t offset;
int at_eof:1;
int has_errno;
} hFILE;
/*!
@abstract Open the named file or URL as a stream
@return An hFILE pointer, or NULL (with errno set) if an error occurred.
*/
hFILE *hopen(const char *filename, const char *mode) HTS_RESULT_USED;
/*!
@abstract Associate a stream with an existing open file descriptor
@return An hFILE pointer, or NULL (with errno set) if an error occurred.
@notes For socket descriptors (on Windows), mode should contain 's'.
*/
hFILE *hdopen(int fd, const char *mode) HTS_RESULT_USED;
/*!
@abstract Report whether the file name or URL denotes remote storage
@return 0 if local, 1 if remote.
@notes "Remote" means involving e.g. explicit network access, with the
implication that callers may wish to cache such files' contents locally.
*/
int hisremote(const char *filename) HTS_RESULT_USED;
/*!
@abstract Flush (for output streams) and close the stream
@return 0 if successful, or EOF (with errno set) if an error occurred.
*/
int hclose(hFILE *fp) HTS_RESULT_USED;
/*!
@abstract Close the stream, without flushing or propagating errors
@notes For use while cleaning up after an error only. Preserves errno.
*/
void hclose_abruptly(hFILE *fp);
/*!
@abstract Return the stream's error indicator
@return Non-zero (in fact, an errno value) if an error has occurred.
@notes This would be called herror() and return true/false to parallel
ferror(3), but a networking-related herror(3) function already exists. */
static inline int herrno(hFILE *fp)
{
return fp->has_errno;
}
/*!
@abstract Clear the stream's error indicator
*/
static inline void hclearerr(hFILE *fp)
{
fp->has_errno = 0;
}
/*!
@abstract Reposition the read/write stream offset
@return The resulting offset within the stream (as per lseek(2)),
or negative if an error occurred.
*/
off_t hseek(hFILE *fp, off_t offset, int whence) HTS_RESULT_USED;
/*!
@abstract Report the current stream offset
@return The offset within the stream, starting from zero.
*/
static inline off_t htell(hFILE *fp)
{
return fp->offset + (fp->begin - fp->buffer);
}
/*!
@abstract Read one character from the stream
@return The character read, or EOF on end-of-file or error
*/
static inline int hgetc(hFILE *fp)
{
extern int hgetc2(hFILE *);
return (fp->end > fp->begin)? (unsigned char) *(fp->begin++) : hgetc2(fp);
}
/*!
@abstract Peek at characters to be read without removing them from buffers
@param fp The file stream
@param buffer The buffer to which the peeked bytes will be written
@param nbytes The number of bytes to peek at; limited by the size of the
internal buffer, which could be as small as 4K.
@return The number of bytes peeked, which may be less than nbytes if EOF
is encountered; or negative, if there was an I/O error.
@notes The characters peeked at remain in the stream's internal buffer,
and will be returned by later hread() etc calls.
*/
ssize_t hpeek(hFILE *fp, void *buffer, size_t nbytes) HTS_RESULT_USED;
/*!
@abstract Read a block of characters from the file
@return The number of bytes read, or negative if an error occurred.
@notes The full nbytes requested will be returned, except as limited
by EOF or I/O errors.
*/
static inline ssize_t HTS_RESULT_USED
hread(hFILE *fp, void *buffer, size_t nbytes)
{
extern ssize_t hread2(hFILE *, void *, size_t, size_t);
size_t n = fp->end - fp->begin;
if (n > nbytes) n = nbytes;
memcpy(buffer, fp->begin, n);
fp->begin += n;
return (n == nbytes)? (ssize_t) n : hread2(fp, buffer, nbytes, n);
}
/*!
@abstract Write a character to the stream
@return The character written, or EOF if an error occurred.
*/
static inline int hputc(int c, hFILE *fp)
{
extern int hputc2(int, hFILE *);
if (fp->begin < fp->limit) *(fp->begin++) = c;
else c = hputc2(c, fp);
return c;
}
/*!
@abstract Write a string to the stream
@return 0 if successful, or EOF if an error occurred.
*/
static inline int hputs(const char *text, hFILE *fp)
{
extern int hputs2(const char *, size_t, size_t, hFILE *);
size_t nbytes = strlen(text), n = fp->limit - fp->begin;
if (n > nbytes) n = nbytes;
memcpy(fp->begin, text, n);
fp->begin += n;
return (n == nbytes)? 0 : hputs2(text, nbytes, n, fp);
}
/*!
@abstract Write a block of characters to the file
@return Either nbytes, or negative if an error occurred.
@notes In the absence of I/O errors, the full nbytes will be written.
*/
static inline ssize_t HTS_RESULT_USED
hwrite(hFILE *fp, const void *buffer, size_t nbytes)
{
extern ssize_t hwrite2(hFILE *, const void *, size_t, size_t);
size_t n = fp->limit - fp->begin;
if (n > nbytes) n = nbytes;
memcpy(fp->begin, buffer, n);
fp->begin += n;
return (n==nbytes)? (ssize_t) n : hwrite2(fp, buffer, nbytes, n);
}
/*!
@abstract For writing streams, flush buffered output to the underlying stream
@return 0 if successful, or EOF if an error occurred.
*/
int hflush(hFILE *fp) HTS_RESULT_USED;
#ifdef __cplusplus
}
#endif
#endif
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