c_cpp/lib/htslib/hts_internal.h

   1 /*  hts_internal.h -- internal functions; not part of the public API.
   2
   3     Copyright (C) 2015-2016 Genome Research Ltd.
   4
   5 Permission is hereby granted, free of charge, to any person obtaining a copy
   6 of this software and associated documentation files (the "Software"), to deal
   7 in the Software without restriction, including without limitation the rights
   8 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
   9 copies of the Software, and to permit persons to whom the Software is
  10 furnished to do so, subject to the following conditions:
  11
  12 The above copyright notice and this permission notice shall be included in
  13 all copies or substantial portions of the Software.
  14
  15 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  16 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  17 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
  18 THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  19 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
  20 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  21 DEALINGS IN THE SOFTWARE.  */
  22
  23 #ifndef HTSLIB_HTS_INTERNAL_H
  24 #define HTSLIB_HTS_INTERNAL_H
  25
  26 #include <stddef.h>
  27 #include <ctype.h>
  28
  29 #include "htslib/hts.h"
  30
  31 #ifdef __cplusplus
  32 extern "C" {
  33 #endif
  34
  35 struct hFILE;
  36
  37 /// Decode percent-encoded (URL-encoded) text
  38 /** On input, _dest_ should be a buffer at least the same size as _s_,
  39     and may be equal to _s_ to decode in place.  On output, _dest_ will be
  40     NUL-terminated and the number of characters written (not including the
  41     NUL) is stored in _destlen_.
  42 */
  43 int hts_decode_percent(char *dest, size_t *destlen, const char *s);
  44
  45 /// Return decoded data length given length of base64-encoded text
  46 /** This gives an upper bound, as it overestimates by a byte or two when
  47     the encoded text ends with (possibly omitted) `=` padding characters.
  48 */
  49 size_t hts_base64_decoded_length(size_t len);
  50
  51 /// Decode base64-encoded data
  52 /** On input, _dest_ should be a sufficient buffer (see `hts_base64_length()`),
  53     and may be equal to _s_ to decode in place.  On output, the number of
  54     bytes writen is stored in _destlen_.
  55 */
  56 int hts_decode_base64(char *dest, size_t *destlen, const char *s);
  57
  58
  59 /// Token structure returned by JSON lexing functions
  60 /** Token types correspond to scalar JSON values and selected punctuation
  61 as follows:
  62   - `s` string
  63   - `n` number
  64   - `b` boolean literal
  65   - `.` null literal
  66   - `{`, `}`, `[`, `]` object and array delimiters
  67   - `?` lexing error
  68   - `\0` terminator at end of input
  69 */
  70 typedef struct hts_json_token {
  71     char type;    ///< Token type
  72     char *str;    ///< Value as a C string (filled in for all token types)
  73     // TODO Add other fields to fill in for particular data types, e.g.
  74     // int inum;
  75     // float fnum;
  76 } hts_json_token;
  77
  78 /// Read one JSON token from a file
  79 /** @param str    The input C string
  80     @param state  The input string state
  81     @param token  On return, filled in with the token read
  82     @return  The type of the token read
  83
  84 On return, `token->str` points into the supplied input string, which
  85 is modified by having token-terminating characters overwritten as NULs.
  86 The `state` argument records the current position within `str` after each
  87 `hts_json_snext()` call, and should be set to 0 before the first call.
  88 */
  89 char hts_json_snext(char *str, size_t *state, hts_json_token *token);
  90
  91 /// Read and discard a complete JSON value from a string
  92 /** @param str    The input C string
  93     @param state  The input string state, as per `hts_json_snext()`
  94     @param type   If the first token of the value to be discarded has already
  95                   been read, provide its type; otherwise `'\0'`
  96     @return  One of `v` (success), `\0` (end of string), and `?` (lexing error)
  97
  98 Skips a complete JSON value, which may be a single token or an entire object
  99 or array.
 100 */
 101 char hts_json_sskip_value(char *str, size_t *state, char type);
 102
 103 /// Read one JSON token from a file
 104 /** @param fp     The file stream
 105     @param token  On return, filled in with the token read
 106     @param kstr   Buffer used to store the token string returned
 107     @return  The type of the token read
 108
 109 The `kstr` buffer is used to store the string value of the token read,
 110 so `token->str` is only valid until the next time `hts_json_fnext()` is
 111 called with the same `kstr` argument.
 112 */
 113 char hts_json_fnext(struct hFILE *fp, hts_json_token *token, kstring_t *kstr);
 114
 115 /// Read and discard a complete JSON value from a file
 116 /** @param fp    The file stream
 117     @param type  If the first token of the value to be discarded has already
 118                  been read, provide its type; otherwise `'\0'`
 119     @return  One of `v` (success), `\0` (EOF), and `?` (lexing error)
 120
 121 Skips a complete JSON value, which may be a single token or an entire object
 122 or array.
 123 */
 124 char hts_json_fskip_value(struct hFILE *fp, char type);
 125
 126
 127 // The <ctype.h> functions operate on ints such as are returned by fgetc(),
 128 // i.e., characters represented as unsigned-char-valued ints, or EOF.
 129 // To operate on plain chars (and to avoid warnings on some platforms),
 130 // technically one must cast to unsigned char everywhere (see CERT STR37-C)
 131 // or less painfully use these *_c() functions that operate on plain chars
 132 // (but not EOF, which must be considered separately where it is applicable).
 133 // TODO We may eventually wish to implement these functions directly without
 134 // using their <ctype.h> equivalents, and thus make them immune to locales.
 135 static inline int isalnum_c(char c) { return isalnum((unsigned char) c); }
 136 static inline int isalpha_c(char c) { return isalpha((unsigned char) c); }
 137 static inline int isdigit_c(char c) { return isdigit((unsigned char) c); }
 138 static inline int isgraph_c(char c) { return isgraph((unsigned char) c); }
 139 static inline int islower_c(char c) { return islower((unsigned char) c); }
 140 static inline int isprint_c(char c) { return isprint((unsigned char) c); }
 141 static inline int isspace_c(char c) { return isspace((unsigned char) c); }
 142 static inline int isupper_c(char c) { return isupper((unsigned char) c); }
 143 static inline char tolower_c(char c) { return tolower((unsigned char) c); }
 144 static inline char toupper_c(char c) { return toupper((unsigned char) c); }
 145
 146
 147 struct cram_fd;
 148
 149 char *hts_idx_getfn(const char *fn, const char *ext);
 150
 151 // The CRAM implementation stores the loaded index within the cram_fd rather
 152 // than separately as is done elsewhere in htslib.  So if p is a pointer to
 153 // an hts_idx_t with p->fmt == HTS_FMT_CRAI, then it actually points to an
 154 // hts_cram_idx_t and should be cast accordingly.
 155 typedef struct hts_cram_idx_t {
 156     int fmt;
 157     struct cram_fd *cram;
 158 } hts_cram_idx_t;
 159
 160
 161 // Entry point to hFILE_multipart backend.
 162 struct hFILE *hopen_json_redirect(struct hFILE *hfile, const char *mode);
 163
 164
 165 struct hts_path_itr {
 166     kstring_t path, entry;
 167     void *dirv;  // DIR * privately
 168     const char *pathdir, *prefix, *suffix;
 169     size_t prefix_len, suffix_len, entry_dir_l;
 170 };
 171
 172 void hts_path_itr_setup(struct hts_path_itr *itr, const char *path,
 173     const char *builtin_path, const char *prefix, size_t prefix_len,
 174     const char *suffix, size_t suffix_len);
 175
 176 const char *hts_path_itr_next(struct hts_path_itr *itr);
 177
 178 void *load_plugin(void **pluginp, const char *filename, const char *symbol);
 179 void *plugin_sym(void *plugin, const char *name, const char **errmsg);
 180 void close_plugin(void *plugin);
 181
 182 #ifdef __cplusplus
 183 }
 184 #endif
 185
 186 #endif