hts_internal.h

/*  hts_internal.h -- internal functions; not part of the public API.

    Copyright (C) 2015-2016 Genome Research Ltd.

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_HTS_INTERNAL_H
#define HTSLIB_HTS_INTERNAL_H

#include <stddef.h>
#include <ctype.h>

#include "htslib/hts.h"

#ifdef __cplusplus
extern "C" {
#endif

struct hFILE;

/// Decode percent-encoded (URL-encoded) text
/** On input, _dest_ should be a buffer at least the same size as _s_,
    and may be equal to _s_ to decode in place.  On output, _dest_ will be
    NUL-terminated and the number of characters written (not including the
    NUL) is stored in _destlen_.
*/
int hts_decode_percent(char *dest, size_t *destlen, const char *s);

/// Return decoded data length given length of base64-encoded text
/** This gives an upper bound, as it overestimates by a byte or two when
    the encoded text ends with (possibly omitted) `=` padding characters.
*/
size_t hts_base64_decoded_length(size_t len);

/// Decode base64-encoded data
/** On input, _dest_ should be a sufficient buffer (see `hts_base64_length()`),
    and may be equal to _s_ to decode in place.  On output, the number of
    bytes writen is stored in _destlen_.
*/
int hts_decode_base64(char *dest, size_t *destlen, const char *s);


/// Token structure returned by JSON lexing functions
/** Token types correspond to scalar JSON values and selected punctuation
as follows:
  - `s` string
  - `n` number
  - `b` boolean literal
  - `.` null literal
  - `{`, `}`, `[`, `]` object and array delimiters
  - `?` lexing error
  - `\0` terminator at end of input
*/
typedef struct hts_json_token {
    char type;    ///< Token type
    char *str;    ///< Value as a C string (filled in for all token types)
    // TODO Add other fields to fill in for particular data types, e.g.
    // int inum;
    // float fnum;
} hts_json_token;

/// Read one JSON token from a file
/** @param str    The input C string
    @param state  The input string state
    @param token  On return, filled in with the token read
    @return  The type of the token read

On return, `token->str` points into the supplied input string, which
is modified by having token-terminating characters overwritten as NULs.
The `state` argument records the current position within `str` after each
`hts_json_snext()` call, and should be set to 0 before the first call.
*/
char hts_json_snext(char *str, size_t *state, hts_json_token *token);

/// Read and discard a complete JSON value from a string
/** @param str    The input C string
    @param state  The input string state, as per `hts_json_snext()`
    @param type   If the first token of the value to be discarded has already
                  been read, provide its type; otherwise `'\0'`
    @return  One of `v` (success), `\0` (end of string), and `?` (lexing error)

Skips a complete JSON value, which may be a single token or an entire object
or array.
*/
char hts_json_sskip_value(char *str, size_t *state, char type);

/// Read one JSON token from a file
/** @param fp     The file stream
    @param token  On return, filled in with the token read
    @param kstr   Buffer used to store the token string returned
    @return  The type of the token read

The `kstr` buffer is used to store the string value of the token read,
so `token->str` is only valid until the next time `hts_json_fnext()` is
called with the same `kstr` argument.
*/
char hts_json_fnext(struct hFILE *fp, hts_json_token *token, kstring_t *kstr);

/// Read and discard a complete JSON value from a file
/** @param fp    The file stream
    @param type  If the first token of the value to be discarded has already
                 been read, provide its type; otherwise `'\0'`
    @return  One of `v` (success), `\0` (EOF), and `?` (lexing error)

Skips a complete JSON value, which may be a single token or an entire object
or array.
*/
char hts_json_fskip_value(struct hFILE *fp, char type);


// The <ctype.h> functions operate on ints such as are returned by fgetc(),
// i.e., characters represented as unsigned-char-valued ints, or EOF.
// To operate on plain chars (and to avoid warnings on some platforms),
// technically one must cast to unsigned char everywhere (see CERT STR37-C)
// or less painfully use these *_c() functions that operate on plain chars
// (but not EOF, which must be considered separately where it is applicable).
// TODO We may eventually wish to implement these functions directly without
// using their <ctype.h> equivalents, and thus make them immune to locales.
static inline int isalnum_c(char c) { return isalnum((unsigned char) c); }
static inline int isalpha_c(char c) { return isalpha((unsigned char) c); }
static inline int isdigit_c(char c) { return isdigit((unsigned char) c); }
static inline int isgraph_c(char c) { return isgraph((unsigned char) c); }
static inline int islower_c(char c) { return islower((unsigned char) c); }
static inline int isprint_c(char c) { return isprint((unsigned char) c); }
static inline int isspace_c(char c) { return isspace((unsigned char) c); }
static inline int isupper_c(char c) { return isupper((unsigned char) c); }
static inline char tolower_c(char c) { return tolower((unsigned char) c); }
static inline char toupper_c(char c) { return toupper((unsigned char) c); }


struct cram_fd;

char *hts_idx_getfn(const char *fn, const char *ext);

// The CRAM implementation stores the loaded index within the cram_fd rather
// than separately as is done elsewhere in htslib.  So if p is a pointer to
// an hts_idx_t with p->fmt == HTS_FMT_CRAI, then it actually points to an
// hts_cram_idx_t and should be cast accordingly.
typedef struct hts_cram_idx_t {
    int fmt;
    struct cram_fd *cram;
} hts_cram_idx_t;


// Entry point to hFILE_multipart backend.
struct hFILE *hopen_htsget_redirect(struct hFILE *hfile, const char *mode);


struct hts_path_itr {
    kstring_t path, entry;
    void *dirv;  // DIR * privately
    const char *pathdir, *prefix, *suffix;
    size_t prefix_len, suffix_len, entry_dir_l;
};

void hts_path_itr_setup(struct hts_path_itr *itr, const char *path,
    const char *builtin_path, const char *prefix, size_t prefix_len,
    const char *suffix, size_t suffix_len);

const char *hts_path_itr_next(struct hts_path_itr *itr);

void *load_plugin(void **pluginp, const char *filename, const char *symbol);
void *plugin_sym(void *plugin, const char *name, const char **errmsg);
void close_plugin(void *plugin);

#ifdef __cplusplus
}
#endif

#endif