struct __ti_iter_t;
typedef struct __ti_iter_t *ti_iter_t;
+typedef struct {
+ BGZF *fp;
+ ti_index_t *idx;
+ char *fn, *fnidx;
+} tabix_t;
+
typedef struct {
int32_t preset;
int32_t sc, bc, ec; // seq col., beg col. and end col.
extern "C" {
#endif
+ /*******************
+ * High-level APIs *
+ *******************/
+
+ tabix_t *ti_open(const char *fn, const char *fnidx);
+ int ti_lazy_index_load(tabix_t *t);
+ void ti_close(tabix_t *t);
+ ti_iter_t ti_query(tabix_t *t, const char *name, int beg, int end);
+ ti_iter_t ti_queryi(tabix_t *t, int tid, int beg, int end);
+ const char *ti_read(tabix_t *t, ti_iter_t iter, int *len);
+
+ /* Destroy the iterator */
+ void ti_iter_destroy(ti_iter_t iter);
+
+ /* Get the list of sequence names. Each "char*" pointer points to a
+ * internal member of the index, so DO NOT modify the returned
+ * pointer; otherwise the index will be corrupted. The returned
+ * pointer should be freed by a single free() call by the routine
+ * calling this function. The number of sequences is returned at *n. */
+ const char **ti_seqname(const ti_index_t *idx, int *n);
+
+ /******************
+ * Low-level APIs *
+ ******************/
+
/* Build the index for file <fn>. File <fn>.tbi will be generated
* and overwrite the file of the same name. Return -1 on failure. */
int ti_index_build(const char *fn, const ti_conf_t *conf);
* downloaded. Return NULL on failure. */
ti_index_t *ti_index_load(const char *fn);
+ ti_index_t *ti_index_load_local(const char *fnidx);
+
/* Destroy the index */
void ti_index_destroy(ti_index_t *idx);
- /* Get the list of sequence names. Each "char*" pointer points to a
- * internal member of the index, so DO NOT modify the returned
- * pointer; otherwise the index will be corrupted. The returned
- * pointer should be freed by a single free() call by the routine
- * calling this function. The number of sequences is returned at *n. */
- const char **ti_seqname(const ti_index_t *idx, int *n);
-
/* Parse a region like: chr2, chr2:100, chr2:100-200. Return -1 on failure. */
- int ti_parse_region(ti_index_t *idx, const char *str, int *tid, int *begin, int *end);
+ int ti_parse_region(const ti_index_t *idx, const char *str, int *tid, int *begin, int *end);
+
+ int ti_get_tid(const ti_index_t *idx, const char *name);
/* Get the iterator pointing to the first record at the current file
* position. If the file is just openned, the iterator points to the
* first record in the file. */
- ti_iter_t ti_first(BGZF *fp);
+ ti_iter_t ti_iter_first(void);
/* Get the iterator pointing to the first record in region tid:beg-end */
- ti_iter_t ti_query(BGZF *fp, const ti_index_t *idx, int tid, int beg, int end);
+ ti_iter_t ti_iter_query(const ti_index_t *idx, int tid, int beg, int end);
/* Get the data line pointed by the iterator and iterate to the next record. */
- const char *ti_iter_read(ti_iter_t iter, int *len);
+ const char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len);
- /* Destroy the iterator */
- void ti_iter_destroy(ti_iter_t iter);
+ /*******************
+ * Deprecated APIs *
+ *******************/
/* The callback version for random access */
int ti_fetch(BGZF *fp, const ti_index_t *idx, int tid, int beg, int end, void *data, ti_fetch_f func);