Changelog entry marking the package released.

[tabix.git] / tabix.h

diff --git a/tabix.h b/tabix.h
index a002d8a1e09a4da451449ab24431abade57c6c76..7b4497a35676b494d8bf1c600601b2945545b8b9 100644 (file)
--- a/tabix.h
+++ b/tabix.h
@@ -46,18 +46,55 @@ typedef struct __ti_index_t ti_index_t;
 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.
        int32_t meta_char, line_skip;
 } ti_conf_t;
 
+typedef struct {
+       int beg, end;
+       char *ss, *se;
+} ti_interval_t;
+
 extern ti_conf_t ti_conf_gff, ti_conf_bed, ti_conf_psltbl, ti_conf_vcf, ti_conf_sam; // preset
 
 #ifdef __cplusplus
 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);
+       ti_iter_t ti_querys(tabix_t *t, const char *reg);
+       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);
@@ -67,32 +104,33 @@ extern "C" {
         * 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);
+       const ti_conf_t *ti_get_conf(ti_index_t *idx);
+       int ti_get_intv(const ti_conf_t *conf, int len, char *line, ti_interval_t *intv);
+
+       /*******************
+        * 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);