+/* The MIT License
+
+ Copyright (c) 2009 Genome Research Ltd (GRL), 2010 Broad Institute
+
+ 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.
+*/
+
+/* Contact: Heng Li <lh3@live.co.uk> */
+
#ifndef __TABIDX_H
#define __TABIDX_H
struct __ti_index_t;
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;
+ int32_t sc, bc, ec; // seq col., beg col. and end col.
int32_t meta_char, line_skip;
} ti_conf_t;
-extern ti_conf_t ti_conf_gff, ti_conf_bed, ti_conf_psltbl, ti_conf_vcf, ti_conf_sam;
+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
- int ti_readline(BGZF *fp, kstring_t *str);
+ /*******************
+ * 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);
+
+ /* Load the index from file <fn>.tbi. If <fn> is a URL and the index
+ * file is not in the working directory, <fn>.tbi will be
+ * 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);
- int ti_parse_region(ti_index_t *idx, const char *str, int *tid, int *begin, int *end);
+
+ /* Parse a region like: chr2, chr2:100, chr2:100-200. Return -1 on failure. */
+ 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_iter_first(void);
+
+ /* Get the iterator pointing to the first record in region tid:beg-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(BGZF *fp, ti_iter_t iter, int *len);
+
+ 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);
+ /* Read one line. */
+ int ti_readline(BGZF *fp, kstring_t *str);
+
#ifdef __cplusplus
}
#endif
projects / tabix.git / blobdiff