X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=tabix.git;a=blobdiff_plain;f=tabix.h;h=7b4497a35676b494d8bf1c600601b2945545b8b9;hp=e608c790dd69842504734935500514713c7519f9;hb=HEAD;hpb=bc08e6c2f34c1367d0fe75dd19cedccfab881229

diff --git a/tabix.h b/tabix.h
index e608c79..7b4497a 100644
--- a/tabix.h
+++ b/tabix.h
@@ -1,3 +1,30 @@
+/* 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
 
@@ -16,26 +43,101 @@ typedef int (*ti_fetch_f)(int l, const char *s, void *data);
 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