3 Copyright (c) 2009 Genome Research Ltd (GRL), 2010 Broad Institute
5 Permission is hereby granted, free of charge, to any person obtaining
6 a copy of this software and associated documentation files (the
7 "Software"), to deal in the Software without restriction, including
8 without limitation the rights to use, copy, modify, merge, publish,
9 distribute, sublicense, and/or sell copies of the Software, and to
10 permit persons to whom the Software is furnished to do so, subject to
11 the following conditions:
13 The above copyright notice and this permission notice shall be
14 included in all copies or substantial portions of the Software.
16 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
17 EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
18 MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
19 NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
20 BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
21 ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
22 CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
26 /* Contact: Heng Li <lh3@live.co.uk> */
35 #define TI_PRESET_GENERIC 0
36 #define TI_PRESET_SAM 1
37 #define TI_PRESET_VCF 2
39 #define TI_FLAG_UCSC 0x10000
41 typedef int (*ti_fetch_f)(int l, const char *s, void *data);
44 typedef struct __ti_index_t ti_index_t;
47 typedef struct __ti_iter_t *ti_iter_t;
57 int32_t sc, bc, ec; // seq col., beg col. and end col.
58 int32_t meta_char, line_skip;
61 extern ti_conf_t ti_conf_gff, ti_conf_bed, ti_conf_psltbl, ti_conf_vcf, ti_conf_sam; // preset
71 tabix_t *ti_open(const char *fn, const char *fnidx);
72 int ti_lazy_index_load(tabix_t *t);
73 void ti_close(tabix_t *t);
74 ti_iter_t ti_query(tabix_t *t, const char *name, int beg, int end);
75 ti_iter_t ti_queryi(tabix_t *t, int tid, int beg, int end);
76 ti_iter_t ti_querys(tabix_t *t, const char *reg);
77 const char *ti_read(tabix_t *t, ti_iter_t iter, int *len);
79 /* Destroy the iterator */
80 void ti_iter_destroy(ti_iter_t iter);
82 /* Get the list of sequence names. Each "char*" pointer points to a
83 * internal member of the index, so DO NOT modify the returned
84 * pointer; otherwise the index will be corrupted. The returned
85 * pointer should be freed by a single free() call by the routine
86 * calling this function. The number of sequences is returned at *n. */
87 const char **ti_seqname(const ti_index_t *idx, int *n);
93 /* Build the index for file <fn>. File <fn>.tbi will be generated
94 * and overwrite the file of the same name. Return -1 on failure. */
95 int ti_index_build(const char *fn, const ti_conf_t *conf);
97 /* Load the index from file <fn>.tbi. If <fn> is a URL and the index
98 * file is not in the working directory, <fn>.tbi will be
99 * downloaded. Return NULL on failure. */
100 ti_index_t *ti_index_load(const char *fn);
102 ti_index_t *ti_index_load_local(const char *fnidx);
104 /* Destroy the index */
105 void ti_index_destroy(ti_index_t *idx);
107 /* Parse a region like: chr2, chr2:100, chr2:100-200. Return -1 on failure. */
108 int ti_parse_region(const ti_index_t *idx, const char *str, int *tid, int *begin, int *end);
110 int ti_get_tid(const ti_index_t *idx, const char *name);
112 /* Get the iterator pointing to the first record at the current file
113 * position. If the file is just openned, the iterator points to the
114 * first record in the file. */
115 ti_iter_t ti_iter_first(void);
117 /* Get the iterator pointing to the first record in region tid:beg-end */
118 ti_iter_t ti_iter_query(const ti_index_t *idx, int tid, int beg, int end);
120 /* Get the data line pointed by the iterator and iterate to the next record. */
121 const char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len);
127 /* The callback version for random access */
128 int ti_fetch(BGZF *fp, const ti_index_t *idx, int tid, int beg, int end, void *data, ti_fetch_f func);
131 int ti_readline(BGZF *fp, kstring_t *str);