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cram_index.h
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1 /*
2 Copyright (c) 2013 Genome Research Ltd.
3 Author: James Bonfield <jkb@sanger.ac.uk>
4 
5 Redistribution and use in source and binary forms, with or without
6 modification, are permitted provided that the following conditions are met:
7 
8  1. Redistributions of source code must retain the above copyright notice,
9 this list of conditions and the following disclaimer.
10 
11  2. Redistributions in binary form must reproduce the above copyright notice,
12 this list of conditions and the following disclaimer in the documentation
13 and/or other materials provided with the distribution.
14 
15  3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
16 Institute nor the names of its contributors may be used to endorse or promote
17 products derived from this software without specific prior written permission.
18 
19 THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
20 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
21 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
22 DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
23 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
24 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
25 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
26 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
27 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
28 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 */
30 
31 #ifndef _CRAM_INDEX_H_
32 #define _CRAM_INDEX_H_
33 
34 #ifdef __cplusplus
35 extern "C" {
36 #endif
37 
38 /*
39  * Loads a CRAM .crai index into memory.
40  * Returns 0 for success
41  * -1 for failure
42  */
43 int cram_index_load(cram_fd *fd, const char *fn);
44 
45 void cram_index_free(cram_fd *fd);
46 
47 /*
48  * Searches the index for the first slice overlapping a reference ID
49  * and position.
50  *
51  * Returns the cram_index pointer on sucess
52  * NULL on failure
53  */
54 cram_index *cram_index_query(cram_fd *fd, int refid, int pos, cram_index *frm);
55 
56 /*
57  * Skips to a container overlapping the start coordinate listed in
58  * cram_range.
59  *
60  * Returns 0 on success
61  * -1 on failure
62  */
64 
65 void cram_index_free(cram_fd *fd);
66 
67 /*
68  * Skips to a container overlapping the start coordinate listed in
69  * cram_range.
70  *
71  * In theory we call cram_index_query multiple times, once per slice
72  * overlapping the range. However slices may be absent from the index
73  * which makes this problematic. Instead we find the left-most slice
74  * and then read from then on, skipping decoding of slices and/or
75  * whole containers when they don't overlap the specified cram_range.
76  *
77  * Returns 0 on success
78  * -1 on failure
79  */
81 
82 /*
83  * Builds an index file.
84  *
85  * fd is a newly opened cram file that we wish to index.
86  * fn_base is the filename of the associated CRAM file. Internally we
87  * add ".crai" to this to get the index filename.
88  *
89  * Returns 0 on success
90  * -1 on failure
91  */
92 int cram_index_build(cram_fd *fd, const char *fn_base);
93 
94 #ifdef __cplusplus
95 }
96 #endif
97 
98 #endif