1 /* 2 Copyright (c) 2013, 2018 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, const char *fn_idx); 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 success 52 * NULL on failure 53 */ 54 cram_index *cram_index_query(cram_fd *fd, int refid, hts_pos_t pos, cram_index *frm); 55 cram_index *cram_index_last(cram_fd *fd, int refid, cram_index *from); 56 cram_index *cram_index_query_last(cram_fd *fd, int refid, hts_pos_t end); 57 58 /* 59 * Skips to a container overlapping the start coordinate listed in 60 * cram_range. 61 * 62 * Returns 0 on success 63 * -1 on failure 64 */ 65 int cram_seek_to_refpos(cram_fd *fd, cram_range *r); 66 67 void cram_index_free(cram_fd *fd); 68 69 /* 70 * Skips to a container overlapping the start coordinate listed in 71 * cram_range. 72 * 73 * In theory we call cram_index_query multiple times, once per slice 74 * overlapping the range. However slices may be absent from the index 75 * which makes this problematic. Instead we find the left-most slice 76 * and then read from then on, skipping decoding of slices and/or 77 * whole containers when they don't overlap the specified cram_range. 78 * 79 * Returns 0 on success 80 * -1 on failure 81 */ 82 int cram_seek_to_refpos(cram_fd *fd, cram_range *r); 83 84 /* 85 * Builds an index file. 86 * 87 * fd is a newly opened cram file that we wish to index. 88 * fn_base is the filename of the associated CRAM file. 89 * fn_idx is the filename of the index file to be written; 90 * if NULL, we add ".crai" to fn_base to get the index filename. 91 * 92 * Returns 0 on success, 93 * negative on failure (-1 for read failure, -4 for write failure) 94 */ 95 int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx); 96 97 /* 98 * Adds a single slice to the index. 99 * 100 * Returns 0 on success, 101 * -1 on failure 102 */ 103 int cram_index_slice(cram_fd *fd, 104 cram_container *c, 105 cram_slice *s, 106 BGZF *fp, 107 off_t cpos, 108 off_t spos, // relative to cpos 109 off_t sz); 110 111 #ifdef __cplusplus 112 } 113 #endif 114 115 #endif 116