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