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1 /*
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2 Copyright (c) 2012-2013 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 /*! \file
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32 * Include cram.h instead.
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33 *
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34 * This is an internal part of the CRAM system and is automatically included
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35 * when you #include cram.h.
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36 *
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37 * Implements the decoding portion of CRAM I/O. Also see
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38 * cram_codecs.[ch] for the actual encoding functions themselves.
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39 */
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40
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41 #ifndef _CRAM_READ_H_
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42 #define _CRAM_READ_H_
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43
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44 #ifdef __cplusplus
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45 extern "C" {
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46 #endif
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47
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48 /* ----------------------------------------------------------------------
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49 * CRAM sequence iterators.
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50 */
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51
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52 /*! Read the next cram record and return it as a cram_record.
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53 *
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54 * Note that to decode cram_record the caller will need to look up some data
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55 * in the current slice, pointed to by fd->ctr->slice. This is valid until
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56 * the next call to cram_get_seq (which may invalidate it).
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57 *
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58 * @return
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59 * Returns record pointer on success (do not free);
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60 * NULL on failure
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61 */
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62 cram_record *cram_get_seq(cram_fd *fd);
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63
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64 /*! Read the next cram record and convert it to a bam_seq_t struct.
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65 *
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66 * @return
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67 * Returns 0 on success;
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68 * -1 on EOF or failure (check fd->err)
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69 */
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70 int cram_get_bam_seq(cram_fd *fd, bam_seq_t **bam);
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71
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72
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73 /* ----------------------------------------------------------------------
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74 * Internal functions
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75 */
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76
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77 /*! INTERNAL:
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78 * Decodes a CRAM block compression header.
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79 *
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80 * @return
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81 * Returns header ptr on success;
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82 * NULL on failure
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83 */
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84 cram_block_compression_hdr *cram_decode_compression_header(cram_fd *fd,
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85 cram_block *b);
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86
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87 /*! INTERNAL:
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88 * Decodes a CRAM (un)mapped slice header block.
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89 *
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90 * @return
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91 * Returns slice header ptr on success;
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92 * NULL on failure
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93 */
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94 cram_block_slice_hdr *cram_decode_slice_header(cram_fd *fd, cram_block *b);
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95
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96
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97 /*! INTERNAL:
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98 * Decode an entire slice from container blocks. Fills out s->crecs[] array.
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99 *
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100 * @return
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101 * Returns 0 on success;
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102 * -1 on failure
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103 */
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104 int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s,
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105 SAM_hdr *hdr);
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106
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107
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108 #ifdef __cplusplus
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109 }
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110 #endif
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111
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112 #endif
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