1 /* 2 Copyright (c) 2012-2013 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 /*! \file 32 * Include cram.h instead. 33 * 34 * This is an internal part of the CRAM system and is automatically included 35 * when you #include cram.h. 36 * 37 * Implements the decoding portion of CRAM I/O. Also see 38 * cram_codecs.[ch] for the actual encoding functions themselves. 39 */ 40 41 #ifndef _CRAM_READ_H_ 42 #define _CRAM_READ_H_ 43 44 #ifdef __cplusplus 45 extern "C" { 46 #endif 47 48 /* ---------------------------------------------------------------------- 49 * CRAM sequence iterators. 50 */ 51 52 /*! Read the next cram record and return it as a cram_record. 53 * 54 * Note that to decode cram_record the caller will need to look up some data 55 * in the current slice, pointed to by fd->ctr->slice. This is valid until 56 * the next call to cram_get_seq (which may invalidate it). 57 * 58 * @return 59 * Returns record pointer on success (do not free); 60 * NULL on failure 61 */ 62 cram_record *cram_get_seq(cram_fd *fd); 63 64 /*! Read the next cram record and convert it to a bam_seq_t struct. 65 * 66 * @return 67 * Returns 0 on success; 68 * -1 on EOF or failure (check fd->err) 69 */ 70 int cram_get_bam_seq(cram_fd *fd, bam_seq_t **bam); 71 72 73 /* ---------------------------------------------------------------------- 74 * Internal functions 75 */ 76 77 /*! INTERNAL: 78 * Decodes a CRAM block compression header. 79 * 80 * @return 81 * Returns header ptr on success; 82 * NULL on failure 83 */ 84 cram_block_compression_hdr *cram_decode_compression_header(cram_fd *fd, 85 cram_block *b); 86 87 /*! INTERNAL: 88 * Decodes a CRAM (un)mapped slice header block. 89 * 90 * @return 91 * Returns slice header ptr on success; 92 * NULL on failure 93 */ 94 cram_block_slice_hdr *cram_decode_slice_header(cram_fd *fd, cram_block *b); 95 96 97 /*! INTERNAL: 98 * Decode an entire slice from container blocks. Fills out s->crecs[] array. 99 * 100 * @return 101 * Returns 0 on success; 102 * -1 on failure 103 */ 104 int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s, 105 SAM_hdr *hdr); 106 107 108 #ifdef __cplusplus 109 } 110 #endif 111 112 #endif 113