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 encoding portion of CRAM I/O. Also see 38 * cram_codecs.[ch] for the actual encoding functions themselves. 39 */ 40 41 #ifndef _CRAM_WRITE_H_ 42 #define _CRAM_WRITE_H_ 43 44 #ifdef __cplusplus 45 extern "C" { 46 #endif 47 48 /* ---------------------------------------------------------------------- 49 * CRAM sequence iterators. 50 */ 51 52 /*! Write iterator: put BAM format sequences into a CRAM file. 53 * 54 * We buffer up a containers worth of data at a time. 55 * 56 * FIXME: break this into smaller pieces. 57 * 58 * @return 59 * Returns 0 on success; 60 * -1 on failure 61 */ 62 int cram_put_bam_seq(cram_fd *fd, bam_seq_t *b); 63 64 65 /* ---------------------------------------------------------------------- 66 * Internal functions 67 */ 68 69 /*! INTERNAL: 70 * Encodes a compression header block into a generic cram_block structure. 71 * 72 * @return 73 * Returns cram_block ptr on success; 74 * NULL on failure 75 */ 76 cram_block *cram_encode_compression_header(cram_fd *fd, cram_container *c, 77 cram_block_compression_hdr *h); 78 79 /*! INTERNAL: 80 * Encodes a slice compression header. 81 * 82 * @return 83 * Returns cram_block on success; 84 * NULL on failure 85 */ 86 cram_block *cram_encode_slice_header(cram_fd *fd, cram_slice *s); 87 88 /*! INTERNAL: 89 * Encodes all slices in a container into blocks. 90 * 91 * @return 92 * Returns 0 on success; 93 * -1 on failure 94 * 95 * FIXME: separate into encode_container and write_container. Ideally 96 * we should be able to do read_container / write_container or 97 * decode_container / encode_container. 98 */ 99 int cram_encode_container(cram_fd *fd, cram_container *c); 100 101 /*! INTERNAL: 102 * 103 * During cram_next_container or before the final flush at end of 104 * file, we update the current slice headers and increment the slice 105 * number to the next slice. 106 * 107 * See cram_next_container() and cram_close(). 108 */ 109 void cram_update_curr_slice(cram_container *c); 110 111 #ifdef __cplusplus 112 } 113 #endif 114 115 #endif 116