|
0
|
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 #ifdef __cplusplus
|
|
|
102 }
|
|
|
103 #endif
|
|
|
104
|
|
|
105 #endif
|
