comparison ezBAMQC/src/htslib/cram/cram_decode.h @ 0:dfa3745e5fd8

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author youngkim
date Thu, 24 Mar 2016 17:12:52 -0400
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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