Gamgee
You miserable little maggot. I'll stove your head in!
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
cram_decode.h
Go to the documentation of this file.
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 
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 
63 
71 
72 
73 /* ----------------------------------------------------------------------
74  * Internal functions
75  */
76 
85  cram_block *b);
86 
95 
96 
105  SAM_hdr *hdr);
106 
107 
108 #ifdef __cplusplus
109 }
110 #endif
111 
112 #endif
cram_block_compression_hdr * cram_decode_compression_header(cram_fd *fd, cram_block *b)
Definition: cram_decode.c:125
Definition: sam_header.h:183
Definition: cram_structs.h:518
Definition: sam.h:170
cram_block_slice_hdr * cram_decode_slice_header(cram_fd *fd, cram_block *b)
Definition: cram_decode.c:946
Definition: cram_structs.h:270
Definition: cram_structs.h:395
Definition: cram_structs.h:247
Definition: hts.h:87
Definition: cram_structs.h:342
cram_record * cram_get_seq(cram_fd *fd)
Definition: cram_decode.c:2639
int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s, SAM_hdr *hdr)
Definition: cram_decode.c:1803
Definition: cram_structs.h:317
int cram_get_bam_seq(cram_fd *fd, bam_seq_t **bam)
Definition: cram_decode.c:2692
Definition: cram_structs.h:655