Gamgee
You miserable little maggot. I'll stove your head in!
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
cram_encode.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_WRITE_H_
42 #define _CRAM_WRITE_H_
43 
44 #ifdef __cplusplus
45 extern "C" {
46 #endif
47 
48 /* ----------------------------------------------------------------------
49  * CRAM sequence iterators.
50  */
51 
63 
64 
65 /* ----------------------------------------------------------------------
66  * Internal functions
67  */
68 
78 
87 
100 
101 #ifdef __cplusplus
102 }
103 #endif
104 
105 #endif
Definition: cram_structs.h:518
cram_block * cram_encode_compression_header(cram_fd *fd, cram_container *c, cram_block_compression_hdr *h)
Definition: cram_encode.c:76
Definition: sam.h:170
int cram_put_bam_seq(cram_fd *fd, bam_seq_t *b)
Definition: cram_encode.c:2886
Definition: cram_structs.h:270
Definition: cram_structs.h:247
Definition: cram_structs.h:342
int cram_encode_container(cram_fd *fd, cram_container *c)
Definition: cram_encode.c:1221
Definition: cram_structs.h:655
cram_block * cram_encode_slice_header(cram_fd *fd, cram_slice *s)
Definition: cram_encode.c:671