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comparison ezBAMQC/src/htslib/cram/cram.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 * CRAM interface.
33 *
34 * Consider using the higher level hts_*() API for programs that wish to
35 * be file format agnostic (see htslib/hts.h).
36 *
37 * This API should be used for CRAM specific code. The specifics of the
38 * public API are implemented in cram_io.h, cram_encode.h and cram_decode.h
39 * although these should not be included directly (use this file instead).
40 */
41
42 #ifdef __cplusplus
43 extern "C" {
44 #endif
45
46 #ifndef _CRAM_H_
47 #define _CRAM_H_
48
49 #include "cram/cram_samtools.h"
50 #include "cram/sam_header.h"
51 #include "cram_structs.h"
52 #include "cram_io.h"
53 #include "cram_encode.h"
54 #include "cram_decode.h"
55 #include "cram_stats.h"
56 #include "cram_codecs.h"
57 #include "cram_index.h"
58
59 #endif
60
61 #ifdef __cplusplus
62 }
63 #endif