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cram_stats.h
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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 #ifndef _CRAM_STATS_H_
32 #define _CRAM_STATS_H_
33 
34 #ifdef __cplusplus
35 extern "C" {
36 #endif
37 
39 void cram_stats_add(cram_stats *st, int32_t val);
40 void cram_stats_del(cram_stats *st, int32_t val);
41 void cram_stats_dump(cram_stats *st);
42 void cram_stats_free(cram_stats *st);
43 
44 /*
45  * Computes entropy from integer frequencies for various encoding methods and
46  * picks the best encoding.
47  *
48  * FIXME: we could reuse some of the code here for the actual encoding
49  * parameters too. Eg the best 'k' for SUBEXP or the code lengths for huffman.
50  *
51  * Returns the best codec to use.
52  */
54 
55 #ifdef __cplusplus
56 }
57 #endif
58 
59 #endif
void cram_stats_add(cram_stats *st, int32_t val)
Definition: cram_stats.c:53
void cram_stats_dump(cram_stats *st)
Definition: cram_stats.c:102
cram_stats * cram_stats_create(void)
Definition: cram_stats.c:49
Definition: cram_structs.h:90
enum cram_encoding cram_stats_encoding(cram_fd *fd, cram_stats *st)
Definition: cram_stats.c:149
cram_encoding
Definition: cram_structs.h:98
void cram_stats_free(cram_stats *st)
Definition: cram_stats.c:446
Definition: cram_structs.h:655
void cram_stats_del(cram_stats *st, int32_t val)
Definition: cram_stats.c:78