Mercurial > repos > youngkim > ezbamqc
comparison ezBAMQC/src/htslib/cram/cram_stats.h @ 0:dfa3745e5fd8
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| author | youngkim |
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| date | Thu, 24 Mar 2016 17:12:52 -0400 |
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| -1:000000000000 | 0:dfa3745e5fd8 |
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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 | |
| 38 cram_stats *cram_stats_create(void); | |
| 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 */ | |
| 53 enum cram_encoding cram_stats_encoding(cram_fd *fd, cram_stats *st); | |
| 54 | |
| 55 #ifdef __cplusplus | |
| 56 } | |
| 57 #endif | |
| 58 | |
| 59 #endif |