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1 /*
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2 Copyright (c) 2012-2013 Genome Research Ltd.
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3 Author: James Bonfield <jkb@sanger.ac.uk>
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4
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5 Redistribution and use in source and binary forms, with or without
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6 modification, are permitted provided that the following conditions are met:
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7
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8 1. Redistributions of source code must retain the above copyright notice,
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9 this list of conditions and the following disclaimer.
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10
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11 2. Redistributions in binary form must reproduce the above copyright notice,
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12 this list of conditions and the following disclaimer in the documentation
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13 and/or other materials provided with the distribution.
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14
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15 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
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16 Institute nor the names of its contributors may be used to endorse or promote
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17 products derived from this software without specific prior written permission.
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18
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19 THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
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20 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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21 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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22 DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
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23 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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24 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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25 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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26 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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27 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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28 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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29 */
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30
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31 #ifndef _CRAM_STATS_H_
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32 #define _CRAM_STATS_H_
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33
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34 #ifdef __cplusplus
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35 extern "C" {
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36 #endif
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37
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38 cram_stats *cram_stats_create(void);
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39 void cram_stats_add(cram_stats *st, int32_t val);
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40 void cram_stats_del(cram_stats *st, int32_t val);
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41 void cram_stats_dump(cram_stats *st);
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42 void cram_stats_free(cram_stats *st);
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43
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44 /*
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45 * Computes entropy from integer frequencies for various encoding methods and
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46 * picks the best encoding.
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47 *
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48 * FIXME: we could reuse some of the code here for the actual encoding
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49 * parameters too. Eg the best 'k' for SUBEXP or the code lengths for huffman.
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50 *
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51 * Returns the best codec to use.
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52 */
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53 enum cram_encoding cram_stats_encoding(cram_fd *fd, cram_stats *st);
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54
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55 #ifdef __cplusplus
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56 }
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57 #endif
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58
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59 #endif
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