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1
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1 /*
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2 * Copyright (c) <2008 - 2012>, University of Washington, Simon Fraser University
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3 * All rights reserved.
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4 *
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5 * Redistribution and use in source and binary forms, with or without modification,
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6 * are permitted provided that the following conditions are met:
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7 *
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8 * Redistributions of source code must retain the above copyright notice, this list
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9 * of conditions and the following disclaimer.
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10 * - Redistributions in binary form must reproduce the above copyright notice, this
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11 * list of conditions and the following disclaimer in the documentation and/or other
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12 * materials provided with the distribution.
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13 * - Neither the names of the University of Washington, Simon Fraser University,
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14 * nor the names of its contributors may be
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15 * used to endorse or promote products derived from this software without specific
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16 * prior written permission.
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17 *
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18 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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19 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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20 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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21 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
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22 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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23 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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24 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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25 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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26 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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27 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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28 * 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 /*
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32 Authors:
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33 Farhad Hormozdiari
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34 Faraz Hach
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35 Can Alkan
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36 Emails:
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37 farhadh AT uw DOT edu
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38 fhach AT cs DOT sfu DOT ca
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39 calkan AT uw DOT edu
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40 */
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41
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42
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43
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44 #ifndef __HASH_TABLE__
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45 #define __HASH_TABLE__
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46
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47 typedef struct HashTable
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48 {
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49 long long hv;
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50 int *locs;
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51 } HashTable;
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52
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53 typedef struct
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54 {
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55 unsigned int *locs;
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56 } IHashTable;
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57
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58 int hashVal(char *seq);
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59 void configHashTable();
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60 char *getRefGenome();
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61 char *getRefGenomeName();
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62 int getRefGenomeOffset();
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63 int initLoadingHashTable(char *fileName);
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64 HashTable *getHashTable();
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65
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66 void (*generateHashTable)(char *fileName, char *indexName);
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67 int (*loadHashTable)(double *loadTime, int errThreshould);
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68 void (*finalizeLoadingHashTable)();
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69 unsigned int *(*getCandidates)(int hv);
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70
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71 #endif
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