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1 /*
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2 * Copyright (c) <2008 - 2009>, 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 name of the <ORGANIZATION> nor the names of its contributors may be
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14 * used to endorse or promote products derived from this software without specific
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15 * prior written permission.
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16 *
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17 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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18 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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19 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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20 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
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21 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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22 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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23 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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24 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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25 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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26 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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27 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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28 */
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29
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30 /*
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31 * Author : Faraz Hach
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32 * Email : fhach AT cs DOT sfu
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33 * Last Update : 2009-12-08
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34 */
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35
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36
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37 #ifndef __MRS_FAST__
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38 #define __MRS_FAST__
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39
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40 #include "Reads.h"
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41
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42 #define MAP_CHUNKS 15
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43
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44 // Pair is used to pre-processing and making the read index table
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45 typedef struct
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46 {
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47 int hv;
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48 int seqInfo;
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49 } Pair;
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50
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51 typedef struct
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52 {
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53 int hv;
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54 unsigned int *seqInfo;
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55 } ReadIndexTable;
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56
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57
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58 typedef struct mn
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59 {
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60 int loc;
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61 char dir;
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62 char err;
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63 float score;
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64 char md[40];
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65 char chr[10];
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66 } FullMappingInfo;
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67
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68 typedef struct lc
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69 {
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70 int loc[MAP_CHUNKS];
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71 struct lc *next;
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72 } MappingLocations;
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73
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74 typedef struct inf
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75 {
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76 int size;
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77 MappingLocations *next;
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78 } MappingInfo;
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79
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80 typedef struct
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81 {
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82 FILE * fp;
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83 char name[400];
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84 } FILE_STRUCT;
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85
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86 extern long long verificationCnt;
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87 extern long long mappingCnt;
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88 extern long long mappedSeqCnt;
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89 extern long long completedSeqCnt;
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90
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91 void initFAST( Read *seqList,
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92 int seqListSize,
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93 int *samplingLocs,
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94 int samplingLocsSize,
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95 char *fileName);
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96
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97 void finalizeFAST();
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98
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99 int mapSingleEndSeq();
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100 int mapPaiedEndSeq();
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101 void outputPairedEnd();
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102 void outputPairedEndDiscPP();
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103 #endif
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