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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 __COMMON__
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45 #define __COMMON__
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46
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47 #include <zlib.h>
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48
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49 #define SEQ_MAX_LENGTH 300 // Seq Max Length
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50 #define CONTIG_OVERLAP 200 // No. of characters overlapped between contings
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51 #define CONTIG_NAME_SIZE 200 // Contig name max size
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52 #define FILE_NAME_LENGTH 400 // Filename Max Length
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53 #define DISCORDANT_CUT_OFF 800
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54 #define MAX_OPEN_FILE 600
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55 #define MAX_TRANS_CHROMOSAL_OUTPUT 50
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56 #define MAX_OEA_OUT 500
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57
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58 extern unsigned int CONTIG_SIZE;
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59 extern unsigned int CONTIG_MAX_SIZE;
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60
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61
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62 extern unsigned char WINDOW_SIZE ; // WINDOW SIZE for indexing/searching
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63 extern unsigned short SEQ_LENGTH; // Sequence(read) length
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64
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65 extern char *versionNumber;
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66 extern char *versionNumberF;
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67 extern unsigned char mrFAST;
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68
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69
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70 extern int maxOEAOutput;
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71 extern int maxDiscordantOutput;
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72 extern int uniqueMode;
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73 extern int indexingMode;
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74 extern int searchingMode;
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75 extern int pairedEndMode;
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76 extern int pairedEndDiscordantMode;
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77 extern int transChromosal;
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78 extern int pairedEndProfilingMode;
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79 extern int bestMode;
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80 extern int nosamMode;
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81 extern int seqCompressed;
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82 extern int outCompressed;
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83 extern int cropSize;
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84 extern int progressRep;
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85 extern char *seqFile1;
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86 extern char *seqFile2;
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87 extern char *seqUnmapped;
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88 extern char *mappingOutput;
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89 extern char *mappingOutputPath;
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90 extern char *unmappedOutput;
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91 extern unsigned char seqFastq;
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92 extern unsigned char errThreshold;
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93 extern unsigned char maxHits;
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94 extern int minPairEndedDiscordantDistance;
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95 extern int maxPairEndedDiscordantDistance;
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96 extern int minPairEndedDistance;
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97 extern int maxPairEndedDistance;
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98 extern char fileName[1000][2][FILE_NAME_LENGTH];
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99 extern int fileCnt;
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100 extern long long memUsage;
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101
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102 FILE * fileOpen(char *fileName, char *mode);
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103 gzFile fileOpenGZ(char *fileName, char *mode);
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104 double getTime(void);
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105 void reverseComplete (char *seq, char *rcSeq , int length);
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106 void * getMem(size_t size);
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107 void freeMem(void * ptr, size_t size);
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108 double getMemUsage();
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109 void reverse (char *seq, char *rcSeq , int length);
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110 void stripPath(char *full, char **path, char **fileName);
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111 #endif
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