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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 #include <stdio.h>
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38 #include <stdlib.h>
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39 #include <string.h>
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40 #include <ctype.h>
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41 #include "Common.h"
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42 #include "RefGenome.h"
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43
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44 FILE *_rg_fp;
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45 char *_rg_gen;
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46 char *_rg_name;
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47 int _rg_offset;
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48 int _rg_contGen;
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49
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50 /**********************************************/
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51 int initLoadingRefGenome(char *fileName)
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52 {
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53 char ch;
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54 _rg_fp = fileOpen (fileName, "r");
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55 if (fscanf(_rg_fp, "%c", &ch))
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56 {
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57 if (ch == '>')
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58 {
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59 _rg_contGen = 0;
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60 _rg_offset = 0;
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61 _rg_gen = getMem(CONTIG_MAX_SIZE);
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62 _rg_name = getMem(CONTIG_NAME_SIZE);
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63 return 1;
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64 }
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65 }
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66 return 0;
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67 }
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68 /**********************************************/
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69 void finalizeLoadingRefGenome()
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70 {
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71 freeMem(_rg_gen, CONTIG_MAX_SIZE);
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72 freeMem(_rg_name, CONTIG_NAME_SIZE);
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73 fclose(_rg_fp);
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74 }
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75 /**********************************************/
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76 int loadRefGenome(char **refGen, char **refGenName, int *refGenOff)
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77 {
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78 char ch;
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79 int i;
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80 int returnVal = 0;
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81 int actualSize=0;
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82 int size;
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83 char *tmp;
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84
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85 // New Conting
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86 if (!_rg_contGen)
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87 {
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88 size = 0;
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89 tmp = fgets(_rg_name, SEQ_MAX_LENGTH, _rg_fp);
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90 int k;
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91 for (k=0; k<strlen(_rg_name);k++)
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92 {
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93 if (_rg_name[k] == ' ')
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94 {
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95 _rg_name[k]='\0';
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96 break;
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97 }
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98 }
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99
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100 }
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101 else
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102 {
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103 size=strlen(_rg_gen);
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104 for( i = 0 ; i < CONTIG_OVERLAP ; i++ )
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105 {
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106
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107 _rg_gen[i] = _rg_gen[size-CONTIG_OVERLAP+i];
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108 if (_rg_gen[i] != 'N')
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109 actualSize++;
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110 }
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111 size = CONTIG_OVERLAP;
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112 }
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113 while( fscanf(_rg_fp, "%c", &ch) > 0 )
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114 {
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115 if (ch == '>')
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116 {
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117 _rg_contGen = 0;
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118 returnVal = 1;
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119 break;
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120 }
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121 else if (!isspace(ch))
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122 {
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123 ch = toupper(ch);
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124 _rg_gen[size++] = ch;
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125 if (ch != 'N')
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126 {
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127 actualSize++;
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128 }
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129 if (actualSize == CONTIG_SIZE || size == CONTIG_MAX_SIZE)
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130 {
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131 _rg_contGen = 1;
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132 returnVal=1;
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133 break;
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134 }
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135 }
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136
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137 }
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138
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139 _rg_gen[size] = '\0';
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140 for (i=strlen(_rg_name)-1; i >= 0; i--)
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141 if (!isspace(_rg_name[i]))
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142 break;
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143 _rg_name[i+1] = '\0';
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144
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145 *refGenOff = _rg_offset;
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146 *refGenName = _rg_name;
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147 *refGen = _rg_gen;
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148
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149 if (_rg_contGen == 1)
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150 {
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151 _rg_offset += size-CONTIG_OVERLAP;
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152 }
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153 else
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154 {
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155 _rg_offset = 0;
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156 }
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157
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158
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159 return returnVal;
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160 }
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161 /**********************************************/
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