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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 #include <stdio.h>
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45 #include <stdlib.h>
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46 #include <sys/time.h>
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47 #include <zlib.h>
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48 #include <string.h>
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49 #include "Common.h"
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50
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51
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52 unsigned short SEQ_LENGTH = 0;
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53 long long memUsage = 0;
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54 /**********************************************/
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55 FILE *fileOpen(char *fileName, char *mode)
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56 {
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57 FILE *fp;
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58 fp = fopen (fileName, mode);
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59 if (fp == NULL)
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60 {
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61 fprintf(stdout, "Error: Cannot Open the file %s\n", fileName);
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62 fflush(stdout);
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63 exit(0);
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64 }
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65 return fp;
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66 }
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67 /**********************************************/
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68 gzFile fileOpenGZ(char *fileName, char *mode)
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69 {
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70 gzFile gzfp;
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71 gzfp = gzopen (fileName, mode);
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72 if (gzfp == Z_NULL)
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73 {
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74 fprintf(stdout, "Error: Cannot Open the file %s\n", fileName);
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75 fflush(stdout);
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76 exit(0);
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77 }
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78 return gzfp;
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79 }
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80 /**********************************************/
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81 double getTime(void)
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82 {
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83 struct timeval t;
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84 gettimeofday(&t, NULL);
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85 return t.tv_sec+t.tv_usec/1000000.0;
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86 }
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87
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88 /**********************************************/
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89 char reverseCompleteChar(char c)
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90 {
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91 char ret;
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92 switch (c)
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93 {
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94 case 'A':
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95 ret = 'T';
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96 break;
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97 case 'T':
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98 ret = 'A';
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99 break;
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100 case 'C':
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101 ret = 'G';
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102 break;
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103 case 'G':
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104 ret = 'C';
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105 break;
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106 default:
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107 ret = 'N';
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108 break;
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109 }
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110 return ret;
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111 }
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112 /**********************************************/
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113 void reverseComplete (char *seq, char *rcSeq , int length)
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114 {
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115 int i;
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116 for (i=0; i<length; i++)
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117 {
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118 rcSeq[i]=reverseCompleteChar (seq[length-1-i]) ;
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119 }
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120 }
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121 /**********************************************/
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122 void * getMem(size_t size)
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123 {
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124 void *ret;
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125 ret = malloc(size);
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126 if (ret == NULL){
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127 fprintf(stderr, "Cannot allocate memory. Currently addressed memory = %0.2f MB, requested memory = %0.2f MB.\nCheck the available main memory, and if you have user limits (ulimit -v).\n", getMemUsage(), (double)size);
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128 exit(0);
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129 }
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130 memUsage+=size;
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131 return ret;
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132 }
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133 /**********************************************/
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134 void freeMem(void *ptr, size_t size)
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135 {
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136 memUsage-=size;
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137 free(ptr);
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138 }
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139 /**********************************************/
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140 double getMemUsage()
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141 {
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142 return memUsage/1048576.0;
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143 }
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144 /**********************************************/
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145 void reverse (char *seq, char *rcSeq , int length)
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146 {
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147 int i;
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148 int l = length;
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149 if(l != strlen(seq))
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150 l = strlen(seq);
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151 for (i=0; i<l; i++)
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152 {
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153 rcSeq[i]=seq[l-1-i] ;
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154 }
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155 rcSeq[l] = '\0';
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156 }
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157 /**********************************************/
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158 void stripPath(char *full, char **path, char **fileName)
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159 {
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160 int i;
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161 int pos = -1;
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162
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163 for (i=strlen(full)-1; i>=0; i--)
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164 {
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165 if (full[i]=='/')
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166 {
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167 pos = i;
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168 break;
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169 }
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170
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171 }
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172
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173 if (pos != -1)
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174 {
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175 sprintf(*fileName, "%s%c", (full+pos+1), '\0');
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176 full[pos+1]='\0';
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177 sprintf(*path,"%s%c", full, '\0');
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178 }
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179 else
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180 {
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181 sprintf(*fileName, "%s%c", full, '\0');
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182 sprintf(*path,"%c", '\0');
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183 }
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184 }
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