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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
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45
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46 #include <stdio.h>
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47 #include <stdlib.h>
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48 #include <string.h>
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49 #include <math.h>
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50 #include "Common.h"
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51 #include "CommandLineParser.h"
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52 #include "Reads.h"
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53 #include "Output.h"
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54 #include "HashTable.h"
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55 #include "MrFAST.h"
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56
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57 char *versionNumber = "2.1"; // Current Version
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58 unsigned char seqFastq;
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59
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60 int main(int argc, char *argv[])
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61 {
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62 if (!parseCommandLine(argc, argv))
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63 return 1;
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64
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65 configHashTable();
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66 /****************************************************
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67 * INDEXING
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68 ***************************************************/
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69 if (indexingMode)
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70 {
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71 int i;
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72 /********************************
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73 * Regular Mode
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74 ********************************/
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75 configHashTable();
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76 for (i = 0; i < fileCnt; i++)
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77 {
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78 generateHashTable(fileName[i][0], fileName[i][1]);
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79 }
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80 }
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81 /****************************************************
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82 * SEARCHING
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83 ***************************************************/
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84 else
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85 {
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86 Read *seqList;
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87 unsigned int seqListSize;
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88 int fc;
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89 int samplingLocsSize;
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90 int *samplingLocs;
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91 double totalLoadingTime = 0;
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92 double totalMappingTime = 0;
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93 double startTime;
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94 double loadingTime;
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95 double mappingTime;
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96 double lstartTime;
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97 double ppTime = 0.0;
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98 double tmpTime;;
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99 char *prevGen = getMem(CONTIG_NAME_SIZE);
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100 prevGen[0]='\0';
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101 char *curGen;
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102 int flag;
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103 double maxMem=0;
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104 char fname1[FILE_NAME_LENGTH];
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105 char fname2[FILE_NAME_LENGTH];
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106 char fname3[FILE_NAME_LENGTH];
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107 char fname4[FILE_NAME_LENGTH];
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108 char fname5[FILE_NAME_LENGTH];
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109
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110 char outputFileName[FILE_NAME_LENGTH];
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111 // Loading Sequences & Sampling Locations
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112 startTime = getTime();
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113 if (!readAllReads(seqFile1, seqFile2, seqCompressed, &seqFastq, pairedEndMode, &seqList, &seqListSize))
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114 {
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115 return 1;
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116 }
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117
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118 loadSamplingLocations(&samplingLocs, &samplingLocsSize);
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119 totalLoadingTime += getTime()-startTime;
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120
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121 if (pairedEndMode)
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122 {
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123 //Switching to Inferred Size
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124 minPairEndedDistance = minPairEndedDistance - SEQ_LENGTH + 2;
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125 maxPairEndedDistance = maxPairEndedDistance - SEQ_LENGTH + 2;
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126 if (pairedEndDiscordantMode)
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127 {
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128 maxPairEndedDiscordantDistance = maxPairEndedDiscordantDistance - SEQ_LENGTH + 2;
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129 minPairEndedDiscordantDistance = minPairEndedDiscordantDistance - SEQ_LENGTH + 2;
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130 }
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131
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132 sprintf(fname1, "__%s__1", mappingOutput);
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133 sprintf(fname2, "__%s__2", mappingOutput);
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134 sprintf(fname3, "__%s__disc", mappingOutput);
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135 sprintf(fname4, "__%s__oea1", mappingOutput);
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136 sprintf(fname5, "__%s__oea2", mappingOutput);
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137 unlink(fname1);
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138 unlink(fname2);
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139 unlink(fname3);
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140 unlink(fname4);
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141 unlink(fname5);
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142 }
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143
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144 sprintf(outputFileName, "%s%s",mappingOutputPath , mappingOutput);
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145 // Preparing output
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146 initOutput(outputFileName, outCompressed);
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147
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148 fprintf(stdout, "-----------------------------------------------------------------------------------------------------------\n");
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149 fprintf(stdout, "| %15s | %15s | %15s | %15s | %15s %15s |\n","Genome Name","Loading Time", "Mapping Time", "Memory Usage(M)","Total Mappings","Mapped reads");
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150 fprintf(stdout, "-----------------------------------------------------------------------------------------------------------\n");
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151
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152 /********************************
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153 * Regular Mode
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154 ********************************/
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155 if (!pairedEndMode)
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156 {
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157 initLookUpTable();
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158 if(bestMode)
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159 initBestMapping(seqListSize);
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160
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161 for (fc = 0; fc <fileCnt; fc++)
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162 {
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163 if (!initLoadingHashTable(fileName[fc][1]))
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164 {
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165 return 1;
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166 }
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167
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168 mappingTime = 0;
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169 loadingTime = 0;
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170 prevGen[0] = '\0';
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171 flag = 1;
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172
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173 do
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174 {
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175 flag = loadHashTable ( &tmpTime, errThreshold); // Reading a fragment
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176 curGen = getRefGenomeName();
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177
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178 // First Time
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179 if (flag && prevGen[0]== '\0')
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180 {
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181 sprintf(prevGen, "%s", curGen);
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182 }
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183
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184 if ( !flag || strcmp(prevGen, curGen)!=0)
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185 {
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186
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187 fprintf(stdout, "| %15s | %15.2f | %15.2f | %15.2f | %15lld %15lld |\n",
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188 prevGen,loadingTime, mappingTime, maxMem, mappingCnt , mappedSeqCnt);
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189 fflush(stdout);
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190
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191 totalMappingTime += mappingTime;
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192 totalLoadingTime += loadingTime;
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193
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194 loadingTime = 0;
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195 mappingTime = 0;
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196 maxMem = 0;
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197
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198 if (!flag)
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199 {
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200 break;
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201 }
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202 }
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203 else if (progressRep && mappingTime != 0)
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204 {
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205 fprintf(stdout, "| %15s | %15.2f | %15.2f | %15.2f | %15lld %15lld |\n",
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206 prevGen,loadingTime, mappingTime, maxMem, mappingCnt , mappedSeqCnt);
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207 fflush(stdout);
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208 }
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209
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210 sprintf(prevGen, "%s", curGen);
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211
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212 loadingTime += tmpTime;
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213 // lstartTime = getTime();
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214
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215 initFAST(seqList, seqListSize, samplingLocs, samplingLocsSize, fileName[fc][0]);
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216
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217 lstartTime = getTime();
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218
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219
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220 mapAllSingleEndSeq();
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221
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222
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223
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224 mappingTime += getTime() - lstartTime;
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225 if (maxMem < getMemUsage())
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226 {
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227 maxMem = getMemUsage();
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228 }
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229 } while (flag);
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230
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231 } // end for;
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232 if(bestMode)
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233 finalizeBestSingleMapping();
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234 finalizeFAST();
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235 finalizeLoadingHashTable();
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236
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237 }
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238 // Pairedend Mapping Mode
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239 else
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240 {
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241 initLookUpTable();
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242 if(pairedEndMode)
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243 initBestConcordantDiscordant(seqListSize);
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244 for (fc = 0; fc < fileCnt; fc++)
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245 {
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246 if (!initLoadingHashTable(fileName[fc][1]))
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247 {
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248 return 1;
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249 }
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250 mappingTime = 0;
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251 loadingTime = 0;
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252 prevGen[0] = '\0';
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253 flag = 1;
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254
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255 do
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256 {
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257 flag = loadHashTable ( &tmpTime , errThreshold); // Reading a fragment
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258 curGen = getRefGenomeName();
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259
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260 // First Time
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261 if (flag && prevGen[0]== '\0')
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262 {
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263 sprintf(prevGen, "%s", curGen);
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264 }
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265
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266 if ( !flag || strcmp(prevGen, curGen)!=0)
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267 {
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268
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269 // DISCORDANT
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270 lstartTime = getTime();
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271 outputPairedEnd();
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272 mappingTime += getTime() - lstartTime;
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273 //DISCORDANT
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274
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275 fprintf(stdout, "| %15s | %15.2f | %15.2f | %15.2f | %15lld %15lld |\n",
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276 prevGen,loadingTime, mappingTime, maxMem, mappingCnt , mappedSeqCnt);
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277 fflush(stdout);
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278
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279 totalMappingTime += mappingTime;
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280 totalLoadingTime += loadingTime;
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281
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282 loadingTime = 0;
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283 mappingTime = 0;
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284 maxMem = 0;
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285
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286 if (!flag)
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287 {
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288 break;
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289 }
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290 }
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291 else if (progressRep && mappingTime != 0)
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292 {
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293 fprintf(stdout, "| %15s | %15.2f | %15.2f | %15.2f | %15lld %15lld |\n",
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294 prevGen,loadingTime, mappingTime, maxMem, mappingCnt , mappedSeqCnt);
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295 fflush(stdout);
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296 }
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297
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298 sprintf(prevGen, "%s", curGen);
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299
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300 loadingTime += tmpTime;
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301 lstartTime = getTime();
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302
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303 initFAST(seqList, seqListSize, samplingLocs, samplingLocsSize, fileName[fc][0]);
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304
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305 mapPairedEndSeq();
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306
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307 mappingTime += getTime() - lstartTime;
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308 if (maxMem < getMemUsage())
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309 {
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310 maxMem = getMemUsage();
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311 }
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312
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313 } while (flag);
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314
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315 } // end for;
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316
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317 if(pairedEndMode)
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318 {
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319 sprintf(outputFileName, "%s%s",mappingOutputPath , mappingOutput);
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320 finalizeOEAReads(outputFileName);
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321 outputAllTransChromosal(transChromosal);
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322 finalizeBestConcordantDiscordant();
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323 }
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324
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325 finalizeLoadingHashTable();
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326
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327 if (pairedEndDiscordantMode)
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328 {
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329 lstartTime = getTime();
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330 outputPairedEndDiscPP();
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331 ppTime = getTime() - lstartTime;
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332 }
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333 finalizeFAST();
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334 } //else
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335
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336 finalizeOutput();
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337
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338 fprintf(stdout, "-----------------------------------------------------------------------------------------------------------\n");
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339 fprintf(stdout, "%19s%16.2f%18.2f\n\n", "Total:",totalLoadingTime, totalMappingTime);
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340 if (pairedEndDiscordantMode)
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341 fprintf(stdout, "Post Processing Time: %18.2f \n", ppTime);
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342 fprintf(stdout, "%-30s%10.2f\n","Total Time:", totalMappingTime+totalLoadingTime);
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343 fprintf(stdout, "%-30s%10d\n","Total No. of Reads:", seqListSize);
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344 fprintf(stdout, "%-30s%10lld\n","Total No. of Mappings:", mappingCnt);
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345 fprintf(stdout, "%-30s%10.0f\n\n","Avg No. of locations verified:", ceil((float)verificationCnt/seqListSize));
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346
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347 int cof = (pairedEndMode)?2:1;
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348
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349 if (progressRep && maxHits != 0)
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350 {
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351 int frequency[maxHits+1];
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352 int i;
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353 for ( i=0 ; i <= maxHits; i++)
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354 {
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355 frequency[i] = 0;
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356 }
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357
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358
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359 for (fc = 0; fc < seqListSize; fc++)
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360 {
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361 frequency[(int)(*(seqList[fc*cof].hits))]++;
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362 }
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363 frequency[maxHits] = completedSeqCnt;
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364 for ( i=0 ; i <= maxHits; i++)
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365 {
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366 fprintf(stdout, "%-30s%10d%10d%10.2f%%\n","Reads Mapped to ", i, frequency[i], 100*(float)frequency[i]/(float)seqListSize);
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367 }
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368 }
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369
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370
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371 finalizeReads(unmappedOutput);
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372 freeMem(prevGen, CONTIG_NAME_SIZE);
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373 }
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374
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375 return 1;
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376 }
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