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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 : 2009-02-01
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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 <math.h>
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41 #include "Common.h"
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42 #include "CommandLineParser.h"
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43 #include "Reads.h"
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44 #include "Output.h"
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45 #include "HashTable.h"
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46 #include "MrsFAST.h"
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47
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48 char *versionNumber = "2.3"; // Current Version
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49 unsigned char seqFastq;
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50
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51 int main(int argc, char *argv[])
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52 {
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53 if (!parseCommandLine(argc, argv))
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54 return 1;
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55
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56 configHashTable();
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57 /****************************************************
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58 * INDEXING
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59 ***************************************************/
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60 if (indexingMode)
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61 {
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62 int i;
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63 /********************************
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64 * Regulard Mode
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65 ********************************/
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66 if (!bisulfiteMode)
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67 {
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68 configHashTable();
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69 for (i = 0; i < fileCnt; i++)
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70 {
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71 generateHashTable(fileName[i][0], fileName[i][1]);
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72 }
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73 }
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74 else
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75 /********************************
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76 * Bisulfite Mode
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77 ********************************/
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78 { // TODO
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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;
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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 // Loading Sequences & Sampling Locations
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110 startTime = getTime();
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111 if (bisulfiteMode && !pairedEndMode && seqFile1 == NULL)
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112 {
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113 //TODO
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114 }
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115 else
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116 {
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117 if (!readAllReads(seqFile1, seqFile2, seqCompressed, &seqFastq, pairedEndMode, &seqList, &seqListSize))
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118 {
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119 return 1;
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120 }
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121 }
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122
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123 //loadSamplingLocations(&samplingLocs, &samplingLocsSize);
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124 totalLoadingTime += getTime()-startTime;
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125
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126
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127
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128
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129 if (pairedEndMode)
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130 {
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131 //Switching to Inferred Size
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132 minPairEndedDistance = minPairEndedDistance - SEQ_LENGTH + 2;
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133 maxPairEndedDistance = maxPairEndedDistance - SEQ_LENGTH + 2;
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134 if (pairedEndDiscordantMode)
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135 {
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136 maxPairEndedDiscordantDistance = maxPairEndedDiscordantDistance - SEQ_LENGTH + 2;
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137 minPairEndedDiscordantDistance = minPairEndedDiscordantDistance - SEQ_LENGTH + 2;
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138 }
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139
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140 /* The size between the ends;
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141 minPairEndedDistance = minPairEndedDistance + SEQ_LENGTH + 1;
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142 maxPairEndedDistance = maxPairEndedDistance + SEQ_LENGTH + 1;
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143 if (pairedEndDiscordantMode)
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144 {
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145 maxPairEndedDiscordantDistance = maxPairEndedDiscordantDistance + SEQ_LENGTH + 1;
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146 minPairEndedDiscordantDistance = minPairEndedDiscordantDistance + SEQ_LENGTH + 1;
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147 }*/
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148 sprintf(fname1, "%s__%s__1", mappingOutputPath, mappingOutput);
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149 sprintf(fname2, "%s__%s__2", mappingOutputPath, mappingOutput);
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150 sprintf(fname3, "%s__%s__disc", mappingOutputPath, mappingOutput);
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151 sprintf(fname4, "%s__%s__oea1", mappingOutputPath, mappingOutput);
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152 sprintf(fname5, "%s__%s__oea2", mappingOutputPath, mappingOutput);
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153 unlink(fname1);
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154 unlink(fname2);
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155 unlink(fname3);
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156 unlink(fname4);
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157 unlink(fname5);
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158 }
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159
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160 // Preparing output
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161 initOutput(mappingOutput, outCompressed);
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162
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163 fprintf(stdout, "-----------------------------------------------------------------------------------------------------------\n");
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164 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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165 fprintf(stdout, "-----------------------------------------------------------------------------------------------------------\n");
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166
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167 /********************************
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168 * Regular Mode
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169 ********************************/
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170 if (!bisulfiteMode)
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171 {
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172 if (!pairedEndMode)
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173 {
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174 for (fc = 0; fc <fileCnt; fc++)
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175 {
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176 if (!initLoadingHashTable(fileName[fc][1]))
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177 {
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178 return 1;
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179 }
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180
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181 loadSamplingLocations(&samplingLocs, &samplingLocsSize);
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182
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183 mappingTime = 0;
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184 loadingTime = 0;
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185 prevGen[0] = '\0';
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186 flag = 1;
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187
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188 do
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189 {
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190 flag = loadHashTable ( &tmpTime ); // Reading a fragment
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191 curGen = getRefGenomeName();
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192
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193 // First Time
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194 if (flag && prevGen[0]== '\0')
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195 {
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196 sprintf(prevGen, "%s", curGen);
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197 }
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198
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199 if ( !flag || strcmp(prevGen, curGen)!=0)
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200 {
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201
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202 fprintf(stdout, "| %15s | %15.2f | %15.2f | %15.2f | %15lld %15lld |\n",
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203 prevGen,loadingTime, mappingTime, maxMem, mappingCnt , mappedSeqCnt);
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204 fflush(stdout);
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205
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206 totalMappingTime += mappingTime;
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207 totalLoadingTime += loadingTime;
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208
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209 loadingTime = 0;
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210 mappingTime = 0;
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211 maxMem = 0;
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212
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213 if (!flag)
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214 {
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215 break;
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216 }
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217 }
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218 else if (progressRep && mappingTime != 0)
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219 {
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220 fprintf(stdout, "| %15s | %15.2f | %15.2f | %15.2f | %15lld %15lld |\n",
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221 prevGen,loadingTime, mappingTime, maxMem, mappingCnt , mappedSeqCnt);
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222 fflush(stdout);
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223 }
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224
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225 sprintf(prevGen, "%s", curGen);
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226
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227 loadingTime += tmpTime;
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228 lstartTime = getTime();
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229
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230 initFAST(seqList, seqListSize, samplingLocs, samplingLocsSize, fileName[fc][0]);
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231
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232 mapSingleEndSeq();
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233
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234 mappingTime += getTime() - lstartTime;
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235 if (maxMem < getMemUsage())
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236 {
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237 maxMem = getMemUsage();
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238 }
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239 } while (flag);
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240
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241 } // end for;
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242 finalizeFAST();
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243 finalizeLoadingHashTable();
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244
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245 }
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246 // Pairedend Mapping Mode
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247 else
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248 {
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249
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250 for (fc = 0; fc <fileCnt; fc++)
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251 {
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252 if (!initLoadingHashTable(fileName[fc][1]))
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253 {
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254 return 1;
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255 }
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256
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257
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258 loadSamplingLocations(&samplingLocs, &samplingLocsSize);
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259
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260 mappingTime = 0;
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261 loadingTime = 0;
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262 prevGen[0] = '\0';
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263 flag = 1;
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264
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265 do
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266 {
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267 flag = loadHashTable ( &tmpTime ); // Reading a fragment
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268 curGen = getRefGenomeName();
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269
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270 // First Time
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271 if (flag && prevGen[0]== '\0')
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272 {
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273 sprintf(prevGen, "%s", curGen);
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274 }
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275
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276 if ( !flag || strcmp(prevGen, curGen)!=0)
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277 {
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278
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279 // DISCORDANT
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280 lstartTime = getTime();
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281 outputPairedEnd();
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282 mappingTime += getTime() - lstartTime;
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283 //DISCORDANT
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284
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285 fprintf(stdout, "| %15s | %15.2f | %15.2f | %15.2f | %15lld %15lld |\n",
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286 prevGen,loadingTime, mappingTime, maxMem, mappingCnt , mappedSeqCnt);
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287 fflush(stdout);
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288
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289 totalMappingTime += mappingTime;
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290 totalLoadingTime += loadingTime;
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291
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292 loadingTime = 0;
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293 mappingTime = 0;
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294 maxMem = 0;
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295
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296 if (!flag)
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297 {
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298 break;
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299 }
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300 }
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301 else if (progressRep && mappingTime != 0)
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302 {
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303 fprintf(stdout, "| %15s | %15.2f | %15.2f | %15.2f | %15lld %15lld |\n",
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304 prevGen,loadingTime, mappingTime, maxMem, mappingCnt , mappedSeqCnt);
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305 fflush(stdout);
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306 }
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307
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308 sprintf(prevGen, "%s", curGen);
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309
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310 loadingTime += tmpTime;
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311 lstartTime = getTime();
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312
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313 initFAST(seqList, seqListSize, samplingLocs, samplingLocsSize, fileName[fc][0]);
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314
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315 mapPairedEndSeq();
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316
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317 mappingTime += getTime() - lstartTime;
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318 if (maxMem < getMemUsage())
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319 {
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320 maxMem = getMemUsage();
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321 }
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322 } while (flag);
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323
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324 } // end for;
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325
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326 finalizeLoadingHashTable();
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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 }
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335 }
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336 /********************************
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337 * Bisulfite Mode
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338 ********************************/
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339 {
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340 //TODO
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341 }
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342
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343
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344 finalizeOutput();
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345
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346 fprintf(stdout, "-----------------------------------------------------------------------------------------------------------\n");
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347 fprintf(stdout, "%19s%16.2f%18.2f\n\n", "Total:",totalLoadingTime, totalMappingTime);
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348 if (pairedEndDiscordantMode)
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349 fprintf(stdout, "Post Processing Time: %18.2f \n", ppTime);
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350 fprintf(stdout, "%-30s%10.2f\n","Total Time:", totalMappingTime+totalLoadingTime);
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351 fprintf(stdout, "%-30s%10d\n","Total No. of Reads:", seqListSize);
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352 fprintf(stdout, "%-30s%10lld\n","Total No. of Mappings:", mappingCnt);
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353 fprintf(stdout, "%-30s%10.0f\n\n","Avg No. of locations verified:", ceil((float)verificationCnt/seqListSize));
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354
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355 int cof = (pairedEndMode)?2:1;
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356
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357 if (progressRep && maxHits != 0)
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358 {
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359 int frequency[maxHits+1];
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360 int i;
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361 for ( i=0 ; i <= maxHits; i++)
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362 {
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363 frequency[i] = 0;
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364 }
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365
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366
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367 for (fc = 0; fc < seqListSize; fc++)
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368 {
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369 frequency[*(seqList[fc*cof].hits)]++;
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370 }
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371 frequency[maxHits] = completedSeqCnt;
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372 for ( i=0 ; i <= maxHits; i++)
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373 {
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374 fprintf(stdout, "%-30s%10d%10d%10.2f%%\n","Reads Mapped to ", i, frequency[i], 100*(float)frequency[i]/(float)seqListSize);
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375 }
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376 }
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377
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378
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379 if (strcmp(unmappedOutput, "") == 0)
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380 {
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381 char fn[strlen(mappingOutputPath) + strlen(mappingOutput) + 6 ];
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382 sprintf(fn, "%s%s.nohit", mappingOutputPath, mappingOutput );
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383 finalizeReads(fn);
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384 }
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385 else
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386 {
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387 finalizeReads(unmappedOutput);
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388 }
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389
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390
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391
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392 freeMem(prevGen, CONTIG_NAME_SIZE);
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393 }
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394
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395
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396
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397 return 1;
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398 }
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