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1 /*****************************************************************************
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2 intersectMain.cpp
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3
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4 (c) 2009 - Aaron Quinlan
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5 Hall Laboratory
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6 Department of Biochemistry and Molecular Genetics
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7 University of Virginia
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8 aaronquinlan@gmail.com
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9
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10 Licenced under the GNU General Public License 2.0 license.
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11 ******************************************************************************/
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12 #include "intersectBed.h"
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13 #include "version.h"
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14
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15 using namespace std;
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16
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17 // define our program name
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18 #define PROGRAM_NAME "intersectBed"
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19
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20
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21 // define our parameter checking macro
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22 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
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23
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24 // function declarations
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25 void ShowHelp(void);
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26
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27 int main(int argc, char* argv[]) {
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28
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29 // our configuration variables
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30 bool showHelp = false;
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31
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32 // input files
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33 string bedAFile;
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34 string bedBFile;
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35
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36 // input arguments
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37 float overlapFraction = 1E-9;
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38
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39 bool haveBedA = false;
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40 bool haveBedB = false;
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41 bool noHit = false;
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42 bool anyHit = false;
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43 bool writeA = false;
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44 bool writeB = false;
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45 bool writeCount = false;
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46 bool writeOverlap = false;
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47 bool writeAllOverlap = false;
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48 bool haveFraction = false;
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49 bool reciprocalFraction = false;
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50 bool sameStrand = false;
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51 bool diffStrand = false;
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52 bool obeySplits = false;
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53 bool inputIsBam = false;
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54 bool outputIsBam = true;
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55 bool uncompressedBam = false;
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56 bool sortedInput = false;
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57 // check to see if we should print out some help
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58 if(argc <= 1) showHelp = true;
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59
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60 for(int i = 1; i < argc; i++) {
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61 int parameterLength = (int)strlen(argv[i]);
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62
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63 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
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64 (PARAMETER_CHECK("--help", 5, parameterLength))) {
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65 showHelp = true;
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66 }
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67 }
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68
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69 if(showHelp) ShowHelp();
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70
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71 // do some parsing (all of these parameters require 2 strings)
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72 for(int i = 1; i < argc; i++) {
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73
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74 int parameterLength = (int)strlen(argv[i]);
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75
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76 if(PARAMETER_CHECK("-a", 2, parameterLength)) {
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77 if ((i+1) < argc) {
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78 haveBedA = true;
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79 outputIsBam = false;
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80 bedAFile = argv[i + 1];
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81 i++;
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82 }
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83 }
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84 else if(PARAMETER_CHECK("-abam", 5, parameterLength)) {
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85 if ((i+1) < argc) {
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86 haveBedA = true;
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87 inputIsBam = true;
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88 bedAFile = argv[i + 1];
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89 i++;
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90 }
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91 }
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92 else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
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93 if ((i+1) < argc) {
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94 haveBedB = true;
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95 bedBFile = argv[i + 1];
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96 i++;
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97 }
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98 }
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99 else if(PARAMETER_CHECK("-bed", 4, parameterLength)) {
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100 outputIsBam = false;
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101 }
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102 else if(PARAMETER_CHECK("-u", 2, parameterLength)) {
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103 anyHit = true;
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104 }
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105 else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
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106 if ((i+1) < argc) {
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107 haveFraction = true;
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108 overlapFraction = atof(argv[i + 1]);
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109 i++;
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110 }
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111 }
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112 else if(PARAMETER_CHECK("-wa", 3, parameterLength)) {
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113 writeA = true;
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114 }
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115 else if(PARAMETER_CHECK("-wb", 3, parameterLength)) {
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116 writeB = true;
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117 }
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118 else if(PARAMETER_CHECK("-wo", 3, parameterLength)) {
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119 writeOverlap = true;
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120 }
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121 else if(PARAMETER_CHECK("-wao", 4, parameterLength)) {
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122 writeAllOverlap = true;
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123 writeOverlap = true;
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124 }
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125 else if(PARAMETER_CHECK("-c", 2, parameterLength)) {
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126 writeCount = true;
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127 }
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128 else if(PARAMETER_CHECK("-r", 2, parameterLength)) {
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129 reciprocalFraction = true;
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130 }
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131 else if (PARAMETER_CHECK("-v", 2, parameterLength)) {
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132 noHit = true;
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133 }
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134 else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
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135 sameStrand = true;
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136 }
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137 else if (PARAMETER_CHECK("-S", 2, parameterLength)) {
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138 diffStrand = true;
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139 }
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140 else if (PARAMETER_CHECK("-split", 6, parameterLength)) {
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141 obeySplits = true;
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142 }
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143 else if(PARAMETER_CHECK("-ubam", 5, parameterLength)) {
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144 uncompressedBam = true;
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145 }
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146 else if(PARAMETER_CHECK("-sorted", 7, parameterLength)) {
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147 sortedInput = true;
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148 }
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149 else {
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150 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
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151 showHelp = true;
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152 }
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153 }
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154
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155 // make sure we have both input files
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156 if (!haveBedA || !haveBedB) {
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157 cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
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158 showHelp = true;
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159 }
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160
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161 if (anyHit && noHit) {
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162 cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -v, not both." << endl << "*****" << endl;
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163 showHelp = true;
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164 }
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165
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166 if (writeB && writeCount) {
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167 cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -c, not both." << endl << "*****" << endl;
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168 showHelp = true;
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169 }
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170
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171 if (writeCount && writeOverlap) {
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172 cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -wo, not both." << endl << "*****" << endl;
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173 showHelp = true;
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174 }
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175
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176 if (writeA && writeOverlap) {
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177 cerr << endl << "*****" << endl << "*****ERROR: Request either -wa OR -wo, not both." << endl << "*****" << endl;
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178 showHelp = true;
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179 }
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180
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181 if (writeB && writeOverlap) {
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182 cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -wo, not both." << endl << "*****" << endl;
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183 showHelp = true;
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184 }
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185
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186 if (reciprocalFraction && !haveFraction) {
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187 cerr << endl << "*****" << endl << "*****ERROR: If using -r, you need to define -f." << endl << "*****" << endl;
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188 showHelp = true;
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189 }
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190
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191 if (anyHit && writeCount) {
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192 cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -c, not both." << endl << "*****" << endl;
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193 showHelp = true;
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194 }
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195
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196 if (anyHit && writeB) {
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197 cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -wb, not both." << endl << "*****" << endl;
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198 showHelp = true;
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199 }
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200
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201 if (anyHit && writeOverlap) {
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202 cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -wo, not both." << endl << "*****" << endl;
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203 showHelp = true;
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204 }
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205
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206 if (sameStrand && diffStrand) {
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207 cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl;
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208 showHelp = true;
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209 }
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210
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211 if (!showHelp) {
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212
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213 BedIntersect *bi = new BedIntersect(bedAFile, bedBFile, anyHit, writeA, writeB, writeOverlap,
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214 writeAllOverlap, overlapFraction, noHit, writeCount, sameStrand, diffStrand,
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215 reciprocalFraction, obeySplits, inputIsBam, outputIsBam, uncompressedBam, sortedInput);
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216 delete bi;
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217 return 0;
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218 }
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219 else {
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220 ShowHelp();
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221 }
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222 }
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223
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224 void ShowHelp(void) {
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225
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226 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
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227
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228 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
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229
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230 cerr << "Summary: Report overlaps between two feature files." << endl << endl;
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231
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232 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
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233
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234 cerr << "Options: " << endl;
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235
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236 cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl << endl;
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237
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238 cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default is to write compressed BAM." << endl << endl;
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239
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240 cerr << "\t-bed\t" << "When using BAM input (-abam), write output as BED. The default" << endl;
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241 cerr << "\t\tis to write output in BAM when using -abam." << endl << endl;
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242
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243 cerr << "\t-wa\t" << "Write the original entry in A for each overlap." << endl << endl;
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244
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245 cerr << "\t-wb\t" << "Write the original entry in B for each overlap." << endl;
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246 cerr << "\t\t- Useful for knowing _what_ A overlaps. Restricted by -f and -r." << endl << endl;
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247
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248 cerr << "\t-wo\t" << "Write the original A and B entries plus the number of base" << endl;
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249 cerr << "\t\tpairs of overlap between the two features." << endl;
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250 cerr << "\t\t- Overlaps restricted by -f and -r." << endl;
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251 cerr << "\t\t Only A features with overlap are reported." << endl << endl;
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252
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253 cerr << "\t-wao\t" << "Write the original A and B entries plus the number of base" << endl;
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254 cerr << "\t\tpairs of overlap between the two features." << endl;
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255 cerr << "\t\t- Overlapping features restricted by -f and -r." << endl;
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256 cerr << "\t\t However, A features w/o overlap are also reported" << endl;
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257 cerr << "\t\t with a NULL B feature and overlap = 0." << endl << endl;
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258
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259 cerr << "\t-u\t" << "Write the original A entry _once_ if _any_ overlaps found in B." << endl;
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260 cerr << "\t\t- In other words, just report the fact >=1 hit was found." << endl;
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261 cerr << "\t\t- Overlaps restricted by -f and -r." << endl << endl;
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262
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263 cerr << "\t-c\t" << "For each entry in A, report the number of overlaps with B." << endl;
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264 cerr << "\t\t- Reports 0 for A entries that have no overlap with B." << endl;
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265 cerr << "\t\t- Overlaps restricted by -f and -r." << endl << endl;
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266
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267 cerr << "\t-v\t" << "Only report those entries in A that have _no overlaps_ with B." << endl;
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268 cerr << "\t\t- Similar to \"grep -v\" (an homage)." << endl << endl;
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269
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270 cerr << "\t-f\t" << "Minimum overlap required as a fraction of A." << endl;
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271 cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl;
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272 cerr << "\t\t- FLOAT (e.g. 0.50)" << endl << endl;
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273
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274 cerr << "\t-r\t" << "Require that the fraction overlap be reciprocal for A and B." << endl;
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275 cerr << "\t\t- In other words, if -f is 0.90 and -r is used, this requires" << endl;
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276 cerr << "\t\t that B overlap 90% of A and A _also_ overlaps 90% of B." << endl << endl;
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277
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278 cerr << "\t-s\t" << "Require same strandedness. That is, only report hits in B that" << endl;
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279 cerr << "\t\toverlap A on the _same_ strand." << endl;
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280 cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
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281
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282 cerr << "\t-S\t" << "Require different strandedness. That is, only report hits in B that" << endl;
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283 cerr << "\t\toverlap A on the _opposite_ strand." << endl;
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284 cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
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285
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286 cerr << "\t-split\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl << endl;
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287
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288 cerr << "\t-sorted\t" << "Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input" << endl;
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289 cerr << "\t\tNOTE: this will trust, but not enforce that data is sorted. Caveat emptor." << endl << endl;
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290
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291 // end the program here
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292 exit(1);
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293
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294 }
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