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1 /*****************************************************************************
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2 pairToBedMain.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 "pairToBed.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 "pairToBed"
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19
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20 // define our parameter checking macro
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21 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
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22
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23 // function declarations
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24 void ShowHelp(void);
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25
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26 int main(int argc, char* argv[]) {
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27
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28 // our configuration variables
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29 bool showHelp = false;
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30
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31 // input files
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32 string bedAFile;
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33 string bedBFile;
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34
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35 // input arguments
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36 float overlapFraction = 1E-9;
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37 string searchType = "either";
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38
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39 // flags to track parameters
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40 bool haveBedA = false;
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41 bool haveBedB = false;
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42 bool haveSearchType = false;
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43 bool haveFraction = false;
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44 bool sameStrand = false;
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45 bool diffStrand = false;
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46 bool useEditDistance = false;
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47 bool inputIsBam = false;
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48 bool outputIsBam = true;
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49 bool uncompressedBam = false;
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50
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51 // check to see if we should print out some help
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52 if(argc <= 1) showHelp = true;
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53
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54 for(int i = 1; i < argc; i++) {
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55 int parameterLength = (int)strlen(argv[i]);
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56
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57 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
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58 (PARAMETER_CHECK("--help", 5, parameterLength))) {
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59 showHelp = true;
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60 }
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61 }
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62
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63 if(showHelp) ShowHelp();
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64
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65 // do some parsing (all of these parameters require 2 strings)
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66 for(int i = 1; i < argc; i++) {
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67
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68 int parameterLength = (int)strlen(argv[i]);
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69
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70 if(PARAMETER_CHECK("-a", 2, parameterLength)) {
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71 if ((i+1) < argc) {
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72 haveBedA = true;
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73 outputIsBam = false;
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74 bedAFile = argv[i + 1];
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75 i++;
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76 }
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77 }
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78 else if(PARAMETER_CHECK("-abam", 5, parameterLength)) {
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79 if ((i+1) < argc) {
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80 haveBedA = true;
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81 inputIsBam = true;
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82 bedAFile = argv[i + 1];
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83 i++;
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84 }
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85 }
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86 else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
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87 if ((i+1) < argc) {
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88 haveBedB = true;
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89 bedBFile = argv[i + 1];
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90 i++;
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91 }
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92 }
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93 else if(PARAMETER_CHECK("-bedpe", 6, parameterLength)) {
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94 outputIsBam = false;
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95 }
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96 else if(PARAMETER_CHECK("-ed", 3, parameterLength)) {
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97 useEditDistance = true;
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98 }
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99 else if(PARAMETER_CHECK("-type", 5, parameterLength)) {
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100 if ((i+1) < argc) {
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101 haveSearchType = true;
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102 searchType = argv[i + 1];
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103 i++;
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104 }
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105 }
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106 else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
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107 if ((i+1) < argc) {
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108 haveFraction = true;
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109 overlapFraction = atof(argv[i + 1]);
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110 i++;
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111 }
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112 }
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113 else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
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114 sameStrand = true;
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115 }
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116 else if (PARAMETER_CHECK("-S", 2, parameterLength)) {
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117 diffStrand = true;
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118 }
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119 else if(PARAMETER_CHECK("-ubam", 5, parameterLength)) {
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120 uncompressedBam = true;
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121 }
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122 else {
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123 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
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124 showHelp = true;
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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 // make sure we have both input files
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130 if (!haveBedA || !haveBedB) {
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131 cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
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132 showHelp = true;
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133 }
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134
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135 if (haveSearchType && (searchType != "either") && (searchType != "neither") && (searchType != "both")
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136 && (searchType != "xor") && (searchType != "notboth") && (searchType != "ispan")
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137 && (searchType != "ospan") && (searchType != "notispan") && (searchType != "notospan")) {
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138 cerr << endl << "*****" << endl << "*****ERROR: Request \"either\" or \"both\" or \"neither\" or \"xor\" or \"notboth\" or \"ispan\" or \"ospan\" or \"notispan\" or \"notospan\"" << endl << "*****" << endl;
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139 showHelp = true;
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140 }
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141
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142 if ( ((searchType == "ispan") || (searchType == "ospan") || (searchType == "notispan") || (searchType == "notospan"))
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143 && (sameStrand || diffStrand) ) {
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144 cerr << endl << "*****" << endl << "*****ERROR: Cannot enforce strandedness with selected searchtype" << endl << "*****" << endl;
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145 showHelp = true;
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146 }
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147
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148 if (useEditDistance && (inputIsBam == false || outputIsBam == true)) {
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149 cerr << endl << "*****" << endl << "*****ERROR: -ed must be used with -bedpe and -abam." << endl << "*****" << endl;
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150 showHelp = true;
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151 }
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152
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153 if (sameStrand && diffStrand) {
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154 cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl;
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155 showHelp = true;
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156 }
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157 if (!showHelp) {
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158
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159 BedIntersectPE *bi = new BedIntersectPE(bedAFile, bedBFile, overlapFraction,
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160 searchType, sameStrand, diffStrand, inputIsBam,
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161 outputIsBam, uncompressedBam, useEditDistance);
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162 delete bi;
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163 return 0;
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164 }
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165 else {
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166 ShowHelp();
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167 }
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168 }
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169
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170
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171 void ShowHelp(void) {
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172
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173 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
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174
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175 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
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176
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177 cerr << "Summary: Report overlaps between a BEDPE file and a BED/GFF/VCF file." << endl << endl;
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178
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179 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bedpe> -b <bed/gff/vcf>" << endl << endl;
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180
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181 cerr << "Options: " << endl;
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182
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183 cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl;
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184 cerr << "\t\t- Requires BAM to be grouped or sorted by query." << endl << endl;
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185
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186 cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default is to write compressed BAM." << endl << endl;
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187 cerr << "\t\tis to write output in BAM when using -abam." << endl << endl;
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188
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189 cerr << "\t-bedpe\t" << "When using BAM input (-abam), write output as BEDPE. The default" << endl;
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190 cerr << "\t\tis to write output in BAM when using -abam." << endl << endl;
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191
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192 cerr << "\t-ed\t" << "Use BAM total edit distance (NM tag) for BEDPE score." << endl;
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193 cerr << "\t\t- Default for BEDPE is to use the minimum of" << endl;
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194 cerr << "\t\t of the two mapping qualities for the pair." << endl;
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195 cerr << "\t\t- When -ed is used the total edit distance" << endl;
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196 cerr << "\t\t from the two mates is reported as the score." << endl << endl;
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197
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198 cerr << "\t-f\t" << "Minimum overlap required as fraction of A (e.g. 0.05)." << endl;
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199 cerr << "\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;
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200
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201 cerr << "\t-s\t" << "Require same strandedness when finding overlaps." << endl;
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202 cerr << "\t\tDefault is to ignore stand." << endl;
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203 cerr << "\t\tNot applicable with -type inspan or -type outspan." << endl << endl;
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204
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205 cerr << "\t-S\t" << "Require different strandedness when finding overlaps." << endl;
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206 cerr << "\t\tDefault is to ignore stand." << endl;
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207 cerr << "\t\tNot applicable with -type inspan or -type outspan." << endl << endl;
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208
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209 cerr << "\t-type \t" << "Approach to reporting overlaps between BEDPE and BED." << endl << endl;
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210 cerr << "\t\teither\tReport overlaps if either end of A overlaps B." << endl;
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211 cerr << "\t\t\t- Default." << endl;
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212
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213 cerr << "\t\tneither\tReport A if neither end of A overlaps B." << endl;
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214
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215 cerr << "\t\tboth\tReport overlaps if both ends of A overlap B." << endl;
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216
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217 cerr << "\t\txor\tReport overlaps if one and only one end of A overlaps B." << endl;
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218
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219 cerr << "\t\tnotboth\tReport overlaps if neither end or one and only one " << endl;
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220 cerr << "\t\t\tend of A overlap B. That is, xor + neither." << endl << endl;
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221
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222 cerr << "\t\tispan\tReport overlaps between [end1, start2] of A and B." << endl;
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223 cerr << "\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl;
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224
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225 cerr << "\t\tospan\tReport overlaps between [start1, end2] of A and B." << endl;
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226 cerr << "\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl;
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227
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228 cerr << "\t\tnotispan\tReport A if ispan of A doesn't overlap B." << endl;
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229 cerr << "\t\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl;
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230
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231 cerr << "\t\tnotospan\tReport A if ospan of A doesn't overlap B." << endl;
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232 cerr << "\t\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl;
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233
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234 cerr << "Refer to the BEDTools manual for BEDPE format." << endl << endl;
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235
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236 exit(1);
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237 }
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