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1 /*****************************************************************************
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2 pairToPairMain.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 "pairToPair.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 "pairToPair"
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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 int slop = 0;
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38 string searchType = "both";
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39
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40 // flags to track parameters
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41 bool haveBedA = false;
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42 bool haveBedB = false;
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43 bool haveSearchType = false;
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44 bool haveFraction = false;
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45 bool ignoreStrand = false;
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46 bool requireDifferentNames = false;
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47 bool haveSlop = false;
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48 bool strandedSlop = false;
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49 // check to see if we should print out some help
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50 if(argc <= 1) showHelp = true;
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51
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52 for(int i = 1; i < argc; i++) {
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53 int parameterLength = (int)strlen(argv[i]);
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54
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55 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
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56 (PARAMETER_CHECK("--help", 5, parameterLength))) {
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57 showHelp = true;
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58 }
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59 }
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60
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61 if(showHelp) ShowHelp();
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62
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63 // do some parsing (all of these parameters require 2 strings)
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64 for(int i = 1; i < argc; i++) {
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65
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66 int parameterLength = (int)strlen(argv[i]);
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67
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68 if(PARAMETER_CHECK("-a", 2, parameterLength)) {
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69 if ((i+1) < argc) {
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70 haveBedA = true;
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71 bedAFile = argv[i + 1];
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72 i++;
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73 }
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74 }
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75 else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
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76 if ((i+1) < argc) {
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77 haveBedB = true;
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78 bedBFile = argv[i + 1];
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79 i++;
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80 }
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81 }
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82 else if(PARAMETER_CHECK("-type", 5, parameterLength)) {
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83 if ((i+1) < argc) {
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84 haveSearchType = true;
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85 searchType = argv[i + 1];
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86 i++;
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87 }
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88 }
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89 else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
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90 if ((i+1) < argc) {
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91 haveFraction = true;
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92 overlapFraction = atof(argv[i + 1]);
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93 i++;
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94 }
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95 }
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96 else if(PARAMETER_CHECK("-slop", 5, parameterLength)) {
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97 if ((i+1) < argc) {
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98 haveSlop = true;
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99 slop = atoi(argv[i + 1]);
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100 i++;
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101 }
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102 }
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103 else if(PARAMETER_CHECK("-ss", 3, parameterLength)) {
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104 strandedSlop = true;
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105 }
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106 else if(PARAMETER_CHECK("-rdn", 4, parameterLength)) {
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107 requireDifferentNames = true;
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108 }
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109 else if(PARAMETER_CHECK("-is", 3, parameterLength)) {
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110 ignoreStrand = true;
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111 }
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112 else {
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113 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
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114 showHelp = true;
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115 }
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116 }
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117
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118
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119 // make sure we have both input files
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120 if (!haveBedA || !haveBedB) {
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121 cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
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122 showHelp = true;
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123 }
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124
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125 if (haveSearchType && (searchType != "neither") && (searchType != "both") && (searchType != "either") && (searchType != "notboth")) {
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126 cerr << endl << "*****" << endl << "*****ERROR: Request \"both\",\"neither\",\"either\",or \"notboth\"" << endl << "*****" << endl;
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127 showHelp = true;
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128 }
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129
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130 if (strandedSlop == true && haveSlop == false) {
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131 cerr << endl << "*****" << endl << "*****ERROR: Need a -slop value if requesting -ss." << 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 (!showHelp) {
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136
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137 PairToPair *bi = new PairToPair(bedAFile, bedBFile, overlapFraction, searchType,
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138 ignoreStrand, requireDifferentNames, slop, strandedSlop);
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139 delete bi;
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140 return 0;
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141 }
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142 else {
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143 ShowHelp();
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144 }
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145 }
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146
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147
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148 void ShowHelp(void) {
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149 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
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150
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151 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
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152
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153 cerr << "Summary: Report overlaps between two paired-end BED files (BEDPE)." << endl << endl;
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154
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155 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <BEDPE> -b <BEDPE>" << endl << endl;
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156
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157 cerr << "Options: " << endl;
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158 cerr << "\t-f\t" << "Minimum overlap required as fraction of A (e.g. 0.05)." << endl;
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159 cerr << "\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;
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160
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161 cerr << "\t-type \t" << "Approach to reporting overlaps between A and B." << endl << endl;
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162 cerr << "\t\tneither\tReport overlaps if neither end of A overlaps B." << endl;
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163 cerr << "\t\teither\tReport overlaps if either ends of A overlap B." << endl;
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164 cerr << "\t\tboth\tReport overlaps if both ends of A overlap B." << endl;
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165 cerr << "\t\tnotboth\tReport overlaps if one or neither of ends of A overlap B." << endl;
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166
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167 cerr << "\t\t- Default = both." << endl << endl;
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168
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169 cerr << "\t-slop \t" << "The amount of slop (in b.p.). to be added to each footprint." << endl;
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170 cerr << "\t\t*Note*: Slop is subtracted from start1 and start2 and added to end1 and end2." << endl << endl;
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171
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172 cerr << "\t-ss\t" << "Add slop based to each BEDPE footprint based on strand." << endl;
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173 cerr << "\t\t- If strand is \"+\", slop is only added to the end coordinates." << endl;
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174 cerr << "\t\t- If strand is \"-\", slop is only added to the start coordinates." << endl;
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175 cerr << "\t\t- By default, slop is added in both directions." << endl << endl;
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176
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177 cerr << "\t-is\t" << "Ignore strands when searching for overlaps." << endl;
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178 cerr << "\t\t- By default, strands are enforced." << endl << endl;
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179
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180 cerr << "\t-rdn\t" << "Require the hits to have different names (i.e. avoid self-hits)." << endl;
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181 cerr << "\t\t- By default, same names are allowed." << endl << endl;
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182
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183
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184 cerr << "Refer to the BEDTools manual for BEDPE format." << endl << endl;
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185
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186 // end the program here
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187 exit(1);
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188 }
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