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1 /*****************************************************************************
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2 annotateMain.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 "annotateBed.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 the version
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18 #define PROGRAM_NAME "annotateBed"
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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 file
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32 string mainFile;
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33
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34 // parm flags
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35 bool sameStrand = false;
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36 bool diffStrand = false;
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37 bool haveBed = false;
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38 bool haveFiles = false;
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39 bool haveTitles = false;
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40 bool reportCounts = false;
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41 bool reportBoth = false;
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42
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43 // list of annotation files / names
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44 vector<string> inputFiles;
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45 vector<string> inputTitles;
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46
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47 // check to see if we should print out some help
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48 if(argc <= 1) showHelp = true;
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49
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50 for(int i = 1; i < argc; i++) {
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51 int parameterLength = (int)strlen(argv[i]);
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52
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53 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
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54 (PARAMETER_CHECK("--help", 5, parameterLength))) {
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55 showHelp = true;
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56 }
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57 }
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58
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59 if(showHelp) ShowHelp();
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60
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61 // do some parsing (all of these parameters require 2 strings)
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62 for(int i = 1; i < argc; i++) {
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63
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64 int parameterLength = (int)strlen(argv[i]);
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65
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66 if(PARAMETER_CHECK("-i", 2, parameterLength)) {
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67 if ((i+1) < argc) {
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68 haveBed = true;
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69 mainFile = argv[i + 1];
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70 i++;
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71 }
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72 }
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73 else if(PARAMETER_CHECK("-files", 6, parameterLength)) {
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74 if ((i+1) < argc) {
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75 haveFiles = true;
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76 i = i+1;
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77 string file = argv[i];
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78 while (file[0] != '-' && i < argc) {
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79 inputFiles.push_back(file);
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80 i++;
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81 if (i < argc)
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82 file = argv[i];
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83 }
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84 i--;
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85 }
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86 }
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87 else if(PARAMETER_CHECK("-names", 6, parameterLength)) {
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88 if ((i+1) < argc) {
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89 haveTitles = true;
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90 i = i+1;
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91 string title = argv[i];
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92 while (title[0] != '-' && i < argc) {
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93 inputTitles.push_back(title);
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94 i++;
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95 if (i < argc)
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96 title = argv[i];
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97 }
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98 i--;
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99 }
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100 }
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101 else if(PARAMETER_CHECK("-counts", 7, parameterLength)) {
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102 reportCounts = true;
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103 }
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104 else if(PARAMETER_CHECK("-both", 5, parameterLength)) {
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105 reportBoth = true;
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106 }
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107 else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
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108 sameStrand = true;
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109 }
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110 else if (PARAMETER_CHECK("-S", 2, parameterLength)) {
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111 diffStrand = true;
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112 }
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113 else {
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114 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
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115 showHelp = true;
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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 (!haveBed || !haveFiles) {
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121 cerr << endl << "*****" << endl << "*****ERROR: Need -i and -files files. " << endl << "*****" << endl;
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122 showHelp = true;
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123 }
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124 if (sameStrand && diffStrand) {
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125 cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl;
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126 showHelp = true;
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127 }
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128
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129 if (!showHelp) {
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130 BedAnnotate *ba = new BedAnnotate(mainFile, inputFiles, inputTitles, sameStrand, diffStrand, reportCounts, reportBoth);
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131 ba->AnnotateBed();
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132 delete ba;
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133 return 0;
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134 }
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135 else {
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136 ShowHelp();
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137 }
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138 }
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139
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140 void ShowHelp(void) {
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141
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142 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
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143
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144 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
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145
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146 cerr << "Summary: Annotates the depth & breadth of coverage of features from multiple files" << endl;
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147 cerr << "\t on the intervals in -i." << endl << endl;
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148
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149 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -files FILE1 FILE2 .. FILEn" << endl << endl;
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150
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151 cerr << "Options: " << endl;
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152
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153 cerr << "\t-names\t" << "A list of names (one / file) to describe each file in -i." << endl;
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154 cerr << "\t\tThese names will be printed as a header line." << endl << endl;
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155
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156 cerr << "\t-counts\t" << "Report the count of features in each file that overlap -i." << endl;
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157 cerr << "\t\t- Default is to report the fraction of -i covered by each file." << endl << endl;
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158
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159 cerr << "\t-both\t" << "Report the counts followed by the % coverage." << endl;
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160 cerr << "\t\t- Default is to report the fraction of -i covered by each file." << endl << endl;
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161
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162 cerr << "\t-s\t" << "Require same strandedness. That is, only counts overlaps" << endl;
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163 cerr << "\t\ton the _same_ strand." << endl;
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164 cerr << "\t\t- By default, overlaps are counted without respect to strand." << endl << endl;
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165
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166 cerr << "\t-S\t" << "Require different strandedness. That is, only count overlaps" << endl;
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167 cerr << "\t\ton the _opposite_ strand." << endl;
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168 cerr << "\t\t- By default, overlaps are counted without respect to strand." << endl << endl;
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169 exit(1);
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170 }
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