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1 /*****************************************************************************
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2 subtractMain.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 "subtractBed.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 "subtractBed"
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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 haveFraction = false;
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42 bool sameStrand = false;
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43 bool diffStrand = false;
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44
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45 // check to see if we should print out some help
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46 if(argc <= 1) showHelp = true;
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47
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48 for(int i = 1; i < argc; i++) {
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49 int parameterLength = (int)strlen(argv[i]);
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50
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51 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
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52 (PARAMETER_CHECK("--help", 5, parameterLength))) {
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53 showHelp = true;
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54 }
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55 }
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56
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57 if(showHelp) ShowHelp();
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58
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59 // do some parsing (all of these parameters require 2 strings)
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60 for(int i = 1; i < argc; i++) {
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61
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62 int parameterLength = (int)strlen(argv[i]);
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63
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64 if(PARAMETER_CHECK("-a", 2, parameterLength)) {
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65 if ((i+1) < argc) {
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66 haveBedA = true;
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67 bedAFile = argv[i + 1];
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68 i++;
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69 }
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70 }
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71 else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
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72 if ((i+1) < argc) {
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73 haveBedB = true;
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74 bedBFile = 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("-f", 2, parameterLength)) {
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79 if ((i+1) < argc) {
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80 haveFraction = true;
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81 overlapFraction = atof(argv[i + 1]);
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82 i++;
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83 }
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84 }
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85 else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
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86 sameStrand = true;
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87 }
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88 else if (PARAMETER_CHECK("-S", 2, parameterLength)) {
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89 diffStrand = true;
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90 }
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91 else {
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92 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
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93 showHelp = true;
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94 }
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95 }
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96
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97 // make sure we have both input files
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98 if (!haveBedA || !haveBedB) {
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99 cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
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100 showHelp = true;
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101 }
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102
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103 if (sameStrand && diffStrand) {
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104 cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl;
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105 showHelp = true;
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106 }
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107
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108 if (!showHelp) {
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109
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110 BedSubtract *bs = new BedSubtract(bedAFile, bedBFile, overlapFraction, sameStrand, diffStrand);
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111 delete bs;
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112 return 0;
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113 }
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114 else {
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115 ShowHelp();
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116 }
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117 }
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118
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119 void ShowHelp(void) {
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120
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121 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
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122
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123 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
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124
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125 cerr << "Summary: Removes the portion(s) of an interval that is overlapped" << endl;
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126 cerr << "\t by another feature(s)." << endl << endl;
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127
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128 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
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129
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130 cerr << "Options: " << endl;
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131 cerr << "\t-f\t" << "Minimum overlap required as a fraction of A." << endl;
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132 cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl;
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133 cerr << "\t\t- (FLOAT) (e.g. 0.50)" << endl << endl;
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134
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135 cerr << "\t-s\t" << "Require same strandedness. That is, only subtract hits in B that" << endl;
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136 cerr << "\t\toverlap A on the _same_ strand." << endl;
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137 cerr << "\t\t- By default, overlaps are subtracted without respect to strand." << endl << endl;
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138
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139 cerr << "\t-S\t" << "Force strandedness. That is, only subtract hits in B that" << endl;
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140 cerr << "\t\toverlap A on the _opposite_ strand." << endl;
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141 cerr << "\t\t- By default, overlaps are subtracted without respect to strand." << endl << endl;
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142
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143 // end the program here
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144 exit(1);
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145 }
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