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1 /*****************************************************************************
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2 overlap.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 <vector>
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13 #include <iostream>
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14 #include <fstream>
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15 #include <stdlib.h>
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16
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17 #include "version.h"
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18 #include "lineFileUtilities.h"
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19 #include "bedFile.h"
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20 using namespace std;
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21
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22
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23 // define our program name
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24 #define PROGRAM_NAME "overlap"
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25
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26 // define our parameter checking macro
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27 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
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28
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29
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30 // function declarations
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31 void ShowHelp(void);
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32 void DetermineInput(string &inFile, short &s1Col, short &e1Col, short &s2Col, short &e2Col);
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33 void ComputeOverlaps(istream &input, short &s1Col, short &e1Col, short &s2Col, short &e2Col);
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34
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35 int main(int argc, char* argv[]) {
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36
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37 // input files
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38 string inFile = "stdin";
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39 string columns;
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40
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41 // our configuration variables
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42 bool showHelp = false;
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43 bool haveInFile = true;
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44 bool haveColumns = false;
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45
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46
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47 for(int i = 1; i < argc; i++) {
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48 int parameterLength = (int)strlen(argv[i]);
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49
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50 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
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51 (PARAMETER_CHECK("--help", 5, parameterLength))) {
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52 showHelp = true;
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53 }
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54 }
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55
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56 if(showHelp) ShowHelp();
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57
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58 // do some parsing (all of these parameters require 2 strings)
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59 for(int i = 1; i < argc; i++) {
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60
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61 int parameterLength = (int)strlen(argv[i]);
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62
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63 if(PARAMETER_CHECK("-i", 2, parameterLength)) {
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64 if ((i+1) < argc) {
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65 inFile = argv[i + 1];
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66 i++;
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67 }
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68 }
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69 else if(PARAMETER_CHECK("-cols", 5, parameterLength)) {
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70 haveColumns = true;
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71 columns = argv[i + 1];
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72 i++;
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73 }
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74 else {
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75 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
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76 showHelp = true;
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77 }
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78 }
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79
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80 // make sure we have an input files
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81 if (!haveInFile ) {
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82 cerr << endl << "*****" << endl << "*****ERROR: Need -i file. " << endl << "*****" << endl;
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83 showHelp = true;
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84 }
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85
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86 if (!showHelp) {
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87
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88 // Split the column string sent by the user into discrete column numbers
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89 // A comma separated string is expected.
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90 vector<string> posColumns;
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91 Tokenize(columns, posColumns, ",");
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92
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93 if (posColumns.size() != 4) {
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94 cerr << endl << "*****" << endl << "*****ERROR: Please specify 4, comma-separated position columns. " << endl << "*****" << endl;
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95 ShowHelp();
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96 }
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97 else {
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98 short s1, e1, s2, e2;
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99 s1 = atoi(posColumns[0].c_str());
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100 e1 = atoi(posColumns[1].c_str());
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101 s2 = atoi(posColumns[2].c_str());
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102 e2 = atoi(posColumns[3].c_str());
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103
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104 DetermineInput(inFile, s1, e1, s2, e2);
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105 }
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106 }
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107 else {
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108 ShowHelp();
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109 }
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110 }
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111
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112 void ShowHelp(void) {
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113
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114 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
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115
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116 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
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117
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118 cerr << "Summary: Computes the amount of overlap (positive values)" << endl;
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119 cerr << "\t or distance (negative values) between genome features" << endl;
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120 cerr << "\t and reports the result at the end of the same line." << endl << endl;
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121
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122 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input> -cols s1,e1,s2,e2 " << endl << endl;
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123
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124 cerr << "Options: " << endl;
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125 cerr << "\t-i\t" << "Input file. Use \"stdin\" for pipes." << endl << endl;
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126
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127 cerr << "\t-cols\t" << "Specify the columns (1-based) for the starts and ends of the" << endl;
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128 cerr << "\t\tfeatures for which you'd like to compute the overlap/distance." << endl;
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129 cerr << "\t\tThe columns must be listed in the following order: " << endl << endl;
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130 cerr << "\t\tstart1,end1,start2,end2" << endl << endl;
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131
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132 cerr << "Example: " << endl;
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133 cerr << "\t$ windowBed -a A.bed -b B.bed -w 10" << endl;
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134 cerr << "\tchr1 10 20 A chr1 15 25 B" << endl;
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135 cerr << "\tchr1 10 20 C chr1 25 35 D" << endl << endl;
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136 cerr << "\t$ windowBed -a A.bed -b B.bed -w 10 | overlap -i stdin -cols 2,3,6,7" << endl;
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137 cerr << "\tchr1 10 20 A chr1 15 25 B 5" << endl;
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138 cerr << "\tchr1 10 20 C chr1 25 35 D -5" << endl;
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139
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140 // end the program here
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141 exit(1);
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142
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143 }
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144
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145
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146 void DetermineInput(string &inFile, short &s1Col, short &e1Col, short &s2Col, short &e2Col) {
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147
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148
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149 if (inFile != "stdin") { // process a file
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150
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151 ifstream in(inFile.c_str(), ios::in);
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152 if ( !in ) {
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153 cerr << "Error: The requested input file (" << inFile << ") could not be opened. Exiting!" << endl;
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154 exit (1);
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155 }
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156 ComputeOverlaps(in, s1Col, e1Col, s2Col, e2Col);
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157 }
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158 else ComputeOverlaps(cin, s1Col, e1Col, s2Col, e2Col);
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159 }
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160
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161
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162 void ComputeOverlaps(istream &input, short &s1Col, short &e1Col, short &s2Col, short &e2Col) {
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163
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164 int lineNum = 0;
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165 string inLine;
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166 vector<string> inFields;
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167
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168 int overlap;
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169
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170 char *s1End, *e1End, *s2End, *e2End;
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171 long s1, e1, s2, e2;
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172
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173 while (getline(input, inLine)) {
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174 lineNum++;
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175 Tokenize(inLine, inFields);
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176
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177 if (inFields.size() > 1) {
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178
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179 // test if columns 2 and 3 are integers. If so, assume BED.
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180 s1 = strtol(inFields[s1Col-1].c_str(), &s1End, 10);
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181 e1 = strtol(inFields[e1Col-1].c_str(), &e1End, 10);
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182 s2 = strtol(inFields[s2Col-1].c_str(), &s2End, 10);
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183 e2 = strtol(inFields[e2Col-1].c_str(), &e2End, 10);
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184
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185 // strtol will set pointers to the start of the string if non-integral, base 10
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186 // if they all check out, we have valid numeric columns. Otherwise, complain.
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187 if (s1End != inFields[s1Col-1].c_str() &&
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188 e1End != inFields[e1Col-1].c_str() &&
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189 s2End != inFields[s2Col-1].c_str() &&
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190 e2End != inFields[e2Col-1].c_str()) {
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191
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192 overlap = overlaps(s1, e1, s2, e2);
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193 printf("%s\t%d\n", inLine.c_str(), overlap);
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194 }
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195 else {
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196 cerr << "One of your columns appears to be non-numeric at line " << lineNum << ". Exiting..." << endl << endl;
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197 exit(1);
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198 }
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199 }
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200 inFields.clear();
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201 }
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202 }
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