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1 /*****************************************************************************
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2 bed12ToBed6.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 "lineFileUtilities.h"
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13 #include "bedFile.h"
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14 #include "version.h"
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15
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16 #include <vector>
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17 #include <iostream>
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18 #include <fstream>
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19 #include <stdlib.h>
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20
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21 using namespace std;
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22
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23
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24 // define our program name
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25 #define PROGRAM_NAME "bed12ToBed6"
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26
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27 // define our parameter checking macro
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28 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
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29
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30
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31 // function declarations
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32 void ShowHelp(void);
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33 void DetermineBedInput(BedFile *bed);
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34 void ProcessBed(istream &bedInput, BedFile *bed);
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35
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36
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37 bool addBlockNums = false;
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38
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39 int main(int argc, char* argv[]) {
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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
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44 // input files
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45 string bedFile = "stdin";
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46 bool haveBed = 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("-i", 2, parameterLength)) {
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65 if ((i+1) < argc) {
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66 bedFile = argv[i + 1];
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67 i++;
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68 }
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69 }
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70 else if(PARAMETER_CHECK("-n", 2, parameterLength)) {
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71 addBlockNums = true;
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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 (!haveBed ) {
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82 cerr << endl << "*****" << endl << "*****ERROR: Need -i (BED) 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 BedFile *bed = new BedFile(bedFile);
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88 DetermineBedInput(bed);
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89 }
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90 else {
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91 ShowHelp();
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92 }
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93 }
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94
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95
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96 void ShowHelp(void) {
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97
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98 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
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99
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100 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
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101
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102 cerr << "Summary: Splits BED12 features into discrete BED6 features." << endl << endl;
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103
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104 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed12>" << endl << endl;
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105
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106 cerr << "Options: " << endl;
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107
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108 cerr << "\t-n\t" << "Force the score to be the (1-based) block number from the BED12." << endl << endl;
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109
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110
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111 // end the program here
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112 exit(1);
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113 }
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114
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115
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116 void DetermineBedInput(BedFile *bed) {
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117
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118 // dealing with a proper file
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119 if (bed->bedFile != "stdin") {
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120
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121 ifstream bedStream(bed->bedFile.c_str(), ios::in);
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122 if ( !bedStream ) {
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123 cerr << "Error: The requested bed file (" << bed->bedFile << ") could not be opened. Exiting!" << endl;
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124 exit (1);
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125 }
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126 ProcessBed(bedStream, bed);
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127 }
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128 // reading from stdin
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129 else {
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130 ProcessBed(cin, bed);
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131 }
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132 }
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133
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134
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135 void ProcessBed(istream &bedInput, BedFile *bed) {
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136
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137 // process each BED entry and convert to BAM
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138 BED bedEntry, nullBed;
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139 int lineNum = 0;
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140 BedLineStatus bedStatus;
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141 // open the BED file for reading.
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142 bed->Open();
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143 while ((bedStatus = bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) {
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144 if (bedStatus == BED_VALID) {
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145
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146 bedVector bedBlocks; // vec to store the discrete BED "blocks" from a
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147 splitBedIntoBlocks(bedEntry, lineNum, bedBlocks);
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148
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149 for (int i = 0; i < (int) bedBlocks.size(); ++i) {
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150 if (addBlockNums == false) {
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151 printf ("%s\t%d\t%d\t%s\t%s\t%s\n", bedBlocks[i].chrom.c_str(), bedBlocks[i].start, bedBlocks[i].end, bedBlocks[i].name.c_str(),
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152 bedBlocks[i].score.c_str(), bedBlocks[i].strand.c_str());
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153 }
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154 else {
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155 if (bedBlocks[i].strand == "+")
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156 printf ("%s\t%d\t%d\t%s\t%d\t%s\n", bedBlocks[i].chrom.c_str(), bedBlocks[i].start, bedBlocks[i].end, bedBlocks[i].name.c_str(),
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157 i+1, bedBlocks[i].strand.c_str());
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158 else
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159 printf ("%s\t%d\t%d\t%s\t%d\t%s\n", bedBlocks[i].chrom.c_str(), bedBlocks[i].start, bedBlocks[i].end, bedBlocks[i].name.c_str(),
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160 (int) ((bedBlocks.size()+1)-i), bedBlocks[i].strand.c_str());
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161 }
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162 }
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163 bedEntry = nullBed;
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164 }
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165 }
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166 // close up
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167 bed->Close();
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168 }
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