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1 /*****************************************************************************
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2 sortBedMain.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 "sortBed.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 "sortBed"
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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 bedFile = "stdin";
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34 bool haveBed = true;
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35 int sortChoices = 0;
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36
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37 bool sortBySizeAsc = false;
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38 bool sortBySizeDesc = false;
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39 bool sortByChromThenSizeAsc = false;
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40 bool sortByChromThenSizeDesc = false;
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41 bool sortByChromThenScoreAsc = false;
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42 bool sortByChromThenScoreDesc = false;
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43
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44
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45 for(int i = 1; i < argc; i++) {
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46 int parameterLength = (int)strlen(argv[i]);
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47
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48 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
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49 (PARAMETER_CHECK("--help", 5, parameterLength))) {
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50 showHelp = true;
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51 }
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52 }
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53
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54 if(showHelp) ShowHelp();
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55
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56 // do some parsing (all of these parameters require 2 strings)
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57 for(int i = 1; i < argc; i++) {
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58
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59 int parameterLength = (int)strlen(argv[i]);
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60
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61 if(PARAMETER_CHECK("-i", 2, parameterLength)) {
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62 if ((i+1) < argc) {
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63 bedFile = argv[i + 1];
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64 i++;
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65 }
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66 }
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67 else if(PARAMETER_CHECK("-sizeA", 6, parameterLength)) {
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68 sortBySizeAsc = true;
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69 sortChoices++;
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70 }
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71 else if(PARAMETER_CHECK("-sizeD", 6, parameterLength)) {
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72 sortBySizeDesc = true;
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73 sortChoices++;
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74 }
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75 else if(PARAMETER_CHECK("-chrThenSizeA", 13, parameterLength)) {
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76 sortByChromThenSizeAsc = true;
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77 sortChoices++;
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78 }
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79 else if(PARAMETER_CHECK("-chrThenSizeD", 13, parameterLength)) {
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80 sortByChromThenSizeDesc = true;
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81 sortChoices++;
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82 }
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83 else if(PARAMETER_CHECK("-chrThenScoreA", 14, parameterLength)) {
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84 sortByChromThenScoreAsc = true;
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85 sortChoices++;
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86 }
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87 else if(PARAMETER_CHECK("-chrThenScoreD", 14, parameterLength)) {
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88 sortByChromThenScoreDesc = true;
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89 sortChoices++;
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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 (!haveBed) {
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99 cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file. " << endl << "*****" << endl;
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100 showHelp = true;
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101 }
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102 if (sortChoices > 1) {
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103 cerr << endl << "*****" << endl << "*****ERROR: Sorting options are mutually exclusive. Please choose just one. " << endl << "*****" << endl;
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104 showHelp = true;
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105 }
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106
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107
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108 if (!showHelp) {
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109 BedSort *bm = new BedSort(bedFile);
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110
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111 if (sortBySizeAsc) {
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112 bm->SortBedBySizeAsc();
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113 }
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114 else if (sortBySizeDesc) {
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115 bm->SortBedBySizeDesc();
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116 }
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117 else if (sortByChromThenSizeAsc) {
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118 bm->SortBedByChromThenSizeAsc();
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119 }
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120 else if (sortByChromThenSizeDesc) {
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121 bm->SortBedByChromThenSizeDesc();
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122 }
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123 else if (sortByChromThenScoreAsc) {
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124 bm->SortBedByChromThenScoreAsc();
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125 }
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126 else if (sortByChromThenScoreDesc) {
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127 bm->SortBedByChromThenScoreDesc();
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128 }
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129 else {
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130 bm->SortBed();
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131 }
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132 return 0;
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133 }
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134 else {
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135 ShowHelp();
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136 }
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137 }
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138
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139 void ShowHelp(void) {
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140
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141 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
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142
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143 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
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144 cerr << "Summary: Sorts a feature file in various and useful ways." << endl << endl;
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145 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf>" << endl << endl;
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146
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147 cerr << "Options: " << endl;
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148 cerr << "\t" << "-sizeA\t\t" << "Sort by feature size in ascending order." << endl;
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149 cerr << "\t" << "-sizeD\t\t" << "Sort by feature size in descending order." << endl;
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150 cerr << "\t" << "-chrThenSizeA\t" << "Sort by chrom (asc), then feature size (asc)." << endl;
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151 cerr << "\t" << "-chrThenSizeD\t" << "Sort by chrom (asc), then feature size (desc)." << endl;
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152 cerr << "\t" << "-chrThenScoreA\t" << "Sort by chrom (asc), then score (asc)." << endl;
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153 cerr << "\t" << "-chrThenScoreD\t" << "Sort by chrom (asc), then score (desc)." << endl << endl;
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154
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155 exit(1);
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156
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157 }
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