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1 /*****************************************************************************
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2 complementBedMain.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 "complementBed.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 "complementBed"
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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 string genomeFile;
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35
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36 bool haveBed = true;
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37 bool haveGenome = false;
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38
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39 for(int i = 1; i < argc; i++) {
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40 int parameterLength = (int)strlen(argv[i]);
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41
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42 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
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43 (PARAMETER_CHECK("--help", 5, parameterLength))) {
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44 showHelp = true;
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45 }
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46 }
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47
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48 if(showHelp) ShowHelp();
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49
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50 // do some parsing (all of these parameters require 2 strings)
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51 for(int i = 1; i < argc; i++) {
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52
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53 int parameterLength = (int)strlen(argv[i]);
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54
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55 if(PARAMETER_CHECK("-i", 2, parameterLength)) {
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56 if ((i+1) < argc) {
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57 bedFile = argv[i + 1];
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58 i++;
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59 }
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60 }
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61 else if(PARAMETER_CHECK("-g", 2, parameterLength)) {
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62 if ((i+1) < argc) {
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63 haveGenome = true;
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64 genomeFile = argv[i + 1];
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65 i++;
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66 }
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67 }
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68 else {
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69 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
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70 showHelp = true;
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71 }
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72 }
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73
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74 // make sure we have both input files
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75 if (!haveBed || !haveGenome) {
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76 cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file and -g Genome file. " << endl << "*****" << endl;
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77 showHelp = true;
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78 }
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79 if (!showHelp) {
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80 BedComplement *bc = new BedComplement(bedFile, genomeFile);
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81 bc->ComplementBed();
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82 return 0;
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83 }
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84 else {
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85 ShowHelp();
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86 }
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87 }
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88
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89 void ShowHelp(void) {
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90
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91 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
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92
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93 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
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94
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95 cerr << "Summary: Returns the base pair complement of a feature file." << endl << endl;
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96
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97 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome>" << endl << endl;
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98
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99 cerr << "Notes: " << endl;
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100 cerr << "\t(1) The genome file should tab delimited and structured as follows:" << endl;
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101 cerr << "\t <chromName><TAB><chromSize>" << endl << endl;
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102 cerr << "\tFor example, Human (hg19):" << endl;
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103 cerr << "\tchr1\t249250621" << endl;
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104 cerr << "\tchr2\t243199373" << endl;
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105 cerr << "\t..." << endl;
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106 cerr << "\tchr18_gl000207_random\t4262" << endl << endl;
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107
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108 cerr << "Tips: " << endl;
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109 cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract" << endl;
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110 cerr << "\tchromosome sizes. For example, H. sapiens:" << endl << endl;
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111 cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\" << endl;
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112 cerr << "\t\"select chrom, size from hg19.chromInfo\" > hg19.genome" << endl << endl;
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113
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114 exit(1);
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115
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116 }
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