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1 /*****************************************************************************
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2 maskFastaFromBedMain.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 "maskFastaFromBed.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 "maskFastaFromBed"
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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 fastaInFile;
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34 string bedFile;
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35
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36 // output files
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37 string fastaOutFile;
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38
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39 // defaults for parameters
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40 bool haveFastaIn = false;
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41 bool haveBed = false;
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42 bool haveFastaOut = false;
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43 bool softMask = false;
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44 char maskChar = 'N';
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45
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46 // check to see if we should print out some help
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47 if(argc <= 1) showHelp = true;
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48
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49 for(int i = 1; i < argc; i++) {
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50 int parameterLength = (int)strlen(argv[i]);
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51
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52 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
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53 (PARAMETER_CHECK("--help", 5, parameterLength))) {
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54 showHelp = true;
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55 }
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56 }
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57
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58 if(showHelp) ShowHelp();
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59
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60 // do some parsing (all of these parameters require 2 strings)
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61 for(int i = 1; i < argc; i++) {
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62
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63 int parameterLength = (int)strlen(argv[i]);
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64
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65 if(PARAMETER_CHECK("-fi", 3, parameterLength)) {
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66 if ((i+1) < argc) {
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67 haveFastaIn = true;
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68 fastaInFile = argv[i + 1];
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69 i++;
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70 }
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71 }
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72 else if(PARAMETER_CHECK("-fo", 3, parameterLength)) {
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73 if ((i+1) < argc) {
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74 haveFastaOut = true;
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75 fastaOutFile = argv[i + 1];
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76 i++;
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77 }
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78 }
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79 else if(PARAMETER_CHECK("-bed", 4, parameterLength)) {
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80 if ((i+1) < argc) {
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81 haveBed = true;
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82 bedFile = argv[i + 1];
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83 i++;
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84 }
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85 }
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86 else if(PARAMETER_CHECK("-soft", 5, parameterLength)) {
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87 softMask = true;
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88 }
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89 else if(PARAMETER_CHECK("-mc", 3, parameterLength)) {
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90 if ((i+1) < argc) {
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91 string mask = argv[i + 1];
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92 if (mask.size() > 1) {
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93 cerr << "*****ERROR: The mask character (-mc) should be a single character.*****" << endl << endl;
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94 showHelp = true;
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95 }
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96 else {
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97 maskChar = mask[0];
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98 }
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99 i++;
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100 }
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101 }
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102 else {
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103 cerr << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << 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 (!haveFastaIn || !haveFastaOut || !haveBed) {
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109 showHelp = true;
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110 }
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111
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112 if (!showHelp) {
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113
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114 MaskFastaFromBed *maskFasta = new MaskFastaFromBed(fastaInFile, bedFile, fastaOutFile, softMask, maskChar);
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115 delete maskFasta;
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116 return 0;
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117 }
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118 else {
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119 ShowHelp();
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120 }
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121 }
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122
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123 void ShowHelp(void) {
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124
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125
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126
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127 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
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128
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129 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
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130
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131 cerr << "Summary: Mask a fasta file based on feature coordinates." << endl << endl;
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132
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133 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -fi <fasta> -out <fasta> -bed <bed/gff/vcf>" << endl << endl;
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134
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135 cerr << "Options:" << endl;
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136 cerr << "\t-fi\tInput FASTA file" << endl;
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137 cerr << "\t-bed\tBED/GFF/VCF file of ranges to mask in -fi" << endl;
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138 cerr << "\t-fo\tOutput FASTA file" << endl;
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139 cerr << "\t-soft\tEnforce \"soft\" masking. That is, instead of masking with Ns," << endl;
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140 cerr << "\t\tmask with lower-case bases." << endl;
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141 cerr << "\t-mc\tReplace masking character. That is, instead of masking with Ns, use another character." << 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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146 }
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