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comparison BEDTools-Version-2.14.3/src/maskFastaFromBed/maskFastaFromBedMain.cpp @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 maskFastaFromBedMain.cpp
3
4 (c) 2009 - Aaron Quinlan
5 Hall Laboratory
6 Department of Biochemistry and Molecular Genetics
7 University of Virginia
8 aaronquinlan@gmail.com
9
10 Licenced under the GNU General Public License 2.0 license.
11 ******************************************************************************/
12 #include "maskFastaFromBed.h"
13 #include "version.h"
14
15 using namespace std;
16
17 // define our program name
18 #define PROGRAM_NAME "maskFastaFromBed"
19
20
21 // define our parameter checking macro
22 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
23
24 // function declarations
25 void ShowHelp(void);
26
27 int main(int argc, char* argv[]) {
28
29 // our configuration variables
30 bool showHelp = false;
31
32 // input files
33 string fastaInFile;
34 string bedFile;
35
36 // output files
37 string fastaOutFile;
38
39 // defaults for parameters
40 bool haveFastaIn = false;
41 bool haveBed = false;
42 bool haveFastaOut = false;
43 bool softMask = false;
44 char maskChar = 'N';
45
46 // check to see if we should print out some help
47 if(argc <= 1) showHelp = true;
48
49 for(int i = 1; i < argc; i++) {
50 int parameterLength = (int)strlen(argv[i]);
51
52 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
53 (PARAMETER_CHECK("--help", 5, parameterLength))) {
54 showHelp = true;
55 }
56 }
57
58 if(showHelp) ShowHelp();
59
60 // do some parsing (all of these parameters require 2 strings)
61 for(int i = 1; i < argc; i++) {
62
63 int parameterLength = (int)strlen(argv[i]);
64
65 if(PARAMETER_CHECK("-fi", 3, parameterLength)) {
66 if ((i+1) < argc) {
67 haveFastaIn = true;
68 fastaInFile = argv[i + 1];
69 i++;
70 }
71 }
72 else if(PARAMETER_CHECK("-fo", 3, parameterLength)) {
73 if ((i+1) < argc) {
74 haveFastaOut = true;
75 fastaOutFile = argv[i + 1];
76 i++;
77 }
78 }
79 else if(PARAMETER_CHECK("-bed", 4, parameterLength)) {
80 if ((i+1) < argc) {
81 haveBed = true;
82 bedFile = argv[i + 1];
83 i++;
84 }
85 }
86 else if(PARAMETER_CHECK("-soft", 5, parameterLength)) {
87 softMask = true;
88 }
89 else if(PARAMETER_CHECK("-mc", 3, parameterLength)) {
90 if ((i+1) < argc) {
91 string mask = argv[i + 1];
92 if (mask.size() > 1) {
93 cerr << "*****ERROR: The mask character (-mc) should be a single character.*****" << endl << endl;
94 showHelp = true;
95 }
96 else {
97 maskChar = mask[0];
98 }
99 i++;
100 }
101 }
102 else {
103 cerr << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
104 showHelp = true;
105 }
106 }
107
108 if (!haveFastaIn || !haveFastaOut || !haveBed) {
109 showHelp = true;
110 }
111
112 if (!showHelp) {
113
114 MaskFastaFromBed *maskFasta = new MaskFastaFromBed(fastaInFile, bedFile, fastaOutFile, softMask, maskChar);
115 delete maskFasta;
116 return 0;
117 }
118 else {
119 ShowHelp();
120 }
121 }
122
123 void ShowHelp(void) {
124
125
126
127 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
128
129 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
130
131 cerr << "Summary: Mask a fasta file based on feature coordinates." << endl << endl;
132
133 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -fi <fasta> -out <fasta> -bed <bed/gff/vcf>" << endl << endl;
134
135 cerr << "Options:" << endl;
136 cerr << "\t-fi\tInput FASTA file" << endl;
137 cerr << "\t-bed\tBED/GFF/VCF file of ranges to mask in -fi" << endl;
138 cerr << "\t-fo\tOutput FASTA file" << endl;
139 cerr << "\t-soft\tEnforce \"soft\" masking. That is, instead of masking with Ns," << endl;
140 cerr << "\t\tmask with lower-case bases." << endl;
141 cerr << "\t-mc\tReplace masking character. That is, instead of masking with Ns, use another character." << endl;
142
143 // end the program here
144 exit(1);
145
146 }