Mercurial > repos > aaronquinlan > multi_intersect

comparison BEDTools-Version-2.14.3/src/linksBed/linksMain.cpp @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 linksBedMain.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 "linksBed.h"
13 #include "version.h"
14
15 using namespace std;
16
17 // define our program name
18 #define PROGRAM_NAME "linksBed"
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 bedFile = "stdin";
34 bool haveBed = true;
35
36 /* Defaults for everyone else */
37 string org = "human";
38 string db = "hg18";
39 string base = "http://genome.ucsc.edu";
40
41 for(int i = 1; i < argc; i++) {
42 int parameterLength = (int)strlen(argv[i]);
43
44 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
45 (PARAMETER_CHECK("--help", 5, parameterLength))) {
46 showHelp = true;
47 }
48 }
49
50 if(showHelp) ShowHelp();
51
52 // do some parsing (all of these parameters require 2 strings)
53 for(int i = 1; i < argc; i++) {
54
55 int parameterLength = (int)strlen(argv[i]);
56
57 if(PARAMETER_CHECK("-i", 2, parameterLength)) {
58 if ((i+1) < argc) {
59 bedFile = argv[i + 1];
60 i++;
61 }
62 }
63 else if(PARAMETER_CHECK("-base", 5, parameterLength)) {
64 if ((i+1) < argc) {
65 base = argv[i + 1];
66 i++;
67 }
68 }
69 else if(PARAMETER_CHECK("-org", 4, parameterLength)) {
70 if ((i+1) < argc) {
71 org = argv[i + 1];
72 i++;
73 }
74 }
75 else if(PARAMETER_CHECK("-db", 3, parameterLength)) {
76 if ((i+1) < argc) {
77 db = argv[i + 1];
78 i++;
79 }
80 }
81 else {
82 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
83 showHelp = true;
84 }
85 }
86
87 // make sure we have both input files
88 if (!haveBed) {
89 cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file. " << endl << "*****" << endl;
90 showHelp = true;
91 }
92
93 if (!showHelp) {
94 BedLinks *bl = new BedLinks(bedFile, base, org, db);
95 delete bl;
96 return 0;
97 }
98 else {
99 ShowHelp();
100 }
101 }
102
103 void ShowHelp(void) {
104
105 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
106
107 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
108
109 cerr << "Summary: Creates HTML links to an UCSC Genome Browser from a feature file." << endl << endl;
110 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> > out.html" << endl << endl;
111
112 cerr << "Options: " << endl;
113 cerr << "\t-base\t" << "The browser basename. Default: http://genome.ucsc.edu " << endl;
114 cerr << "\t-org\t" << "The organism. Default: human" << endl;
115 cerr << "\t-db\t" << "The build. Default: hg18" << endl << endl;
116
117 cerr << "Example: " << endl;
118 cerr << "\t" << "By default, the links created will point to human (hg18) UCSC browser." << endl;
119 cerr << "\tIf you have a local mirror, you can override this behavior by supplying" << endl;
120 cerr << "\tthe -base, -org, and -db options." << endl << endl;
121 cerr << "\t" << "For example, if the URL of your local mirror for mouse MM9 is called: " << endl;
122 cerr << "\thttp://mymirror.myuniversity.edu, then you would use the following:" << endl;
123 cerr << "\t" << "-base http://mymirror.myuniversity.edu" << endl;
124 cerr << "\t" << "-org mouse" << endl;
125 cerr << "\t" << "-db mm9" << endl;
126
127
128 exit(1);
129 }