Mercurial > repos > aaronquinlan > multi_intersect

comparison BEDTools-Version-2.14.3/src/complementBed/complementMain.cpp @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 complementBedMain.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 "complementBed.h"
13 #include "version.h"
14
15 using namespace std;
16
17 // define our program name
18 #define PROGRAM_NAME "complementBed"
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 string genomeFile;
35
36 bool haveBed = true;
37 bool haveGenome = false;
38
39 for(int i = 1; i < argc; i++) {
40 int parameterLength = (int)strlen(argv[i]);
41
42 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
43 (PARAMETER_CHECK("--help", 5, parameterLength))) {
44 showHelp = true;
45 }
46 }
47
48 if(showHelp) ShowHelp();
49
50 // do some parsing (all of these parameters require 2 strings)
51 for(int i = 1; i < argc; i++) {
52
53 int parameterLength = (int)strlen(argv[i]);
54
55 if(PARAMETER_CHECK("-i", 2, parameterLength)) {
56 if ((i+1) < argc) {
57 bedFile = argv[i + 1];
58 i++;
59 }
60 }
61 else if(PARAMETER_CHECK("-g", 2, parameterLength)) {
62 if ((i+1) < argc) {
63 haveGenome = true;
64 genomeFile = argv[i + 1];
65 i++;
66 }
67 }
68 else {
69 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
70 showHelp = true;
71 }
72 }
73
74 // make sure we have both input files
75 if (!haveBed || !haveGenome) {
76 cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file and -g Genome file. " << endl << "*****" << endl;
77 showHelp = true;
78 }
79 if (!showHelp) {
80 BedComplement *bc = new BedComplement(bedFile, genomeFile);
81 bc->ComplementBed();
82 return 0;
83 }
84 else {
85 ShowHelp();
86 }
87 }
88
89 void ShowHelp(void) {
90
91 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
92
93 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
94
95 cerr << "Summary: Returns the base pair complement of a feature file." << endl << endl;
96
97 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome>" << endl << endl;
98
99 cerr << "Notes: " << endl;
100 cerr << "\t(1) The genome file should tab delimited and structured as follows:" << endl;
101 cerr << "\t <chromName><TAB><chromSize>" << endl << endl;
102 cerr << "\tFor example, Human (hg19):" << endl;
103 cerr << "\tchr1\t249250621" << endl;
104 cerr << "\tchr2\t243199373" << endl;
105 cerr << "\t..." << endl;
106 cerr << "\tchr18_gl000207_random\t4262" << endl << endl;
107
108 cerr << "Tips: " << endl;
109 cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract" << endl;
110 cerr << "\tchromosome sizes. For example, H. sapiens:" << endl << endl;
111 cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\" << endl;
112 cerr << "\t\"select chrom, size from hg19.chromInfo\" > hg19.genome" << endl << endl;
113
114 exit(1);
115
116 }