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comparison BEDTools-Version-2.14.3/src/annotateBed/annotateMain.cpp @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 annotateMain.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 "annotateBed.h"
13 #include "version.h"
14
15 using namespace std;
16
17 // define the version
18 #define PROGRAM_NAME "annotateBed"
19
20 // define our parameter checking macro
21 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
22
23 // function declarations
24 void ShowHelp(void);
25
26 int main(int argc, char* argv[]) {
27
28 // our configuration variables
29 bool showHelp = false;
30
31 // input file
32 string mainFile;
33
34 // parm flags
35 bool sameStrand = false;
36 bool diffStrand = false;
37 bool haveBed = false;
38 bool haveFiles = false;
39 bool haveTitles = false;
40 bool reportCounts = false;
41 bool reportBoth = false;
42
43 // list of annotation files / names
44 vector<string> inputFiles;
45 vector<string> inputTitles;
46
47 // check to see if we should print out some help
48 if(argc <= 1) showHelp = true;
49
50 for(int i = 1; i < argc; i++) {
51 int parameterLength = (int)strlen(argv[i]);
52
53 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
54 (PARAMETER_CHECK("--help", 5, parameterLength))) {
55 showHelp = true;
56 }
57 }
58
59 if(showHelp) ShowHelp();
60
61 // do some parsing (all of these parameters require 2 strings)
62 for(int i = 1; i < argc; i++) {
63
64 int parameterLength = (int)strlen(argv[i]);
65
66 if(PARAMETER_CHECK("-i", 2, parameterLength)) {
67 if ((i+1) < argc) {
68 haveBed = true;
69 mainFile = argv[i + 1];
70 i++;
71 }
72 }
73 else if(PARAMETER_CHECK("-files", 6, parameterLength)) {
74 if ((i+1) < argc) {
75 haveFiles = true;
76 i = i+1;
77 string file = argv[i];
78 while (file[0] != '-' && i < argc) {
79 inputFiles.push_back(file);
80 i++;
81 if (i < argc)
82 file = argv[i];
83 }
84 i--;
85 }
86 }
87 else if(PARAMETER_CHECK("-names", 6, parameterLength)) {
88 if ((i+1) < argc) {
89 haveTitles = true;
90 i = i+1;
91 string title = argv[i];
92 while (title[0] != '-' && i < argc) {
93 inputTitles.push_back(title);
94 i++;
95 if (i < argc)
96 title = argv[i];
97 }
98 i--;
99 }
100 }
101 else if(PARAMETER_CHECK("-counts", 7, parameterLength)) {
102 reportCounts = true;
103 }
104 else if(PARAMETER_CHECK("-both", 5, parameterLength)) {
105 reportBoth = true;
106 }
107 else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
108 sameStrand = true;
109 }
110 else if (PARAMETER_CHECK("-S", 2, parameterLength)) {
111 diffStrand = true;
112 }
113 else {
114 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
115 showHelp = true;
116 }
117 }
118
119 // make sure we have both input files
120 if (!haveBed || !haveFiles) {
121 cerr << endl << "*****" << endl << "*****ERROR: Need -i and -files files. " << endl << "*****" << endl;
122 showHelp = true;
123 }
124 if (sameStrand && diffStrand) {
125 cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl;
126 showHelp = true;
127 }
128
129 if (!showHelp) {
130 BedAnnotate *ba = new BedAnnotate(mainFile, inputFiles, inputTitles, sameStrand, diffStrand, reportCounts, reportBoth);
131 ba->AnnotateBed();
132 delete ba;
133 return 0;
134 }
135 else {
136 ShowHelp();
137 }
138 }
139
140 void ShowHelp(void) {
141
142 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
143
144 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
145
146 cerr << "Summary: Annotates the depth & breadth of coverage of features from multiple files" << endl;
147 cerr << "\t on the intervals in -i." << endl << endl;
148
149 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -files FILE1 FILE2 .. FILEn" << endl << endl;
150
151 cerr << "Options: " << endl;
152
153 cerr << "\t-names\t" << "A list of names (one / file) to describe each file in -i." << endl;
154 cerr << "\t\tThese names will be printed as a header line." << endl << endl;
155
156 cerr << "\t-counts\t" << "Report the count of features in each file that overlap -i." << endl;
157 cerr << "\t\t- Default is to report the fraction of -i covered by each file." << endl << endl;
158
159 cerr << "\t-both\t" << "Report the counts followed by the % coverage." << endl;
160 cerr << "\t\t- Default is to report the fraction of -i covered by each file." << endl << endl;
161
162 cerr << "\t-s\t" << "Require same strandedness. That is, only counts overlaps" << endl;
163 cerr << "\t\ton the _same_ strand." << endl;
164 cerr << "\t\t- By default, overlaps are counted without respect to strand." << endl << endl;
165
166 cerr << "\t-S\t" << "Require different strandedness. That is, only count overlaps" << endl;
167 cerr << "\t\ton the _opposite_ strand." << endl;
168 cerr << "\t\t- By default, overlaps are counted without respect to strand." << endl << endl;
169 exit(1);
170 }