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comparison BEDTools-Version-2.14.3/src/pairToPair/pairToPairMain.cpp @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 pairToPairMain.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 "pairToPair.h"
13 #include "version.h"
14
15 using namespace std;
16
17 // define our program name
18 #define PROGRAM_NAME "pairToPair"
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 files
32 string bedAFile;
33 string bedBFile;
34
35 // input arguments
36 float overlapFraction = 1E-9;
37 int slop = 0;
38 string searchType = "both";
39
40 // flags to track parameters
41 bool haveBedA = false;
42 bool haveBedB = false;
43 bool haveSearchType = false;
44 bool haveFraction = false;
45 bool ignoreStrand = false;
46 bool requireDifferentNames = false;
47 bool haveSlop = false;
48 bool strandedSlop = false;
49 // check to see if we should print out some help
50 if(argc <= 1) showHelp = true;
51
52 for(int i = 1; i < argc; i++) {
53 int parameterLength = (int)strlen(argv[i]);
54
55 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
56 (PARAMETER_CHECK("--help", 5, parameterLength))) {
57 showHelp = true;
58 }
59 }
60
61 if(showHelp) ShowHelp();
62
63 // do some parsing (all of these parameters require 2 strings)
64 for(int i = 1; i < argc; i++) {
65
66 int parameterLength = (int)strlen(argv[i]);
67
68 if(PARAMETER_CHECK("-a", 2, parameterLength)) {
69 if ((i+1) < argc) {
70 haveBedA = true;
71 bedAFile = argv[i + 1];
72 i++;
73 }
74 }
75 else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
76 if ((i+1) < argc) {
77 haveBedB = true;
78 bedBFile = argv[i + 1];
79 i++;
80 }
81 }
82 else if(PARAMETER_CHECK("-type", 5, parameterLength)) {
83 if ((i+1) < argc) {
84 haveSearchType = true;
85 searchType = argv[i + 1];
86 i++;
87 }
88 }
89 else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
90 if ((i+1) < argc) {
91 haveFraction = true;
92 overlapFraction = atof(argv[i + 1]);
93 i++;
94 }
95 }
96 else if(PARAMETER_CHECK("-slop", 5, parameterLength)) {
97 if ((i+1) < argc) {
98 haveSlop = true;
99 slop = atoi(argv[i + 1]);
100 i++;
101 }
102 }
103 else if(PARAMETER_CHECK("-ss", 3, parameterLength)) {
104 strandedSlop = true;
105 }
106 else if(PARAMETER_CHECK("-rdn", 4, parameterLength)) {
107 requireDifferentNames = true;
108 }
109 else if(PARAMETER_CHECK("-is", 3, parameterLength)) {
110 ignoreStrand = true;
111 }
112 else {
113 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
114 showHelp = true;
115 }
116 }
117
118
119 // make sure we have both input files
120 if (!haveBedA || !haveBedB) {
121 cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
122 showHelp = true;
123 }
124
125 if (haveSearchType && (searchType != "neither") && (searchType != "both") && (searchType != "either") && (searchType != "notboth")) {
126 cerr << endl << "*****" << endl << "*****ERROR: Request \"both\",\"neither\",\"either\",or \"notboth\"" << endl << "*****" << endl;
127 showHelp = true;
128 }
129
130 if (strandedSlop == true && haveSlop == false) {
131 cerr << endl << "*****" << endl << "*****ERROR: Need a -slop value if requesting -ss." << endl << "*****" << endl;
132 showHelp = true;
133 }
134
135 if (!showHelp) {
136
137 PairToPair *bi = new PairToPair(bedAFile, bedBFile, overlapFraction, searchType,
138 ignoreStrand, requireDifferentNames, slop, strandedSlop);
139 delete bi;
140 return 0;
141 }
142 else {
143 ShowHelp();
144 }
145 }
146
147
148 void ShowHelp(void) {
149 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
150
151 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
152
153 cerr << "Summary: Report overlaps between two paired-end BED files (BEDPE)." << endl << endl;
154
155 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <BEDPE> -b <BEDPE>" << endl << endl;
156
157 cerr << "Options: " << endl;
158 cerr << "\t-f\t" << "Minimum overlap required as fraction of A (e.g. 0.05)." << endl;
159 cerr << "\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;
160
161 cerr << "\t-type \t" << "Approach to reporting overlaps between A and B." << endl << endl;
162 cerr << "\t\tneither\tReport overlaps if neither end of A overlaps B." << endl;
163 cerr << "\t\teither\tReport overlaps if either ends of A overlap B." << endl;
164 cerr << "\t\tboth\tReport overlaps if both ends of A overlap B." << endl;
165 cerr << "\t\tnotboth\tReport overlaps if one or neither of ends of A overlap B." << endl;
166
167 cerr << "\t\t- Default = both." << endl << endl;
168
169 cerr << "\t-slop \t" << "The amount of slop (in b.p.). to be added to each footprint." << endl;
170 cerr << "\t\t*Note*: Slop is subtracted from start1 and start2 and added to end1 and end2." << endl << endl;
171
172 cerr << "\t-ss\t" << "Add slop based to each BEDPE footprint based on strand." << endl;
173 cerr << "\t\t- If strand is \"+\", slop is only added to the end coordinates." << endl;
174 cerr << "\t\t- If strand is \"-\", slop is only added to the start coordinates." << endl;
175 cerr << "\t\t- By default, slop is added in both directions." << endl << endl;
176
177 cerr << "\t-is\t" << "Ignore strands when searching for overlaps." << endl;
178 cerr << "\t\t- By default, strands are enforced." << endl << endl;
179
180 cerr << "\t-rdn\t" << "Require the hits to have different names (i.e. avoid self-hits)." << endl;
181 cerr << "\t\t- By default, same names are allowed." << endl << endl;
182
183
184 cerr << "Refer to the BEDTools manual for BEDPE format." << endl << endl;
185
186 // end the program here
187 exit(1);
188 }