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comparison BEDTools-Version-2.14.3/src/fjoin/fjoinMain.cpp @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 intersectMain.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 "fjoin.h"
13 #include "version.h"
14
15 using namespace std;
16
17 // define our program name
18 #define PROGRAM_NAME "fjoin"
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 bedAFile;
34 string bedBFile;
35
36 // input arguments
37 float overlapFraction = 1E-9;
38
39 bool haveBedA = false;
40 bool haveBedB = false;
41 bool noHit = false;
42 bool anyHit = false;
43 bool writeA = false;
44 bool writeB = false;
45 bool writeCount = false;
46 bool writeOverlap = false;
47 bool writeAllOverlap = false;
48 bool haveFraction = false;
49 bool reciprocalFraction = false;
50 bool forceStrand = false;
51 bool obeySplits = false;
52 bool inputIsBam = false;
53 bool outputIsBam = true;
54
55 // check to see if we should print out some help
56 if(argc <= 1) showHelp = true;
57
58 for(int i = 1; i < argc; i++) {
59 int parameterLength = (int)strlen(argv[i]);
60
61 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
62 (PARAMETER_CHECK("--help", 5, parameterLength))) {
63 showHelp = true;
64 }
65 }
66
67 if(showHelp) ShowHelp();
68
69 // do some parsing (all of these parameters require 2 strings)
70 for(int i = 1; i < argc; i++) {
71
72 int parameterLength = (int)strlen(argv[i]);
73
74 if(PARAMETER_CHECK("-a", 2, parameterLength)) {
75 if ((i+1) < argc) {
76 haveBedA = true;
77 outputIsBam = false;
78 bedAFile = argv[i + 1];
79 i++;
80 }
81 }
82 else if(PARAMETER_CHECK("-abam", 5, parameterLength)) {
83 if ((i+1) < argc) {
84 haveBedA = true;
85 inputIsBam = true;
86 bedAFile = argv[i + 1];
87 i++;
88 }
89 }
90 else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
91 if ((i+1) < argc) {
92 haveBedB = true;
93 bedBFile = argv[i + 1];
94 i++;
95 }
96 }
97 else if(PARAMETER_CHECK("-bed", 4, parameterLength)) {
98 outputIsBam = false;
99 }
100 else if(PARAMETER_CHECK("-u", 2, parameterLength)) {
101 anyHit = true;
102 }
103 else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
104 if ((i+1) < argc) {
105 haveFraction = true;
106 overlapFraction = atof(argv[i + 1]);
107 i++;
108 }
109 }
110 else if(PARAMETER_CHECK("-wa", 3, parameterLength)) {
111 writeA = true;
112 }
113 else if(PARAMETER_CHECK("-wb", 3, parameterLength)) {
114 writeB = true;
115 }
116 else if(PARAMETER_CHECK("-wo", 3, parameterLength)) {
117 writeOverlap = true;
118 }
119 else if(PARAMETER_CHECK("-wao", 4, parameterLength)) {
120 writeAllOverlap = true;
121 writeOverlap = true;
122 }
123 else if(PARAMETER_CHECK("-c", 2, parameterLength)) {
124 writeCount = true;
125 }
126 else if(PARAMETER_CHECK("-r", 2, parameterLength)) {
127 reciprocalFraction = true;
128 }
129 else if (PARAMETER_CHECK("-v", 2, parameterLength)) {
130 noHit = true;
131 }
132 else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
133 forceStrand = true;
134 }
135 else if (PARAMETER_CHECK("-split", 6, parameterLength)) {
136 obeySplits = true;
137 }
138 else {
139 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
140 showHelp = true;
141 }
142 }
143
144 // make sure we have both input files
145 if (!haveBedA || !haveBedB) {
146 cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
147 showHelp = true;
148 }
149
150 if (anyHit && noHit) {
151 cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -v, not both." << endl << "*****" << endl;
152 showHelp = true;
153 }
154
155 if (writeB && writeCount) {
156 cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -c, not both." << endl << "*****" << endl;
157 showHelp = true;
158 }
159
160 if (writeCount && writeOverlap) {
161 cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -wo, not both." << endl << "*****" << endl;
162 showHelp = true;
163 }
164
165 if (writeA && writeOverlap) {
166 cerr << endl << "*****" << endl << "*****ERROR: Request either -wa OR -wo, not both." << endl << "*****" << endl;
167 showHelp = true;
168 }
169
170 if (writeB && writeOverlap) {
171 cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -wo, not both." << endl << "*****" << endl;
172 showHelp = true;
173 }
174
175 if (reciprocalFraction && !haveFraction) {
176 cerr << endl << "*****" << endl << "*****ERROR: If using -r, you need to define -f." << endl << "*****" << endl;
177 showHelp = true;
178 }
179
180 if (anyHit && writeCount) {
181 cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -c, not both." << endl << "*****" << endl;
182 showHelp = true;
183 }
184
185 if (anyHit && writeB) {
186 cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -wb, not both." << endl << "*****" << endl;
187 showHelp = true;
188 }
189
190 if (anyHit && writeOverlap) {
191 cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -wo, not both." << endl << "*****" << endl;
192 showHelp = true;
193 }
194
195
196 if (!showHelp) {
197
198 BedIntersect *bi = new BedIntersect(bedAFile, bedBFile, anyHit, writeA, writeB, writeOverlap,
199 writeAllOverlap, overlapFraction, noHit, writeCount, forceStrand,
200 reciprocalFraction, obeySplits, inputIsBam, outputIsBam);
201 delete bi;
202 return 0;
203 }
204 else {
205 ShowHelp();
206 }
207 }
208
209 void ShowHelp(void) {
210
211 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
212
213 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
214
215 cerr << "Summary: Report overlaps between two feature files." << endl << endl;
216
217 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
218
219 cerr << "Options: " << endl;
220
221 cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl << endl;
222
223 cerr << "\t-bed\t" << "When using BAM input (-abam), write output as BED. The default" << endl;
224 cerr << "\t\tis to write output in BAM when using -abam." << endl << endl;
225
226 cerr << "\t-wa\t" << "Write the original entry in A for each overlap." << endl << endl;
227
228 cerr << "\t-wb\t" << "Write the original entry in B for each overlap." << endl;
229 cerr << "\t\t- Useful for knowing _what_ A overlaps. Restricted by -f and -r." << endl << endl;
230
231 cerr << "\t-wo\t" << "Write the original A and B entries plus the number of base" << endl;
232 cerr << "\t\tpairs of overlap between the two features." << endl;
233 cerr << "\t\t- Overlaps restricted by -f and -r." << endl;
234 cerr << "\t\t Only A features with overlap are reported." << endl << endl;
235
236 cerr << "\t-wao\t" << "Write the original A and B entries plus the number of base" << endl;
237 cerr << "\t\tpairs of overlap between the two features." << endl;
238 cerr << "\t\t- Overlapping features restricted by -f and -r." << endl;
239 cerr << "\t\t However, A features w/o overlap are also reported" << endl;
240 cerr << "\t\t with a NULL B feature and overlap = 0." << endl << endl;
241
242 cerr << "\t-u\t" << "Write the original A entry _once_ if _any_ overlaps found in B." << endl;
243 cerr << "\t\t- In other words, just report the fact >=1 hit was found." << endl;
244 cerr << "\t\t- Overlaps restricted by -f and -r." << endl << endl;
245
246 cerr << "\t-c\t" << "For each entry in A, report the number of overlaps with B." << endl;
247 cerr << "\t\t- Reports 0 for A entries that have no overlap with B." << endl;
248 cerr << "\t\t- Overlaps restricted by -f and -r." << endl << endl;
249
250 cerr << "\t-v\t" << "Only report those entries in A that have _no overlaps_ with B." << endl;
251 cerr << "\t\t- Similar to \"grep -v\" (an homage)." << endl << endl;
252
253 cerr << "\t-f\t" << "Minimum overlap required as a fraction of A." << endl;
254 cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl;
255 cerr << "\t\t- FLOAT (e.g. 0.50)" << endl << endl;
256
257 cerr << "\t-r\t" << "Require that the fraction overlap be reciprocal for A and B." << endl;
258 cerr << "\t\t- In other words, if -f is 0.90 and -r is used, this requires" << endl;
259 cerr << "\t\t that B overlap 90% of A and A _also_ overlaps 90% of B." << endl << endl;
260
261 cerr << "\t-s\t" << "Force strandedness. That is, only report hits in B that" << endl;
262 cerr << "\t\toverlap A on the same strand." << endl;
263 cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
264
265 cerr << "\t-split\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl << endl;
266
267
268 // end the program here
269 exit(1);
270
271 }