Mercurial > repos > aaronquinlan > multi_intersect
comparison BEDTools-Version-2.14.3/src/fjoin/fjoinMain.cpp @ 0:dfcd8b6c1bda
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author | aaronquinlan |
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date | Thu, 03 Nov 2011 10:25:04 -0400 |
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-1:000000000000 | 0:dfcd8b6c1bda |
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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 } |