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comparison BEDTools-Version-2.14.3/src/windowBed/windowMain.cpp @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 windowMain.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 "windowBed.h"
13 #include "version.h"
14
15 using namespace std;
16
17 // define the version
18 #define PROGRAM_NAME "windowBed"
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
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 int leftSlop = 1000;
38 int rightSlop = 1000;
39
40 bool haveBedA = false;
41 bool haveBedB = false;
42 bool noHit = false;
43 bool anyHit = false;
44 bool writeCount = false;
45 bool haveSlop = false;
46 bool haveLeft = false;
47 bool haveRight = false;
48 bool strandWindows = false;
49 bool matchOnSameStrand = false;
50 bool matchOnDiffStrand = false;
51 bool inputIsBam = false;
52 bool outputIsBam = true;
53 bool uncompressedBam = false;
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 bedAFile = argv[i + 1];
78 i++;
79 }
80 }
81 else if(PARAMETER_CHECK("-abam", 5, parameterLength)) {
82 if ((i+1) < argc) {
83 haveBedA = true;
84 inputIsBam = true;
85 bedAFile = argv[i + 1];
86 i++;
87 }
88 }
89 else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
90 if ((i+1) < argc) {
91 haveBedB = true;
92 bedBFile = argv[i + 1];
93 i++;
94 }
95 }
96 else if(PARAMETER_CHECK("-bed", 4, parameterLength)) {
97 outputIsBam = false;
98 }
99 else if(PARAMETER_CHECK("-u", 2, parameterLength)) {
100 anyHit = true;
101 }
102 else if(PARAMETER_CHECK("-c", 2, parameterLength)) {
103 writeCount = true;
104 }
105 else if (PARAMETER_CHECK("-v", 2, parameterLength)) {
106 noHit = true;
107 }
108 else if (PARAMETER_CHECK("-sw", 3, parameterLength)) {
109 strandWindows = true;
110 }
111 else if (PARAMETER_CHECK("-sm", 3, parameterLength)) {
112 matchOnSameStrand = true;
113 }
114 else if (PARAMETER_CHECK("-Sm", 3, parameterLength)) {
115 matchOnDiffStrand = true;
116 }
117 else if (PARAMETER_CHECK("-w", 2, parameterLength)) {
118 if ((i+1) < argc) {
119 haveSlop = true;
120 leftSlop = atoi(argv[i + 1]);
121 rightSlop = leftSlop;
122 i++;
123 }
124 }
125 else if (PARAMETER_CHECK("-l", 2, parameterLength)) {
126 if ((i+1) < argc) {
127 haveLeft = true;
128 leftSlop = atoi(argv[i + 1]);
129 i++;
130 }
131 }
132 else if (PARAMETER_CHECK("-r", 2, parameterLength)) {
133 if ((i+1) < argc) {
134 haveRight = true;
135 rightSlop = atoi(argv[i + 1]);
136 i++;
137 }
138 }
139 else if(PARAMETER_CHECK("-ubam", 5, parameterLength)) {
140 uncompressedBam = true;
141 }
142 else {
143 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
144 showHelp = true;
145 }
146 }
147
148 // make sure we have both input files
149 if (!haveBedA || !haveBedB) {
150 cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
151 showHelp = true;
152 }
153
154 if (anyHit && noHit) {
155 cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -v, not both." << endl << "*****" << endl;
156 showHelp = true;
157 }
158
159 if (anyHit && writeCount) {
160 cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -c, not both." << endl << "*****" << endl;
161 showHelp = true;
162 }
163
164 if (haveLeft && (leftSlop < 0)) {
165 cerr << endl << "*****" << endl << "*****ERROR: Upstream window (-l) must be positive." << endl << "*****" << endl;
166 showHelp = true;
167 }
168
169 if (haveRight && (rightSlop < 0)) {
170 cerr << endl << "*****" << endl << "*****ERROR: Downstream window (-r) must be positive." << endl << "*****" << endl;
171 showHelp = true;
172 }
173
174 if (haveSlop && (haveLeft || haveRight)) {
175 cerr << endl << "*****" << endl << "*****ERROR: Cannot choose -w with -l or -r. Either specify -l and -r or specify solely -w" << endl << "*****" << endl;
176 showHelp = true;
177 }
178
179 if ((haveLeft && !haveRight) || (haveRight && !haveLeft)) {
180 cerr << endl << "*****" << endl << "*****ERROR: Please specify both -l and -r." << endl << "*****" << endl;
181 showHelp = true;
182 }
183
184 if (matchOnSameStrand && matchOnDiffStrand) {
185 cerr << endl << "*****" << endl << "*****ERROR: Use either -sm or -Sm, not both." << endl << "*****" << endl;
186 showHelp = true;
187 }
188
189 if (!showHelp) {
190 BedWindow *bi = new BedWindow(bedAFile, bedBFile, leftSlop, rightSlop, anyHit,
191 noHit, writeCount, strandWindows, matchOnSameStrand, matchOnDiffStrand,
192 inputIsBam, outputIsBam, uncompressedBam);
193 delete bi;
194 return 0;
195 }
196 else {
197 ShowHelp();
198 }
199 }
200
201
202 void ShowHelp(void) {
203
204 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
205
206 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
207
208 cerr << "Summary: Examines a \"window\" around each feature in A and" << endl;
209 cerr << "\t reports all features in B that overlap the window. For each" << endl;
210 cerr << "\t overlap the entire entry in A and B are reported." << endl << endl;
211
212 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
213
214 cerr << "Options: " << endl;
215
216 cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl << endl;
217
218 cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default is to write compressed BAM." << endl << endl;
219
220 cerr << "\t-bed\t" << "When using BAM input (-abam), write output as BED. The default" << endl;
221 cerr << "\t\tis to write output in BAM when using -abam." << endl << endl;
222
223 cerr << "\t-w\t" << "Base pairs added upstream and downstream of each entry" << endl;
224 cerr << "\t\tin A when searching for overlaps in B." << endl;
225 cerr << "\t\t- Creates symterical \"windows\" around A." << endl;
226 cerr << "\t\t- Default is 1000 bp." << endl;
227 cerr << "\t\t- (INTEGER)" << endl << endl;
228
229 cerr << "\t-l\t" << "Base pairs added upstream (left of) of each entry" << endl;
230 cerr << "\t\tin A when searching for overlaps in B." << endl;
231 cerr << "\t\t- Allows one to define assymterical \"windows\"." << endl;
232 cerr << "\t\t- Default is 1000 bp." << endl;
233 cerr << "\t\t- (INTEGER)" << endl << endl;
234
235 cerr << "\t-r\t" << "Base pairs added downstream (right of) of each entry" << endl;
236 cerr << "\t\tin A when searching for overlaps in B." << endl;
237 cerr << "\t\t- Allows one to define assymterical \"windows\"." << endl;
238 cerr << "\t\t- Default is 1000 bp." << endl;
239 cerr << "\t\t- (INTEGER)" << endl << endl;
240
241 cerr << "\t-sw\t" << "Define -l and -r based on strand. For example if used, -l 500" << endl;
242 cerr << "\t\tfor a negative-stranded feature will add 500 bp downstream." << endl;
243 cerr << "\t\t- Default = disabled." << endl << endl;
244
245 cerr << "\t-sm\t" << "Only report hits in B that overlap A on the _same_ strand." << endl;
246 cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
247
248 cerr << "\t-Sm\t" << "Only report hits in B that overlap A on the _opposite_ strand." << endl;
249 cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
250
251 cerr << "\t-u\t" << "Write the original A entry _once_ if _any_ overlaps found in B." << endl;
252 cerr << "\t\t- In other words, just report the fact >=1 hit was found." << endl << endl;
253
254 cerr << "\t-c\t" << "For each entry in A, report the number of overlaps with B." << endl;
255 cerr << "\t\t- Reports 0 for A entries that have no overlap with B." << endl;
256 cerr << "\t\t- Overlaps restricted by -f." << endl << endl;
257
258 cerr << "\t-v\t" << "Only report those entries in A that have _no overlaps_ with B." << endl;
259 cerr << "\t\t- Similar to \"grep -v.\"" << endl << endl;
260
261 // end the program here
262 exit(1);
263 }