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comparison BEDTools-Version-2.14.3/src/pairToBed/pairToBedMain.cpp @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 pairToBedMain.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 "pairToBed.h"
13 #include "version.h"
14
15 using namespace std;
16
17 // define our program name
18 #define PROGRAM_NAME "pairToBed"
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 string searchType = "either";
38
39 // flags to track parameters
40 bool haveBedA = false;
41 bool haveBedB = false;
42 bool haveSearchType = false;
43 bool haveFraction = false;
44 bool sameStrand = false;
45 bool diffStrand = false;
46 bool useEditDistance = false;
47 bool inputIsBam = false;
48 bool outputIsBam = true;
49 bool uncompressedBam = false;
50
51 // check to see if we should print out some help
52 if(argc <= 1) showHelp = true;
53
54 for(int i = 1; i < argc; i++) {
55 int parameterLength = (int)strlen(argv[i]);
56
57 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
58 (PARAMETER_CHECK("--help", 5, parameterLength))) {
59 showHelp = true;
60 }
61 }
62
63 if(showHelp) ShowHelp();
64
65 // do some parsing (all of these parameters require 2 strings)
66 for(int i = 1; i < argc; i++) {
67
68 int parameterLength = (int)strlen(argv[i]);
69
70 if(PARAMETER_CHECK("-a", 2, parameterLength)) {
71 if ((i+1) < argc) {
72 haveBedA = true;
73 outputIsBam = false;
74 bedAFile = argv[i + 1];
75 i++;
76 }
77 }
78 else if(PARAMETER_CHECK("-abam", 5, parameterLength)) {
79 if ((i+1) < argc) {
80 haveBedA = true;
81 inputIsBam = true;
82 bedAFile = argv[i + 1];
83 i++;
84 }
85 }
86 else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
87 if ((i+1) < argc) {
88 haveBedB = true;
89 bedBFile = argv[i + 1];
90 i++;
91 }
92 }
93 else if(PARAMETER_CHECK("-bedpe", 6, parameterLength)) {
94 outputIsBam = false;
95 }
96 else if(PARAMETER_CHECK("-ed", 3, parameterLength)) {
97 useEditDistance = true;
98 }
99 else if(PARAMETER_CHECK("-type", 5, parameterLength)) {
100 if ((i+1) < argc) {
101 haveSearchType = true;
102 searchType = argv[i + 1];
103 i++;
104 }
105 }
106 else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
107 if ((i+1) < argc) {
108 haveFraction = true;
109 overlapFraction = atof(argv[i + 1]);
110 i++;
111 }
112 }
113 else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
114 sameStrand = true;
115 }
116 else if (PARAMETER_CHECK("-S", 2, parameterLength)) {
117 diffStrand = true;
118 }
119 else if(PARAMETER_CHECK("-ubam", 5, parameterLength)) {
120 uncompressedBam = true;
121 }
122 else {
123 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
124 showHelp = true;
125 }
126 }
127
128
129 // make sure we have both input files
130 if (!haveBedA || !haveBedB) {
131 cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
132 showHelp = true;
133 }
134
135 if (haveSearchType && (searchType != "either") && (searchType != "neither") && (searchType != "both")
136 && (searchType != "xor") && (searchType != "notboth") && (searchType != "ispan")
137 && (searchType != "ospan") && (searchType != "notispan") && (searchType != "notospan")) {
138 cerr << endl << "*****" << endl << "*****ERROR: Request \"either\" or \"both\" or \"neither\" or \"xor\" or \"notboth\" or \"ispan\" or \"ospan\" or \"notispan\" or \"notospan\"" << endl << "*****" << endl;
139 showHelp = true;
140 }
141
142 if ( ((searchType == "ispan") || (searchType == "ospan") || (searchType == "notispan") || (searchType == "notospan"))
143 && (sameStrand || diffStrand) ) {
144 cerr << endl << "*****" << endl << "*****ERROR: Cannot enforce strandedness with selected searchtype" << endl << "*****" << endl;
145 showHelp = true;
146 }
147
148 if (useEditDistance && (inputIsBam == false || outputIsBam == true)) {
149 cerr << endl << "*****" << endl << "*****ERROR: -ed must be used with -bedpe and -abam." << endl << "*****" << endl;
150 showHelp = true;
151 }
152
153 if (sameStrand && diffStrand) {
154 cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl;
155 showHelp = true;
156 }
157 if (!showHelp) {
158
159 BedIntersectPE *bi = new BedIntersectPE(bedAFile, bedBFile, overlapFraction,
160 searchType, sameStrand, diffStrand, inputIsBam,
161 outputIsBam, uncompressedBam, useEditDistance);
162 delete bi;
163 return 0;
164 }
165 else {
166 ShowHelp();
167 }
168 }
169
170
171 void ShowHelp(void) {
172
173 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
174
175 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
176
177 cerr << "Summary: Report overlaps between a BEDPE file and a BED/GFF/VCF file." << endl << endl;
178
179 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bedpe> -b <bed/gff/vcf>" << endl << endl;
180
181 cerr << "Options: " << endl;
182
183 cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl;
184 cerr << "\t\t- Requires BAM to be grouped or sorted by query." << endl << endl;
185
186 cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default is to write compressed BAM." << endl << endl;
187 cerr << "\t\tis to write output in BAM when using -abam." << endl << endl;
188
189 cerr << "\t-bedpe\t" << "When using BAM input (-abam), write output as BEDPE. The default" << endl;
190 cerr << "\t\tis to write output in BAM when using -abam." << endl << endl;
191
192 cerr << "\t-ed\t" << "Use BAM total edit distance (NM tag) for BEDPE score." << endl;
193 cerr << "\t\t- Default for BEDPE is to use the minimum of" << endl;
194 cerr << "\t\t of the two mapping qualities for the pair." << endl;
195 cerr << "\t\t- When -ed is used the total edit distance" << endl;
196 cerr << "\t\t from the two mates is reported as the score." << endl << endl;
197
198 cerr << "\t-f\t" << "Minimum overlap required as fraction of A (e.g. 0.05)." << endl;
199 cerr << "\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;
200
201 cerr << "\t-s\t" << "Require same strandedness when finding overlaps." << endl;
202 cerr << "\t\tDefault is to ignore stand." << endl;
203 cerr << "\t\tNot applicable with -type inspan or -type outspan." << endl << endl;
204
205 cerr << "\t-S\t" << "Require different strandedness when finding overlaps." << endl;
206 cerr << "\t\tDefault is to ignore stand." << endl;
207 cerr << "\t\tNot applicable with -type inspan or -type outspan." << endl << endl;
208
209 cerr << "\t-type \t" << "Approach to reporting overlaps between BEDPE and BED." << endl << endl;
210 cerr << "\t\teither\tReport overlaps if either end of A overlaps B." << endl;
211 cerr << "\t\t\t- Default." << endl;
212
213 cerr << "\t\tneither\tReport A if neither end of A overlaps B." << endl;
214
215 cerr << "\t\tboth\tReport overlaps if both ends of A overlap B." << endl;
216
217 cerr << "\t\txor\tReport overlaps if one and only one end of A overlaps B." << endl;
218
219 cerr << "\t\tnotboth\tReport overlaps if neither end or one and only one " << endl;
220 cerr << "\t\t\tend of A overlap B. That is, xor + neither." << endl << endl;
221
222 cerr << "\t\tispan\tReport overlaps between [end1, start2] of A and B." << endl;
223 cerr << "\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl;
224
225 cerr << "\t\tospan\tReport overlaps between [start1, end2] of A and B." << endl;
226 cerr << "\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl;
227
228 cerr << "\t\tnotispan\tReport A if ispan of A doesn't overlap B." << endl;
229 cerr << "\t\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl;
230
231 cerr << "\t\tnotospan\tReport A if ospan of A doesn't overlap B." << endl;
232 cerr << "\t\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl;
233
234 cerr << "Refer to the BEDTools manual for BEDPE format." << endl << endl;
235
236 exit(1);
237 }