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comparison BEDTools-Version-2.14.3/src/genomeCoverageBed/genomeCoverageMain.cpp @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 genomeCoverageMain.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 "genomeCoverageBed.h"
13 #include "version.h"
14
15 using namespace std;
16
17 // define our program name
18 #define PROGRAM_NAME "genomeCoverageBed"
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 bedFile;
34 string genomeFile;
35 int max = INT_MAX;
36 float scale = 1.0;
37
38 bool haveBed = false;
39 bool bamInput = false;
40 bool haveGenome = false;
41 bool startSites = false;
42 bool bedGraph = false;
43 bool bedGraphAll = false;
44 bool eachBase = false;
45 bool eachBaseZeroBased = false;
46 bool obeySplits = false;
47 bool haveScale = false;
48 bool filterByStrand = false;
49 bool only_5p_end = false;
50 bool only_3p_end = false;
51 bool add_gb_track_line = false;
52 string gb_track_opts;
53 string requestedStrand = "X";
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("-i", 2, parameterLength)) {
75 if ((i+1) < argc) {
76 haveBed = true;
77 bedFile = argv[i + 1];
78 i++;
79 }
80 }
81 else if(PARAMETER_CHECK("-ibam", 5, parameterLength)) {
82 if ((i+1) < argc) {
83 haveBed = true;
84 bamInput = true;
85 bedFile = argv[i + 1];
86 i++;
87 }
88 }
89 else if(PARAMETER_CHECK("-g", 2, parameterLength)) {
90 if ((i+1) < argc) {
91 haveGenome = true;
92 genomeFile = argv[i + 1];
93 i++;
94 }
95 }
96 else if(PARAMETER_CHECK("-d", 2, parameterLength)) {
97 eachBase = true;
98 }
99 else if(PARAMETER_CHECK("-dz", 3, parameterLength)) {
100 eachBase = true;
101 eachBaseZeroBased = true;
102 }
103 else if(PARAMETER_CHECK("-bg", 3, parameterLength)) {
104 bedGraph = true;
105 }
106 else if(PARAMETER_CHECK("-bga", 4, parameterLength)) {
107 bedGraphAll = true;
108 }
109 else if(PARAMETER_CHECK("-max", 4, parameterLength)) {
110 if ((i+1) < argc) {
111 max = atoi(argv[i + 1]);
112 i++;
113 }
114 }
115 else if(PARAMETER_CHECK("-scale", 6, parameterLength)) {
116 if ((i+1) < argc) {
117 haveScale = true;
118 scale = atof(argv[i + 1]);
119 i++;
120 }
121 }
122 else if(PARAMETER_CHECK("-split", 6, parameterLength)) {
123 obeySplits = true;
124 }
125 else if(PARAMETER_CHECK("-strand", 7, parameterLength)) {
126 if ((i+1) < argc) {
127 filterByStrand = true;
128 requestedStrand = argv[i+1][0];
129 if (!(requestedStrand == "-" || requestedStrand == "+")) {
130 cerr << "*****ERROR: invalid -strand value (" << requestedStrand << "). Allowed options are + or -" << endl;
131 showHelp = true;
132 }
133 i++;
134 }
135 else {
136 cerr << "*****ERROR: -strand options requires a value: + or -" << endl;
137 showHelp = true;
138 }
139 }
140 else if(PARAMETER_CHECK("-3", 2, parameterLength)) {
141 only_3p_end = true;
142 }
143 else if(PARAMETER_CHECK("-5", 2, parameterLength)) {
144 only_5p_end = true;
145 }
146 else if(PARAMETER_CHECK("-trackline", 10, parameterLength)) {
147 add_gb_track_line = true;
148 }
149 else if(PARAMETER_CHECK("-trackopts", 10, parameterLength)) {
150 if ((i+1) < argc) {
151 add_gb_track_line = true;
152 gb_track_opts = argv[i+1];
153 i++;
154 } else {
155 cerr << "*****ERROR: -trackopts options requires a value (UCSC/GB track definition parameters)" << endl;
156 showHelp = true;
157 }
158 }
159 else {
160 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
161 showHelp = true;
162 }
163 }
164
165 // make sure we have both input files
166 if (!haveBed && !haveGenome && !bamInput) {
167 cerr << endl << "*****" << endl << "*****ERROR: Need both a BED (-i) and a genome (-g) file. " << endl << "*****" << endl;
168 showHelp = true;
169 }
170 if (bedGraph && eachBase) {
171 cerr << endl << "*****" << endl << "*****ERROR: Use -d/-dz or -bg, not both" << endl << "*****" << endl;
172 showHelp = true;
173 }
174 if (bedGraphAll && eachBase) {
175 cerr << endl << "*****" << endl << "*****ERROR: Use -d/-dz or -bga, not both" << endl << "*****" << endl;
176 showHelp = true;
177 }
178
179 if (only_3p_end && only_5p_end) {
180 cerr << endl << "*****" << endl << "*****ERROR: Use -3 or -5, not both " << endl << "*****" << endl;
181 showHelp = true;
182 }
183
184 if ( (only_3p_end||only_5p_end) && obeySplits) {
185 cerr << endl << "*****" << endl << "*****ERROR: Use -split can't be used with -3 or -5." << endl << "*****" << endl;
186 showHelp = true;
187 }
188
189 if (add_gb_track_line && !(bedGraph||bedGraphAll)) {
190 cerr << endl << "*****" << endl << "*****ERROR: Using -trackline requires bedGraph output (use -bg or -bga)." << endl << "*****" << endl;
191 showHelp = true;
192 }
193
194 if (haveScale && !(bedGraph||bedGraphAll||eachBase)) {
195 cerr << endl << "*****" << endl << "*****ERROR: Using -scale requires bedGraph output (use -bg or -bga) or per base depth (-d)." << endl << "*****" << endl;
196 showHelp = true;
197 }
198
199 if (!showHelp) {
200 BedGenomeCoverage *bc = new BedGenomeCoverage(bedFile, genomeFile, eachBase,
201 startSites, bedGraph, bedGraphAll,
202 max, scale, bamInput, obeySplits,
203 filterByStrand, requestedStrand,
204 only_5p_end, only_3p_end,
205 eachBaseZeroBased,
206 add_gb_track_line, gb_track_opts);
207 delete bc;
208
209 return 0;
210 }
211 else {
212 ShowHelp();
213 }
214 }
215
216 void ShowHelp(void) {
217
218 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
219
220 cerr << "Authors: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
221 cerr << " Assaf Gordon, CSHL" << endl << endl;
222
223 cerr << "Summary: Compute the coverage of a feature file among a genome." << endl << endl;
224
225 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome>" << endl << endl;
226
227 cerr << "Options: " << endl;
228
229 cerr << "\t-ibam\t\t" << "The input file is in BAM format." << endl;
230 cerr << "\t\t\tNote: BAM _must_ be sorted by position" << endl << endl;
231
232 cerr << "\t-d\t\t" << "Report the depth at each genome position (with one-based coordinates)." << endl;
233 cerr << "\t\t\tDefault behavior is to report a histogram." << endl << endl;
234
235 cerr << "\t-dz\t\t" << "Report the depth at each genome position (with zero-based coordinates)." << endl;
236 cerr << "\t\t\tReports only non-zero positions." << endl;
237 cerr << "\t\t\tDefault behavior is to report a histogram." << endl << endl;
238
239 cerr << "\t-bg\t\t" << "Report depth in BedGraph format. For details, see:" << endl;
240 cerr << "\t\t\tgenome.ucsc.edu/goldenPath/help/bedgraph.html" << endl << endl;
241
242 cerr << "\t-bga\t\t" << "Report depth in BedGraph format, as above (-bg)." << endl;
243 cerr << "\t\t\tHowever with this option, regions with zero " << endl;
244 cerr << "\t\t\tcoverage are also reported. This allows one to" << endl;
245 cerr << "\t\t\tquickly extract all regions of a genome with 0 " << endl;
246 cerr << "\t\t\tcoverage by applying: \"grep -w 0$\" to the output." << endl << endl;
247
248 cerr << "\t-split\t\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl;
249 cerr << "\t\t\twhen computing coverage." << endl;
250 cerr << "\t\t\tFor BAM files, this uses the CIGAR \"N\" and \"D\" operations " << endl;
251 cerr << "\t\t\tto infer the blocks for computing coverage." << endl;
252 cerr << "\t\t\tFor BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds" << endl;
253 cerr << "\t\t\tfields (i.e., columns 10,11,12)." << endl << endl;
254
255 cerr << "\t-strand\t\t" << "Calculate coverage of intervals from a specific strand." << endl;
256 cerr << "\t\t\tWith BED files, requires at least 6 columns (strand is column 6). " << endl;
257 cerr << "\t\t\t- (STRING): can be + or -" << endl << endl;
258
259 cerr << "\t-5\t\t" << "Calculate coverage of 5\" positions (instead of entire interval)." << endl << endl;
260
261 cerr << "\t-3\t\t" << "Calculate coverage of 3\" positions (instead of entire interval)." << endl << endl;
262
263 cerr << "\t-max\t\t" << "Combine all positions with a depth >= max into" << endl;
264 cerr << "\t\t\ta single bin in the histogram. Irrelevant" << endl;
265 cerr << "\t\t\tfor -d and -bedGraph" << endl;
266 cerr << "\t\t\t- (INTEGER)" << endl << endl;
267
268 cerr << "\t-scale\t\t" << "Scale the coverage by a constant factor." << endl;
269 cerr << "\t\t\tEach coverage value is multiplied by this factor before being reported." << endl;
270 cerr << "\t\t\tUseful for normalizing coverage by, e.g., reads per million (RPM)." << endl;
271 cerr << "\t\t\t- Default is 1.0; i.e., unscaled." << endl;
272 cerr << "\t\t\t- (FLOAT)" << endl << endl;
273
274 cerr << "\t-trackline\t" << "Adds a UCSC/Genome-Browser track line definition in the first line of the output." << endl;
275 cerr <<"\t\t\t- See here for more details about track line definition:" << endl;
276 cerr <<"\t\t\t http://genome.ucsc.edu/goldenPath/help/bedgraph.html" << endl;
277 cerr <<"\t\t\t- NOTE: When adding a trackline definition, the output BedGraph can be easily" << endl;
278 cerr <<"\t\t\t uploaded to the Genome Browser as a custom track," << endl;
279 cerr <<"\t\t\t BUT CAN NOT be converted into a BigWig file (w/o removing the first line)." << endl << endl;
280
281 cerr << "\t-trackopts\t"<<"Writes additional track line definition parameters in the first line." << endl;
282 cerr <<"\t\t\t- Example:" << endl;
283 cerr <<"\t\t\t -trackopts 'name=\"My Track\" visibility=2 color=255,30,30'" << endl;
284 cerr <<"\t\t\t Note the use of single-quotes if you have spaces in your parameters." << endl;
285 cerr <<"\t\t\t- (TEXT)" << endl << endl;
286
287 cerr << "Notes: " << endl;
288 cerr << "\t(1) The genome file should tab delimited and structured as follows:" << endl;
289 cerr << "\t <chromName><TAB><chromSize>" << endl << endl;
290 cerr << "\tFor example, Human (hg19):" << endl;
291 cerr << "\tchr1\t249250621" << endl;
292 cerr << "\tchr2\t243199373" << endl;
293 cerr << "\t..." << endl;
294 cerr << "\tchr18_gl000207_random\t4262" << endl << endl;
295
296 cerr << "\t(2) The input BED (-i) file must be grouped by chromosome." << endl;
297 cerr << "\t A simple \"sort -k 1,1 <BED> > <BED>.sorted\" will suffice."<< endl << endl;
298
299 cerr << "\t(3) The input BAM (-ibam) file must be sorted by position." << endl;
300 cerr << "\t A \"samtools sort <BAM>\" should suffice."<< endl << endl;
301
302 cerr << "Tips: " << endl;
303 cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract" << endl;
304 cerr << "\tchromosome sizes. For example, H. sapiens:" << endl << endl;
305 cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\" << endl;
306 cerr << "\t\"select chrom, size from hg19.chromInfo\" > hg19.genome" << endl << endl;
307
308
309 // end the program here
310 exit(1);
311 }
312