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 "bedtools genomecov"
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 genomecoverage_help(void);
26 
genomecoverage_main(int argc,char * argv[])27 int genomecoverage_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     float fragmentSize = 146; //Nucleosome :)
38 
39     bool haveBed = false;
40     bool bamInput = false;
41     bool haveGenome = false;
42     bool startSites = false;
43     bool bedGraph = false;
44     bool bedGraphAll = false;
45     bool eachBase = false;
46     bool eachBaseZeroBased = false;
47     bool obeySplits = false;
48     bool ignoreD = false;
49     bool haveScale = false;
50     bool filterByStrand = false;
51     bool pair_chip = false;
52     bool haveSize = false;
53     bool dUTP = false;
54     bool only_5p_end = false;
55     bool only_3p_end = false;
56     bool add_gb_track_line = false;
57     string gb_track_opts;
58     string requestedStrand = "X";
59 
60     // check to see if we should print out some help
61     if(argc <= 1) showHelp = true;
62 
63     for(int i = 1; i < argc; i++) {
64         int parameterLength = (int)strlen(argv[i]);
65 
66         if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
67         (PARAMETER_CHECK("--help", 5, parameterLength))) {
68             showHelp = true;
69         }
70     }
71 
72     if(showHelp) genomecoverage_help();
73 
74     // do some parsing (all of these parameters require 2 strings)
75     for(int i = 1; i < argc; i++) {
76 
77         int parameterLength = (int)strlen(argv[i]);
78 
79         if(PARAMETER_CHECK("-i", 2, parameterLength)) {
80             if ((i+1) < argc) {
81                 haveBed = true;
82                 bedFile = argv[i + 1];
83                 i++;
84             }
85         }
86         else if(PARAMETER_CHECK("-ibam", 5, parameterLength)) {
87             if ((i+1) < argc) {
88                 haveBed = true;
89                 bamInput = true;
90                 bedFile = argv[i + 1];
91                 i++;
92             }
93         }
94         else if(PARAMETER_CHECK("-g", 2, parameterLength)) {
95             if ((i+1) < argc) {
96                 haveGenome = true;
97                 genomeFile = argv[i + 1];
98                 i++;
99             }
100         }
101         else if(PARAMETER_CHECK("-d", 2, parameterLength)) {
102             eachBase = true;
103         }
104         else if(PARAMETER_CHECK("-dz", 3, parameterLength)) {
105             eachBase = true;
106             eachBaseZeroBased = true;
107         }
108         else if(PARAMETER_CHECK("-bg", 3, parameterLength)) {
109             bedGraph = true;
110         }
111         else if(PARAMETER_CHECK("-bga", 4, parameterLength)) {
112             bedGraphAll = true;
113         }
114         else if(PARAMETER_CHECK("-max", 4, parameterLength)) {
115             if ((i+1) < argc) {
116                 max = atoi(argv[i + 1]);
117                 i++;
118             }
119         }
120         else if(PARAMETER_CHECK("-scale", 6, parameterLength)) {
121             if ((i+1) < argc) {
122                 haveScale = true;
123                 scale = atof(argv[i + 1]);
124                 i++;
125             }
126         }
127         else if(PARAMETER_CHECK("-split", 6, parameterLength)) {
128             obeySplits = true;
129         }
130         else if(PARAMETER_CHECK("-ignoreD", 8, parameterLength)) {
131             ignoreD = true;
132         }
133         else if(PARAMETER_CHECK("-strand", 7, parameterLength)) {
134             if ((i+1) < argc) {
135                 filterByStrand = true;
136                 requestedStrand = argv[i+1][0];
137                 if (!(requestedStrand == "-" || requestedStrand == "+")) {
138                     cerr << "*****ERROR: invalid -strand value (" << requestedStrand << "). Allowed options are + or -" << endl;
139                     showHelp = true;
140                 }
141                 i++;
142             }
143             else {
144                 cerr << "*****ERROR: -strand options requires a value: + or -" << endl;
145                 showHelp = true;
146             }
147         }
148         else if(PARAMETER_CHECK("-3", 2, parameterLength)) {
149                 only_3p_end = true;
150         }
151         else if(PARAMETER_CHECK("-5", 2, parameterLength)) {
152                 only_5p_end = true;
153         }
154         else if(PARAMETER_CHECK("-pc", 3, parameterLength)) {
155                 pair_chip = true;
156         }
157         else if(PARAMETER_CHECK("-fs", 3, parameterLength)) {
158             if ((i+1) < argc) {
159                 haveSize = true;
160                 fragmentSize = atoi(argv[i + 1]);
161                 i++;
162             }
163         }
164         else if(PARAMETER_CHECK("-du", 3, parameterLength)) {
165             dUTP = true;
166         }
167         else if(PARAMETER_CHECK("-trackline", 10, parameterLength)) {
168                 add_gb_track_line = true;
169         }
170         else if(PARAMETER_CHECK("-trackopts", 10, parameterLength)) {
171                 if ((i+1) < argc) {
172                     add_gb_track_line = true;
173                     gb_track_opts = argv[i+1];
174                     i++;
175                 } else {
176                     cerr << "*****ERROR: -trackopts options requires a value (UCSC/GB track definition parameters)" << endl;
177                     showHelp = true;
178                 }
179         }
180         else {
181           cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
182             showHelp = true;
183         }
184     }
185 
186     // make sure we have both input files
187     if (!haveBed && !haveGenome && !bamInput) {
188       cerr << endl << "*****" << endl << "*****ERROR: Need both a BED (-i) and a genome (-g) file. " << endl << "*****" << endl;
189       showHelp = true;
190     }
191     // make sure we have both input files
192     if (bamInput && haveGenome) {
193       cerr << endl << "*****" << endl << "*****WARNING: Genome (-g) files are ignored when BAM input is provided. " << endl << "*****" << endl;
194     }
195     if (bedGraph && eachBase) {
196       cerr << endl << "*****" << endl << "*****ERROR: Use -d/-dz or -bg, not both" << endl << "*****" << endl;
197       showHelp = true;
198     }
199     if (bedGraphAll && eachBase) {
200       cerr << endl << "*****" << endl << "*****ERROR: Use -d/-dz or -bga, not both" << endl << "*****" << endl;
201       showHelp = true;
202     }
203 
204     if (only_3p_end && only_5p_end) {
205       cerr << endl << "*****" << endl << "*****ERROR: Use -3 or -5, not both " << endl << "*****" << endl;
206       showHelp = true;
207     }
208 
209     if ( (only_3p_end||only_5p_end) && obeySplits) {
210       cerr << endl << "*****" << endl << "*****ERROR: Use -split can't be used with -3 or -5." << endl << "*****" << endl;
211       showHelp = true;
212     }
213 
214     if (add_gb_track_line && !(bedGraph||bedGraphAll)) {
215       cerr << endl << "*****" << endl << "*****ERROR: Using -trackline requires bedGraph output (use -bg or -bga)." << endl << "*****" << endl;
216       showHelp = true;
217     }
218 
219     if (haveScale && !(bedGraph||bedGraphAll||eachBase)) {
220       cerr << endl << "*****" << endl << "*****ERROR: Using -scale requires bedGraph output (use -bg or -bga) or per base depth (-d)." << endl << "*****" << endl;
221       showHelp = true;
222     }
223 
224     if (!showHelp) {
225         BedGenomeCoverage *bc = new BedGenomeCoverage(bedFile, genomeFile, eachBase,
226                                                       startSites, bedGraph, bedGraphAll,
227                                                       max, scale, bamInput, obeySplits, ignoreD,
228                                                       filterByStrand, requestedStrand,
229                                                       only_5p_end, only_3p_end,
230                                                       pair_chip, haveSize, fragmentSize, dUTP,
231                                                       eachBaseZeroBased,
232                                                       add_gb_track_line, gb_track_opts);
233         delete bc;
234     }
235     else {
236         genomecoverage_help();
237     }
238     return 0;
239 }
240 
genomecoverage_help(void)241 void genomecoverage_help(void) {
242 
243     cerr << "\nTool:    bedtools genomecov (aka genomeCoverageBed)" << endl;
244     cerr << "Version: " << VERSION << "\n";
245     cerr << "Summary: Compute the coverage of a feature file among a genome." << endl << endl;
246 
247     cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome>" << endl << endl;
248 
249     cerr << "Options: " << endl;
250 
251     cerr << "\t-ibam\t\t" << "The input file is in BAM format." << endl;
252     cerr << "\t\t\tNote: BAM _must_ be sorted by position" << endl << endl;
253 
254     cerr << "\t-d\t\t" << "Report the depth at each genome position (with one-based coordinates)." << endl;
255     cerr << "\t\t\tDefault behavior is to report a histogram." << endl << endl;
256 
257     cerr << "\t-dz\t\t" << "Report the depth at each genome position (with zero-based coordinates)." << endl;
258     cerr << "\t\t\tReports only non-zero positions." << endl;
259     cerr << "\t\t\tDefault behavior is to report a histogram." << endl << endl;
260 
261     cerr << "\t-bg\t\t" << "Report depth in BedGraph format. For details, see:" << endl;
262     cerr << "\t\t\tgenome.ucsc.edu/goldenPath/help/bedgraph.html" << endl << endl;
263 
264     cerr << "\t-bga\t\t" << "Report depth in BedGraph format, as above (-bg)." << endl;
265     cerr << "\t\t\tHowever with this option, regions with zero " << endl;
266     cerr << "\t\t\tcoverage are also reported. This allows one to" << endl;
267     cerr << "\t\t\tquickly extract all regions of a genome with 0 " << endl;
268     cerr << "\t\t\tcoverage by applying: \"grep -w 0$\" to the output." << endl << endl;
269 
270     cerr << "\t-split\t\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl;
271     cerr << "\t\t\twhen computing coverage." << endl;
272     cerr << "\t\t\tFor BAM files, this uses the CIGAR \"N\" and \"D\" operations " << endl;
273     cerr << "\t\t\tto infer the blocks for computing coverage." << endl;
274     cerr << "\t\t\tFor BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds" << endl;
275     cerr << "\t\t\tfields (i.e., columns 10,11,12)." << endl << endl;
276 
277     cerr << "\t-ignoreD\t" << "Ignore local deletions (CIGAR \"D\" operations) in BAM entries" << endl;
278     cerr << "\t\t\twhen computing coverage." << endl << endl;
279 
280     cerr << "\t-strand\t\t" << "Calculate coverage of intervals from a specific strand." << endl;
281     cerr << "\t\t\tWith BED files, requires at least 6 columns (strand is column 6). " << endl;
282     cerr << "\t\t\t- (STRING): can be + or -" << endl << endl;
283 
284     cerr << "\t-pc\t\t" << "Calculate coverage of pair-end fragments." << endl;
285     cerr << "\t\t\tWorks for BAM files only" << endl;
286 
287     cerr << "\t-fs\t\t" << "Force to use provided fragment size instead of read length" << endl;
288     cerr << "\t\t\tWorks for BAM files only" << endl;
289 
290     cerr << "\t-du\t\t" << "Change strand af the mate read (so both reads from the same strand) useful for strand specific" << endl;
291     cerr << "\t\t\tWorks for BAM files only" << endl;
292 
293     cerr << "\t-5\t\t" << "Calculate coverage of 5\" positions (instead of entire interval)." << endl << endl;
294 
295     cerr << "\t-3\t\t" << "Calculate coverage of 3\" positions (instead of entire interval)." << endl << endl;
296 
297     cerr << "\t-max\t\t" << "Combine all positions with a depth >= max into" << endl;
298     cerr << "\t\t\ta single bin in the histogram. Irrelevant" << endl;
299     cerr << "\t\t\tfor -d and -bedGraph" << endl;
300     cerr << "\t\t\t- (INTEGER)" << endl << endl;
301 
302     cerr << "\t-scale\t\t" << "Scale the coverage by a constant factor." << endl;
303     cerr << "\t\t\tEach coverage value is multiplied by this factor before being reported." << endl;
304     cerr << "\t\t\tUseful for normalizing coverage by, e.g., reads per million (RPM)." << endl;
305     cerr << "\t\t\t- Default is 1.0; i.e., unscaled." << endl;
306     cerr << "\t\t\t- (FLOAT)" << endl << endl;
307 
308     cerr << "\t-trackline\t" << "Adds a UCSC/Genome-Browser track line definition in the first line of the output." << endl;
309     cerr <<"\t\t\t- See here for more details about track line definition:" << endl;
310     cerr <<"\t\t\t      http://genome.ucsc.edu/goldenPath/help/bedgraph.html" << endl;
311     cerr <<"\t\t\t- NOTE: When adding a trackline definition, the output BedGraph can be easily" << endl;
312     cerr <<"\t\t\t      uploaded to the Genome Browser as a custom track," << endl;
313     cerr <<"\t\t\t      BUT CAN NOT be converted into a BigWig file (w/o removing the first line)." << endl << endl;
314 
315     cerr << "\t-trackopts\t"<<"Writes additional track line definition parameters in the first line." << endl;
316     cerr <<"\t\t\t- Example:" << endl;
317     cerr <<"\t\t\t   -trackopts 'name=\"My Track\" visibility=2 color=255,30,30'" << endl;
318     cerr <<"\t\t\t   Note the use of single-quotes if you have spaces in your parameters." << endl;
319     cerr <<"\t\t\t- (TEXT)" << endl << endl;
320 
321     cerr << "Notes: " << endl;
322     cerr << "\t(1) The genome file should tab delimited and structured as follows:" << endl;
323     cerr << "\t <chromName><TAB><chromSize>" << endl << endl;
324     cerr << "\tFor example, Human (hg19):" << endl;
325     cerr << "\tchr1\t249250621" << endl;
326     cerr << "\tchr2\t243199373" << endl;
327     cerr << "\t..." << endl;
328     cerr << "\tchr18_gl000207_random\t4262" << endl << endl;
329 
330     cerr << "\t(2) The input BED (-i) file must be grouped by chromosome." << endl;
331     cerr << "\t A simple \"sort -k 1,1 <BED> > <BED>.sorted\" will suffice."<< endl << endl;
332 
333     cerr << "\t(3) The input BAM (-ibam) file must be sorted by position." << endl;
334     cerr << "\t A \"samtools sort <BAM>\" should suffice."<< endl << endl;
335 
336     cerr << "Tips: " << endl;
337     cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract" << endl;
338     cerr << "\tchromosome sizes. For example, H. sapiens:" << endl << endl;
339     cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\" << endl;
340     cerr << "\t\"select chrom, size from hg19.chromInfo\" > hg19.genome" << endl << endl;
341 
342 
343     // end the program here
344     exit(1);
345 }
346 
347