| 13 | |
| 14 | |
| 15 | void coverage_help(void) { |
| 16 | |
| 17 | cerr << "\nTool: bedtools coverage (aka coverageBed)" << endl; |
| 18 | cerr << "Version: " << VERSION << "\n"; |
| 19 | cerr << "Summary: Returns the depth and breadth of coverage of features from B" << endl; |
| 20 | cerr << "\t on the intervals in A." << endl << endl; |
| 21 | |
| 22 | cerr << "Usage: " << "bedtools coverage" << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl; |
| 23 | |
| 24 | cerr << "Options: " << endl; |
| 25 | |
| 26 | cerr << "\t-hist\t" << "Report a histogram of coverage for each feature in A" << endl; |
| 27 | cerr << "\t\tas well as a summary histogram for _all_ features in A." << endl << endl; |
| 28 | cerr << "\t\tOutput (tab delimited) after each feature in A:" << endl; |
| 29 | cerr << "\t\t 1) depth\n\t\t 2) # bases at depth\n\t\t 3) size of A\n\t\t 4) % of A at depth" << endl << endl; |
| 30 | |
| 31 | cerr << "\t-d\t" << "Report the depth at each position in each A feature." << endl; |
| 32 | cerr << "\t\tPositions reported are one based. Each position" << endl; |
| 33 | cerr << "\t\tand depth follow the complete A feature." << endl << endl; |
| 34 | |
| 35 | cerr << "\t-counts\t" << "Only report the count of overlaps, don't compute fraction, etc." << endl << endl; |
| 36 | |
| 37 | cerr << "\t-mean\t" << "Report the mean depth of all positions in each A feature." << endl << endl; |
| 38 | |
| 39 | |
| 40 | IntersectCommonHelp(); |
| 41 | sortedHelp(); |
| 42 | allToolsCommonHelp(); |
| 43 | |
| 44 | cerr << "Default Output: " << endl; |
| 45 | cerr << "\t" << " After each entry in A, reports: " << endl; |
| 46 | cerr << "\t 1) The number of features in B that overlapped the A interval." << endl; |
| 47 | cerr << "\t 2) The number of bases in A that had non-zero coverage." << endl; |
| 48 | cerr << "\t 3) The length of the entry in A." << endl; |
| 49 | cerr << "\t 4) The fraction of bases in A that had non-zero coverage." << endl << endl; |
| 50 | } |
no test coverage detected