| 13 | #include "CommonHelp.h" |
| 14 | |
| 15 | void intersect_help(void) { |
| 16 | |
| 17 | cerr << "\nTool: bedtools intersect (aka intersectBed)" << endl; |
| 18 | cerr << "Version: " << VERSION << "\n"; |
| 19 | cerr << "Summary: Report overlaps between two feature files." << endl << endl; |
| 20 | |
| 21 | cerr << "Usage: " << "bedtools intersect" << " [OPTIONS] -a <bed/gff/vcf/bam> -b <bed/gff/vcf/bam>" << endl << endl; |
| 22 | |
| 23 | cerr << "\t" << "Note: -b may be followed with multiple databases and/or " << endl; |
| 24 | cerr << "\t" "wildcard (*) character(s). " << endl; |
| 25 | |
| 26 | cerr << "Options: " << endl; |
| 27 | |
| 28 | // -abam is obsolete. |
| 29 | // cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl << endl; |
| 30 | |
| 31 | |
| 32 | IntersectOutputHelp(); |
| 33 | IntersectCommonHelp(); |
| 34 | |
| 35 | sortedHelp(); |
| 36 | multiDbOutputHelp(); |
| 37 | allToolsCommonHelp(); |
| 38 | |
| 39 | cerr << "Notes: " << endl; |
| 40 | cerr << "\t(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist," << endl; |
| 41 | cerr << "\tand excluded if an overlap cannot be found. If multiple overlaps exist, they are not" << endl; |
| 42 | cerr << "\treported, as we are only testing for one or more overlaps." << endl << endl; |
| 43 | |
| 44 | } |
no test coverage detected