Commit 509e6fee authored by Neil Kindlon's avatar Neil Kindlon
Browse files

Added -wb and -wo to subtract help

parent 706608e5
......@@ -64,6 +64,14 @@ void subtract_help(void) {
cerr << "\t-N\t" << "Same as -A except when used with -f, the amount is the sum" << endl;
cerr << "\t\tof all features (not any single feature)." << endl << endl;
cerr << "\t-wb\t" << "Write the original entry in B for each overlap." << endl;
cerr << "\t\t- Useful for knowing _what_ A overlaps. Restricted by -f and -r." << endl << endl;
cerr << "\t-wo\t" << "Write the original A and B entries plus the number of base" << endl;
cerr << "\t\tpairs of overlap between the two features." << endl;
cerr << "\t\t- Overlaps restricted by -f and -r." << endl;
cerr << "\t\t Only A features with overlap are reported." << endl << endl;
cerr << "\t-split\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl << endl;
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