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Commit 397aa79e authored by Aaron's avatar Aaron
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Changed windowBed help message.

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......@@ -166,7 +166,7 @@ void ShowHelp(void) {
cerr << "\t" << "-w (def. 1000)\t\t" << "Base pairs added upstream and downstream of each entry in A when searching for overlaps in B." << endl << endl;
cerr << "\t" << "-l (def. 1000)\t\t" << "Base pairs added upstream (left of) of each entry in A when searching for overlaps in B." << endl << endl;
cerr << "\t" << "-r (def. 1000)\t\t" << "Base pairs added downstream (right of) of each entry in A when searching for overlaps in B." << endl << endl;
cerr << "\t" << "-sw\t\t\t" << "Define -l and -r based on strand. E.g. if used, -l 500 for a negative-stranded feature will add 500 bp downstream. Default = false." << endl << "\t\t\t\tBy default, overlaps are reported without respect to strand." << endl << endl;
cerr << "\t" << "-sw\t\t\t" << "Define -l and -r based on strand. E.g. if used, -l 500 for a negative-stranded " << endl << "\t\t\t\tfeature will add 500 bp downstream. Default = false." << endl << endl;
cerr << "\t" << "-sm\t\t\t" << "Only report hits in B that overlap A on the same strand." << endl << "\t\t\t\tBy default, overlaps are reported without respect to strand." << endl << endl;
cerr << "\t" << "-u\t\t\t" << "Write ORIGINAL a.bed entry ONCE if ANY overlap with B.bed." << endl << "\t\t\t\tIn other words, just report the fact >=1 hit was found." << endl << endl;
cerr << "\t" << "-v \t\t\t" << "Only report those entries in A that have NO OVERLAP in B within the requested window." << endl << "\t\t\t\tSimilar to grep -v." << endl << endl;
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