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Commit 45a0cc47 authored by Aaron Quinlan's avatar Aaron Quinlan
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Updated usage statement for windowBed.

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......@@ -128,7 +128,7 @@ void ShowHelp(void) {
cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
cerr << "OPTIONS: " << endl;
cerr << "\t" << "-w (e.g. 100000)\t" << "Base pairs added before and after each entry in A when searching for overlaps in B" << endl << endl;
cerr << "\t" << "-w (e.g. 100000)\t" << "Base pairs added before and after each entry in A when searching for overlaps in B (default=0)" << 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;
cerr << "\t" << "-c \t\t\t" << "For each entry in A, report the number of hits in B within the requested window." << endl << "\t\t\t\tReports 0 for A entries that have no overlap with B." << endl << endl;
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