Updated windowBed to 80 char width.

src/windowBed/windowMain.cpp

@@ -156,26 +156,45 @@ void ShowHelp(void) {
 	cerr << " Aaron Quinlan, Ph.D. (aaronquinlan@gmail.com)  " << endl ;
 	cerr << " Hall Laboratory, University of Virginia" << endl;
 	cerr << "===============================================" << endl << endl;
-	cerr << "Description: Examines a \"window\" around each feature in A.bed and" << endl;
-	cerr << "reports all features in B.bed that are within the window. For each" << endl;
+	cerr << "Description: Examines a \"window\" around each feature in A and" << endl;
+	cerr << "reports all features in B that overlap the window. For each" << endl;
 	cerr << "overlap the entire entry in A and B are reported." << endl << endl;
 
 	cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
 
 	cerr << "OPTIONS: " << endl;
-	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 " << 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;
-	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;
-
-	cerr << "NOTES: " << endl;
-	cerr << "\t" << "-i stdin\t\t"	<< "Allows BED file A to be read from stdin.  E.g.: cat a.bed | windowBed -a stdin -b B.bed" << endl << endl;
-	cerr << "\t***Only tab-delimited BED3 - BED6 formats allowed.***"<< endl << endl;
+	cerr << "  " << "-w\t"		<< "Base pairs added upstream and downstream of each entry" << endl;
+	cerr						<< "\tin A when searching for overlaps in B." << endl;
+	cerr						<< "\t  - Creates symterical \"windows\" around A." << endl;		
+	cerr						<< "\t  - Default is 1000 bp." << endl << endl;
+	
+	cerr << "  " << "-l\t"		<< "Base pairs added upstream (left of) of each entry" << endl;
+	cerr						<< "\tin A when searching for overlaps in B." << endl;	
+	cerr						<< "\t  - Allows one to define assymterical \"windows\"." << endl;
+	cerr						<< "\t  - Default is 1000 bp." << endl << endl;
+
+	cerr << "  " << "-r\t"		<< "Base pairs added downstream (right of) of each entry" << endl;
+	cerr						<< "\tin A when searching for overlaps in B." << endl;	
+	cerr						<< "\t  - Allows one to define assymterical \"windows\"." << endl;
+	cerr						<< "\t  - Default is 1000 bp." << endl << endl;
+		
+
+	cerr << "  " << "-sw\t"     << "Define -l and -r based on strand.  For example if used, -l 500" << endl;
+	cerr 						<< "\tfor a negative-stranded feature will add 500 bp downstream." << endl;
+	cerr						<< "\t  - Default = disabled." << endl << endl;	
+
+	cerr << "  " << "-sm\t"     << "Only report hits in B that overlap A on the same strand." << endl;
+	cerr						<< "\t  - By default, overlaps are reported without respect to strand." << endl << endl;	
+
+	cerr << "  " << "-u\t"      << "Write the original A entry _once_ if _any_ overlaps found in B." << endl;
+	cerr 						<< "\t  - In other words, just report the fact >=1 hit was found." << endl << endl;
+
+	cerr << "  " << "-c\t"		<< "For each entry in A, report the number of overlaps with B." << endl; 
+	cerr 						<< "\t  - Reports 0 for A entries that have no overlap with B." << endl;
+	cerr						<< "\t  - Overlaps restricted by -f." << endl << endl;
 
+	cerr << "  " << "-v\t"      << "Only report those entries in A that have _no overlaps_ with B." << endl;
+	cerr 						<< "\t  - Similar to \"grep -v.\"" << endl << endl;
 
 	// end the program here
 	exit(1);