Further standardization of the option listings.

src/closestBed/closestMain.cpp

@@ -107,7 +107,7 @@ void ShowHelp(void) {
 	cerr << "Author:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
 
 	cerr << "Summary: For each feature in BED A, finds the closest " << endl;
-	cerr << "\t\t feature (upstream or downstream) in BED B." << endl << endl;
+	cerr << "\t feature (upstream or downstream) in BED B." << endl << endl;
 
 	cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
 

src/pairToPair/pairToPairMain.cpp

@@ -139,7 +139,7 @@ void ShowHelp(void) {
 	cerr 								<< "\t\tneither\tReport overlaps if neither end of A overlaps B." << endl;
 
 	cerr 								<< "\t\tboth\tReport overlaps if both ends of A overlap B." << endl;
-	cerr									<< "\t\t\t- Default." << endl << endl;
+	cerr									<< "\t\t- Default." << endl << endl;
 
 	cerr << "\t-is\t"	    			<< "Ignore strands when searching for overlaps." << endl;
 	cerr 								<< "\t\t- By default, strands are enforced." << endl << endl;

src/subtractBed/subtractMain.cpp

@@ -112,7 +112,7 @@ void ShowHelp(void) {
 	cerr << "Author:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
 
 	cerr << "Summary: Removes the portion(s) of an interval that is overlapped" << endl;
-	cerr << "\t\t by another feature(s)." << endl << endl;
+	cerr << "\t by another feature(s)." << endl << endl;
 
 	cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
 

src/windowBed/windowMain.cpp

@@ -167,8 +167,8 @@ void ShowHelp(void) {
 	cerr << "Author:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
 
 	cerr << "Summary: Examines a \"window\" around each feature in A and" << endl;
-	cerr << "\t\t reports all features in B that overlap the window. For each" << endl;
-	cerr << "\t\t overlap the entire entry in A and B are reported." << endl << endl;
+	cerr << "\t reports all features in B that overlap the window. For each" << endl;
+	cerr << "\t 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;