Updated usage statement for pairToBed.

src/pairToBed/pairToBedMain.cpp

@@ -136,6 +136,11 @@ int main(int argc, char* argv[]) {
 		cerr << endl << "*****" << endl << "*****ERROR: Cannot enforce strandedness with selected searchtype" << endl << "*****" << endl;
 		showHelp = true;		
 	}
+	
+	if (useEditDistance && (inputIsBam == false || outputIsBam == true)) {
+		cerr << endl << "*****" << endl << "*****ERROR: -ed must be used with -bedpe and -abam." << endl << "*****" << endl;
+		showHelp = true;		
+	}
 
 	if (!showHelp) {
 
@@ -163,16 +168,17 @@ void ShowHelp(void) {
 
 	cerr << "Options: " << endl;
 
-	cerr << "\t-abam\t"			<< "The A input file is in BAM format.  Output will be BAM as well." << endl << endl;
-
+	cerr << "\t-abam\t"			<< "The A input file is in BAM format.  Output will be BAM as well." << endl;
+	cerr 					    << "\t\t- Requires BAM to be grouped or sorted by query." << endl << endl;
+	
 	cerr << "\t-bedpe\t"		<< "When using BAM input (-abam), write output as BEDPE. The default" << endl;
 	cerr 						<< "\t\tis to write output in BAM when using -abam." << endl << endl;
 	
-	cerr << "\t-ed\t"		<< "Use BAM total edit distance (NM tag) for BEDPE score." << endl;
-	cerr 					<< "\t\t- Default for BEDPE is to use the minimum of" << endl;
-	cerr 					<< "\t\t  of the two mapping qualities for the pair." << endl;
-	cerr 					<< "\t\t- When -ed is used the total edit distance" << endl;
-	cerr 					<< "\t\t  from the two mates is reported as the score." << endl << endl;
+	cerr << "\t-ed\t"	   		<< "Use BAM total edit distance (NM tag) for BEDPE score." << endl;
+	cerr 				   		<< "\t\t- Default for BEDPE is to use the minimum of" << endl;
+	cerr 				   		<< "\t\t  of the two mapping qualities for the pair." << endl;
+	cerr 				   		<< "\t\t- When -ed is used the total edit distance" << endl;
+	cerr 				   		<< "\t\t  from the two mates is reported as the score." << endl << endl;
 	
 	cerr << "\t-f\t"	    			<< "Minimum overlap required as fraction of A (e.g. 0.05)." << endl;
 	cerr 								<< "\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;