shuffleBed assumes stdin.

src/shuffleBed/shuffleBedMain.cpp

@@ -30,19 +30,17 @@ int main(int argc, char* argv[]) {
 	bool showHelp = false;
 
 	// input files
-	string bedFile;
+	string bedFile = "stdin";
 	string excludeFile;	
 	string genomeFile;
 	
-	bool haveBed = false;
-	bool haveGenome = false;
+	bool haveBed     = true;
+	bool haveGenome  = false;
 	bool haveExclude = false;
-	bool haveSeed = false;
-	int seed = -1;
-	bool sameChrom = false;
+	bool haveSeed    = false;
+	int seed         = -1;
+	bool sameChrom   = false;
 
-	// check to see if we should print out some help
-	if(argc <= 1) showHelp = true;
 
 	for(int i = 1; i < argc; i++) {
 		int parameterLength = (int)strlen(argv[i]);
@@ -62,7 +60,6 @@ int main(int argc, char* argv[]) {
 
  		if(PARAMETER_CHECK("-i", 2, parameterLength)) {
 			if ((i+1) < argc) {
-				haveBed = true;
 				bedFile = argv[i + 1];
 				i++;
 			}