bamToBed assumes stdin.

src/bamToBed/bamToBed.cpp

@@ -55,11 +55,11 @@ int main(int argc, char* argv[]) {
 	bool showHelp = false;
 
 	// input files
-	string bamFile;
-	string color = "255,0,0";
-    string tag   = "";
+	string bamFile = "stdin";
+	string color   = "255,0,0";
+    string tag     = "";
 	
-	bool haveBam           = false;
+	bool haveBam           = true;
 	bool haveColor         = false;
     bool haveOtherTag      = false;	
 	bool writeBedPE        = false;
@@ -69,7 +69,6 @@ int main(int argc, char* argv[]) {
 	bool obeySplits        = 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]);
@@ -89,7 +88,6 @@ int main(int argc, char* argv[]) {
 
 		if(PARAMETER_CHECK("-i", 2, parameterLength)) {
 			if ((i+1) < argc) {
-				haveBam = true;
 				bamFile = argv[i + 1];
 				i++;
 			}