Did #147: don't print usage on errors.

src/bedtools.cpp

@@ -96,7 +96,7 @@ int main(int argc, char *argv[])
     if (btDriver.supports(subCmd)) {
 		if (btDriver.subMain(argc, argv)) {
 			return 0;
-		} else {
+		} else if (!btDriver.hadError()) {
 			showHelp(subCmd);
 			return 1;
 		}

src/utils/Contexts/ContextBase.h

@@ -70,6 +70,7 @@ public:
 	ContextFileType getOutputFileType() const { return _outputFileType; }
 
 	virtual bool testCmdArgs(int argc, char **argv);
+	virtual bool errorEncountered() const { return !_errorMsg.empty(); }
 
 	 //isValidState checks that parameters to context are in an acceptable state.
 	// If not, the error msg string will be set with a reason why it failed.

src/utils/aux/BedtoolsDriver.cpp

@@ -24,7 +24,8 @@
 #include "fisher.h"
 #include "coverageFile.h"
 
-BedtoolsDriver::BedtoolsDriver() {
+BedtoolsDriver::BedtoolsDriver()
+: _hadError(false) {
 	_supported.insert("intersect");
 	_supported.insert("map");
 	_supported.insert("closest");
@@ -50,6 +51,7 @@ bool BedtoolsDriver::subMain(int argc, char **argv) {
 	//process all command line arguments, check for valid usage,
 	//show help and error messages if needed.
 	if (!context->testCmdArgs(argc - 1, argv + 1)) {
+		_hadError = context->errorEncountered();
 		delete context;
 		return false;
 	}

src/utils/aux/BedtoolsDriver.h

@@ -8,9 +8,11 @@ public:
 	bool supports(const QuickString &tool);
 	ContextBase *getContext();
 	ToolBase *getTool(ContextBase *context);
+	bool hadError() const { return _hadError; }
 protected:
 	QuickString _subCmd;
 	typedef set<QuickString> supportType;
 	supportType _supported;
+	bool _hadError;
 
 };