Removed -debug/--debug_mode.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5697 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java

@@ -54,20 +54,12 @@ public abstract class CommandLineProgram {
               required = false)
     protected String toFile = null;
 
-    /** do we want to generate debugging information with the logs */
-    @Argument(fullName = "debug_mode",
-              shortName = "debug",
-              doc = "Set the logging file string to include a lot of debugging information (SLOW!)",
-              required = false)
-    protected Boolean debugMode = false;
-
     /** this is used to indicate if they've asked for help */
     @Argument(fullName = "help", shortName = "h", doc = "Generate this help message", required = false)
     public Boolean help = false;
 
     /** our logging output patterns */
-    private static String patternString = "%-5p %d{HH:mm:ss,SSS} %C{1} - %m %n";
+    private static final String patternString = "%-5p %d{HH:mm:ss,SSS} %C{1} - %m %n";
-    private static String debugPatternString = "%n[level] %p%n[date]\t\t %d{dd MMM yyyy HH:mm:ss,SSS} %n[class]\t\t %C %n[location]\t %l %n[line number]\t %L %n[message]\t %m %n";
 
     static {
         /**
@@ -250,14 +242,8 @@ public abstract class CommandLineProgram {
      * level that was provided.
      * @param layout Pattern layout to format based on the logger level.
      */
-    @SuppressWarnings("unchecked")
     private void setupLoggerLevel(PatternLayout layout) {
-        // if we're in debug mode, set the mode up
-        if (debugMode) {
-            layout.setConversionPattern(debugPatternString);
-        } else {
         layout.setConversionPattern(patternString);
-        }
 
         // set the default logger level
         Level par;

scala/src/org/broadinstitute/sting/queue/QCommandLine.scala

@@ -47,7 +47,7 @@ object QCommandLine {
 
     Runtime.getRuntime.addShutdownHook(new Thread {
       /** Cleanup as the JVM shuts down. */
-      override def run = {
+      override def run() {
         ProcessController.shutdown()
         qCommandLine.shutdown()
       }
@@ -94,13 +94,12 @@ class QCommandLine extends CommandLineProgram with Logging {
    */
   def execute = {
     qGraph.settings = settings
-    qGraph.debugMode = debugMode == true
 
     for (script <- pluginManager.createAllTypes()) {
       logger.info("Scripting " + pluginManager.getName(script.getClass.asSubclass(classOf[QScript])))
       loadArgumentsIntoObject(script)
       try {
-        script.script
+        script.script()
       } catch {
         case e: Exception =>
           throw new UserException.CannotExecuteQScript(script.getClass.getSimpleName + ".script() threw the following exception: " + e, e)

scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala

@@ -44,7 +44,6 @@ import org.broadinstitute.sting.queue.function.scattergather.{ScatterFunction, C
  */
 class QGraph extends Logging {
   var settings: QGraphSettings = _
-  var debugMode = false
 
   private def dryRun = !settings.run
   private var numMissingValues = 0
@@ -147,8 +146,6 @@ class QGraph extends Logging {
         val functions = scatterGather.asInstanceOf[FunctionEdge]
                 .function.asInstanceOf[ScatterGatherableFunction]
                 .generateFunctions()
-        if (this.debugMode)
-          logger.debug("Scattered into %d parts: %n%s".format(functions.size, functions.mkString(nl)))
         addedFunctions ++= functions
       }