Logging layout is now done with properties files

biopet-framework/src/main/resources/log4j.properties

+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=INFO, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala

 package nl.lumc.sasc.biopet.core
 
-import java.text.SimpleDateFormat
-import java.util.Calendar
 import org.apache.log4j.Logger
-import org.apache.log4j.WriterAppender
-import org.apache.log4j.helpers.DateLayout
 
 trait Logging {
   def logger = Logging.logger
 }
 
 object Logging {
-  val logger = Logger.getLogger("Logging")
-
-  val logLayout = new DateLayout() {
-    val ignoresThrowable = false
-    def format(event: org.apache.log4j.spi.LoggingEvent): String = {
-      val calendar: Calendar = Calendar.getInstance
-      calendar.setTimeInMillis(event.getTimeStamp)
-      val formatter: SimpleDateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
-      val formattedDate: String = formatter.format(calendar.getTime)
-      var logLevel = event.getLevel.toString
-      while (logLevel.size < 6) logLevel += " "
-      val className = event.getLocationInformation.getClassName.split("\\.").last.split("\\$").head
-      logLevel + " [" + formattedDate + "] [" + className + "] " + event.getMessage + "\n"
-    }
-  }
-
-  val stderrAppender = new WriterAppender(logLayout, sys.process.stderr)
-
-  logger.setLevel(org.apache.log4j.Level.INFO)
-  logger.addAppender(Logging.stderrAppender)
+  val logger = Logger.getRootLogger
 }
\ No newline at end of file

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala

 package nl.lumc.sasc.biopet.core
 
-import org.apache.log4j.WriterAppender
-import java.io.File
-
 trait ToolCommand extends MainCommand with Logging {
   abstract class AbstractArgs {
   }
 
   abstract class AbstractOptParser extends scopt.OptionParser[Args](commandName) {
-    opt[Unit]("log_nostderr") foreach { _ =>
-      logger.removeAppender(Logging.stderrAppender)
-    } text ("No output to stderr")
-    opt[File]("log_file") foreach { x =>
-      logger.addAppender(new WriterAppender(Logging.logLayout, new java.io.PrintStream(x)))
-    } text ("Log file") valueName ("<file>")
     opt[String]('l', "log_level") foreach { x =>
       x.toLowerCase match {
         case "debug" => logger.setLevel(org.apache.log4j.Level.DEBUG)

biopet-framework/src/test/resources/log4j.properties

+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file