Fixing own comments

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CommandLineGATK.scala

@@ -421,5 +421,8 @@ trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with
 
 object CommandLineGATK {
 
-  def isFileWithTag(file: File, tag: String): Boolean = file.isInstanceOf[TaggedFile] && file.asInstanceOf[TaggedFile].tag == tag
+  def isFileWithTag(file: File, tag: String): Boolean = file match {
+    case f:TaggedFile => f.tag == tag
+    case _ => false
+  }
 }
\ No newline at end of file

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala

@@ -38,10 +38,17 @@ object Logging {
 
   private[biopet] val errors: ListBuffer[Exception] = ListBuffer()
 
-  def addError(error: String, debug: String = null, cause: Exception = null): Unit = {
-    val msg = error + (if (debug != null && logger.isDebugEnabled) "; " + debug else "")
-    logger.error(msg, cause)
-    errors.append(if (cause != null) new Exception(msg, cause) else new Exception(msg))
+  def addError(error: String, debug: Option[String] = None, cause: Option[Exception] = None): Unit = {
+    val msg = error + debug.map("; " + _).getOrElse("")
+
+    cause match {
+      case Some(e) =>
+        logger.error(msg, e)
+        errors.append(new Exception(msg, e))
+      case _ =>
+        logger.error(msg)
+        errors.append(new Exception(msg))
+    }
   }
 
   def checkErrors(debug: Boolean = false): Unit = {

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala

@@ -160,8 +160,10 @@ class ShivaVariantcalling(val parent: Configurable)
       caller.namePrefix = namePrefix
       caller.outputDir = new File(outputDir, caller.name)
       caller.genders = genders
-      if (caller.isInstanceOf[SomaticVariantCaller])
-        caller.asInstanceOf[SomaticVariantCaller].tnPairs = tumorSamples
+      caller match {
+        case c:SomaticVariantCaller => c.tnPairs = tumorSamples
+        case _ =>
+      }
 
       add(caller)
       addStats(caller.outputFile, caller.name)