Change to option types

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

@@ -177,51 +177,51 @@ object BiopetQScript {
     require(outputDir.getAbsoluteFile.canWrite, s"No premision to write outputdir: $outputDir")
   }
 
-  def safeInputs(function: QFunction): Seq[File] = {
+  def safeInputs(function: QFunction): Option[Seq[File]] = {
     try {
-      function.inputs
+      Some(function.inputs)
     } catch {
-      case e: NullPointerException => Seq()
+      case e: NullPointerException => None
     }
   }
 
-  def safeOutputs(function: QFunction): Seq[File] = {
+  def safeOutputs(function: QFunction): Option[Seq[File]] = {
     try {
-      function.outputs
+      Some(function.outputs)
     } catch {
-      case e: NullPointerException => Seq()
+      case e: NullPointerException => None
     }
   }
 
-  def safeDoneFiles(function: QFunction): Seq[File] = {
+  def safeDoneFiles(function: QFunction): Option[Seq[File]] = {
     try {
-      function.doneOutputs
+      Some(function.doneOutputs)
     } catch {
-      case e: NullPointerException => Seq()
+      case e: NullPointerException => None
     }
   }
 
-  def safeFailFiles(function: QFunction): Seq[File] = {
+  def safeFailFiles(function: QFunction): Option[Seq[File]] = {
     try {
-      function.failOutputs
+      Some(function.failOutputs)
     } catch {
-      case e: NullPointerException => Seq()
+      case e: NullPointerException => None
     }
   }
 
-  def safeIsDone(function: QFunction): Boolean = {
+  def safeIsDone(function: QFunction): Option[Boolean] = {
     try {
-      function.isDone
+      Some(function.isDone)
     } catch {
-      case e: NullPointerException => false
+      case e: NullPointerException => None
     }
   }
 
-  def safeIsFail(function: QFunction): Boolean = {
+  def safeIsFail(function: QFunction): Option[Boolean] = {
     try {
-      function.isFail
+      Some(function.isFail)
     } catch {
-      case e: NullPointerException => false
+      case e: NullPointerException => None
     }
   }
 

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala

@@ -91,12 +91,12 @@ object WriteDependencies extends Logging with Configurable {
     val files: mutable.Map[File, QueueFile] = mutable.Map()
 
     for (function <- functions) {
-      for (input <- BiopetQScript.safeInputs(function)) {
+      for (input <- BiopetQScript.safeInputs(function).getOrElse(Seq())) {
         val file = files.getOrElse(input, QueueFile(input))
         file.addInputJob(function)
         files += input -> file
       }
-      for (output <- BiopetQScript.safeOutputs(function)) {
+      for (output <- BiopetQScript.safeOutputs(function).getOrElse(Seq())) {
         val file = files.getOrElse(output, QueueFile(output))
         file.addOutputJob(function)
         files += output -> file
@@ -113,13 +113,13 @@ object WriteDependencies extends Logging with Configurable {
           case s: WriteSummary if s.qscript.root == null => true
           case _                                         => false
         }), "intermediate" -> f.isIntermediate,
-          "depends_on_intermediate" -> BiopetQScript.safeOutputs(f).exists(files(_).isIntermediate),
-          "depends_on_jobs" -> BiopetQScript.safeOutputs(f).toList.flatMap(files(_).outputJobNames).distinct,
-          "output_used_by_jobs" -> BiopetQScript.safeOutputs(f).toList.flatMap(files(_).inputJobNames).distinct,
-          "outputs" -> BiopetQScript.safeOutputs(f).toList,
-          "inputs" -> BiopetQScript.safeOutputs(f).toList,
-          "done_files" -> BiopetQScript.safeDoneFiles(f).toList,
-          "fail_files" -> BiopetQScript.safeFailFiles(f).toList,
+          "depends_on_intermediate" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).exists(files(_).isIntermediate),
+          "depends_on_jobs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList.flatMap(files(_).outputJobNames).distinct,
+          "output_used_by_jobs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList.flatMap(files(_).inputJobNames).distinct,
+          "outputs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList,
+          "inputs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList,
+          "done_files" -> BiopetQScript.safeDoneFiles(f).getOrElse(Seq()).toList,
+          "fail_files" -> BiopetQScript.safeFailFiles(f).getOrElse(Seq()).toList,
           "stdout_file" -> f.jobOutputFile,
           "done_at_start" -> BiopetQScript.safeIsDone(f),
           "fail_at_start" -> BiopetQScript.safeIsFail(f))