Merge branch 'fix-BIOPET-458' into 'develop'

Fixed nullpointer



See merge request !474

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

@@ -38,8 +38,6 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
     if (config.contains("output_dir", path = Nil)) config("output_dir", path = Nil).asFile
     else new File(".")
   }
-  require(outputDir.canRead, s"No premision to read outputdir: $outputDir")
-  require(outputDir.canWrite, s"No premision to read outputdir: $outputDir")
 
   @Argument(doc = "Disable all scatters", shortName = "DSC", required = false)
   var disableScatter: Boolean = false
@@ -161,10 +159,10 @@ object BiopetQScript {
 
   def checkOutputDir(outputDir: File): Unit = {
     // Sanity checks
-    require(outputDir.getParentFile.canRead, s"No premision to read parent of outputdir: ${outputDir.getParentFile}")
-    require(outputDir.getParentFile.canWrite, s"No premision to write parent of outputdir: ${outputDir.getParentFile}")
+    require(outputDir.getAbsoluteFile.getParentFile.canRead, s"No premision to read parent of outputdir: ${outputDir.getParentFile}")
+    require(outputDir.getAbsoluteFile.getParentFile.canWrite, s"No premision to write parent of outputdir: ${outputDir.getParentFile}")
     outputDir.mkdir()
-    require(outputDir.canRead, s"No premision to read outputdir: $outputDir")
-    require(outputDir.canWrite, s"No premision to write outputdir: $outputDir")
+    require(outputDir.getAbsoluteFile.canRead, s"No premision to read outputdir: $outputDir")
+    require(outputDir.getAbsoluteFile.canWrite, s"No premision to write outputdir: $outputDir")
   }
 }