Merge pull request #65 from biopet/fix-BIOPET-642

Fixing nullpointer

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

@@ -99,7 +99,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
     beforeGraph()
     internalBeforeGraph()
 
-    this.commandDirectory = this.jobOutputFile.getParentFile
+    if (jobOutputFile != null) this.commandDirectory = this.jobOutputFile.getAbsoluteFile.getParentFile
 
     super.freezeFieldValues()
   }

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala

@@ -23,13 +23,13 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 class BedtoolsIntersect(val parent: Configurable) extends Bedtools {
 
   @Input(doc = "Input file (bed/gff/vcf/bam)")
-  var input: File = null
+  var input: File = _
 
   @Input(doc = "Intersect file (bed/gff/vcf)")
-  var intersectFile: File = null
+  var intersectFile: File = _
 
   @Output(doc = "output File")
-  var output: File = null
+  var output: File = _
 
   @Argument(doc = "Min overlap", required = false)
   var minOverlap: Option[Double] = config("minoverlap")
@@ -46,7 +46,8 @@ class BedtoolsIntersect(val parent: Configurable) extends Bedtools {
   }
 
   /** Returns command to execute */
-  def cmdLine = required(executable) + required("intersect") +
+  def cmdLine: String = required(executable) +
+    required("intersect") +
     required(inputTag, input) +
     required("-b", intersectFile) +
     optional("-f", minOverlap) +