Fix unit testing

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala

@@ -42,7 +42,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
   var opt_front: Set[String] = Set()
   if (config.contains("front")) for (adapter <- config("front").asList) opt_front += adapter.toString
 
-  var opt_discard: Boolean = config("discard")
+  var opt_discard: Boolean = config("discard", default = false)
   var opt_minimum_length: String = config("minimum_length", 1)
   var opt_maximum_length: String = config("maximum_length")
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala

@@ -39,9 +39,9 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
   executable = config("exe", default = "fastqc")
   var java_exe: String = config("exe", default = "java", submodule = "java", freeVar = false)
   var kmers: Option[Int] = config("kmers")
-  var quiet: Boolean = config("quiet")
-  var noextract: Boolean = config("noextract")
-  var nogroup: Boolean = config("nogroup")
+  var quiet: Boolean = config("quiet", default = false)
+  var noextract: Boolean = config("noextract", default = false)
+  var nogroup: Boolean = config("nogroup", default = false)
   var extract: Boolean = config("extract", default = true)
 
   override val versionRegex = """FastQC (.*)""".r

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala

@@ -42,10 +42,10 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
   var iterations: Option[Int] = config("iterations")
   var minSnps: Option[Int] = config("min_snps")
   var convergeMethod: String = config("converge_method")
-  var useTimeStamp: Boolean = config("use_time_stamp")
+  var useTimeStamp: Boolean = config("use_time_stamp", default = false)
   var prefix: String = config("prefix")
-  var verbose: Boolean = config("verbose")
-  var noCleanup: Boolean = config("no_cleanup")
+  var verbose: Boolean = config("verbose", default = false)
+  var noCleanup: Boolean = config("no_cleanup", default = false)
 
   override def afterGraph: Unit = {
     super.afterGraph

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala

@@ -46,9 +46,9 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
   var qualityType: String = config("qualitytype")
   var qualityThreshold: Option[Int] = config("qualityThreshold")
   var lengthThreshold: Option[Int] = config("lengthThreshold")
-  var noFiveprime: Boolean = config("noFiveprime")
-  var discardN: Boolean = config("discardN")
-  var quiet: Boolean = config("quiet")
+  var noFiveprime: Boolean = config("noFiveprime", default = false)
+  var discardN: Boolean = config("discardN", default = false)
+  var quiet: Boolean = config("quiet", default = false)
   var defaultQualityType: String = config("defaultqualitytype", default = "sanger")
   override val versionRegex = """sickle version (.*)""".r
   override def versionCommand = executable + " --version"

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/aligners/Bwa.scala

@@ -36,7 +36,7 @@ class Bwa(val root: Configurable) extends BiopetCommandLineFunction {
   var R: String = config("R")
   var k: Option[Int] = config("k")
   var r: Option[Float] = config("r")
-  var S: Boolean = config("S")
+  var S: Boolean = config("S", default = false)
   var M: Boolean = config("M", default = true)
   var w: Option[Int] = config("w")
   var d: Option[Int] = config("d")
@@ -44,8 +44,8 @@ class Bwa(val root: Configurable) extends BiopetCommandLineFunction {
   var D: Option[Float] = config("D")
   var W: Option[Int] = config("W")
   var m: Option[Int] = config("m")
-  var P: Boolean = config("P")
-  var e: Boolean = config("e")
+  var P: Boolean = config("P", default = false)
+  var e: Boolean = config("e", default = false)
   var A: Option[Int] = config("A")
   var B: Option[Int] = config("B")
   var O: String = config("O")
@@ -53,13 +53,13 @@ class Bwa(val root: Configurable) extends BiopetCommandLineFunction {
   var L: String = config("L")
   var U: Option[Int] = config("U")
   var x: String = config("x")
-  var p: Boolean = config("p")
+  var p: Boolean = config("p", default = false)
   var v: Option[Int] = config("v")
   var T: Option[Int] = config("T")
   var h: Option[Int] = config("h")
-  var a: Boolean = config("a")
-  var C: Boolean = config("C")
-  var Y: Boolean = config("Y")
+  var a: Boolean = config("a", default = false)
+  var C: Boolean = config("C", default = false)
+  var Y: Boolean = config("Y", default = false)
   var I: String = config("I")
 
   executable = config("exe", default = "bwa", freeVar = false)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala

@@ -29,7 +29,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard {
   var maxInstertSize: Option[Int] = config("maxInstertSize")
 
   @Argument(doc = "ADAPTER_SEQUENCE", required = false)
-  var adapterSequence: List[String] = config("adapterSequence")
+  var adapterSequence: List[String] = config("adapterSequence", default = Nil)
 
   @Argument(doc = "IS_BISULFITE_SEQUENCED", required = false)
   var isBisulfiteSequenced: Option[Boolean] = config("isBisulfiteSequenced")
@@ -44,7 +44,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard {
   var assumeSorted: Boolean = config("assumeSorted", default = true)
 
   @Argument(doc = "METRIC_ACCUMULATION_LEVEL", required = false)
-  var metricAccumulationLevel: List[String] = config("metricaccumulationlevel")
+  var metricAccumulationLevel: List[String] = config("metricaccumulationlevel", default = Nil)
 
   @Argument(doc = "STOP_AFTER", required = false)
   var stopAfter: Option[Long] = config("stopAfter")

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala

@@ -19,6 +19,8 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
+import scala.collection.immutable.Nil
+
 class CollectInsertSizeMetrics(val root: Configurable) extends Picard {
   javaMainClass = "picard.analysis.CollectInsertSizeMetrics"
 
@@ -47,7 +49,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard {
   var stopAfter: Option[Long] = config("stopAfter")
 
   @Argument(doc = "METRIC_ACCUMULATION_LEVEL", required = false)
-  var metricAccumulationLevel: List[String] = config("metricaccumulationlevel")
+  var metricAccumulationLevel: List[String] = config("metricaccumulationlevel", default = Nil)
 
   @Argument(doc = "HISTOGRAM_WIDTH", required = false)
   var histogramWidth: Option[Int] = config("histogramWidth")

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala

@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 
 abstract class Samtools extends BiopetCommandLineFunction {
   override def subPath = "samtools" :: super.subPath
-  executable = config("exe", default = "samtools", freeVar = false)
+  executable = config("exe", default = "samtools")
   override def versionCommand = executable
   override val versionRegex = """Version: (.*)""".r
   override val versionExitcode = List(0, 1)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala

@@ -58,28 +58,28 @@ class SeqtkSeq(val root: Configurable) extends Seqtk {
   var L: Option[Int] = config("L")
 
   /** mask complement region (effective with -M) */
-  var c: Boolean = config("c")
+  var c: Boolean = config("c", default = false)
 
   /** reverse complement */
-  var r: Boolean = config("r")
+  var r: Boolean = config("r", default = false)
 
   /** force FASTA output (discard quality) */
-  var A: Boolean = config("A")
+  var A: Boolean = config("A", default = false)
 
   /** drop comments at the header lines */
-  var C: Boolean = config("C")
+  var C: Boolean = config("C", default = false)
 
   /** drop sequences containing ambiguous bases */
-  var N: Boolean = config("N")
+  var N: Boolean = config("N", default = false)
 
   /** output the 2n-1 reads only */
-  var flag1: Boolean = config("1")
+  var flag1: Boolean = config("1", default = false)
 
   /** output the 2n reads only */
-  var flag2: Boolean = config("2")
+  var flag2: Boolean = config("2", default = false)
 
   /** shift quality by '(-Q) - 33' */
-  var V: Boolean = config("V")
+  var V: Boolean = config("V", default = false)
 
   def cmdLine = {
     required(executable) +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala

@@ -40,7 +40,7 @@ class VcfFilter(val root: Configurable) extends BiopetJavaCommandLineFunction {
   var minTotalDepth: Option[Int] = config("min_total_depth")
   var minAlternateDepth: Option[Int] = config("min_alternate_depth")
   var minSamplesPass: Option[Int] = config("min_samples_pass")
-  var filterRefCalls: Boolean = config("filter_ref_calls")
+  var filterRefCalls: Boolean = config("filter_ref_calls", default = false)
 
   override val defaultVmem = "8G"
   memoryLimit = Option(4.0)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala

@@ -354,7 +354,8 @@ object ConfigUtils extends Logging {
      * @return
      */
     implicit def configValue2long(value: ConfigValue): Long = {
-      if (value != null && value.value != null && value.value != None) any2long(value.value) else 0
+      if (value != null && value.value != null && value.value != None) any2long(value.value)
+      else throw new IllegalStateException("Value does not exist")
     }
 
     /**
@@ -372,7 +373,8 @@ object ConfigUtils extends Logging {
      * @return
      */
     implicit def configValue2int(value: ConfigValue): Int = {
-      if (value != null && value.value != null && value.value != None) any2int(value.value) else 0
+      if (value != null && value.value != null && value.value != None) any2int(value.value)
+      else throw new IllegalStateException("Value does not exist")
     }
 
     /**
@@ -390,7 +392,8 @@ object ConfigUtils extends Logging {
      * @return
      */
     implicit def configValue2double(value: ConfigValue): Double = {
-      if (value != null && value.value != null && value.value != None) any2double(value.value) else 0
+      if (value != null && value.value != null && value.value != None) any2double(value.value)
+      else throw new IllegalStateException("Value does not exist")
     }
 
     /**
@@ -408,7 +411,8 @@ object ConfigUtils extends Logging {
      * @return
      */
     implicit def configValue2float(value: ConfigValue): Float = {
-      if (value != null && value.value != null && value.value != None) any2float(value.value) else 0
+      if (value != null && value.value != null && value.value != None) any2float(value.value)
+      else throw new IllegalStateException("Value does not exist")
     }
 
     /**
@@ -426,7 +430,8 @@ object ConfigUtils extends Logging {
      * @return
      */
     implicit def configValue2boolean(value: ConfigValue): Boolean = {
-      if (value != null && value.value != null && value.value != None) any2boolean(value.value) else false
+      if (value != null && value.value != null && value.value != None) any2boolean(value.value)
+      else throw new IllegalStateException("Value does not exist")
     }
 
     /**
@@ -444,7 +449,8 @@ object ConfigUtils extends Logging {
      * @return
      */
     implicit def configValue2list(value: ConfigValue): List[Any] = {
-      if (value != null && value.value != null && value.value != None) any2list(value.value) else null
+      if (value != null && value.value != null && value.value != None) any2list(value.value)
+      else throw new IllegalStateException("Value does not exist")
     }
 
     /**
@@ -453,7 +459,8 @@ object ConfigUtils extends Logging {
      * @return
      */
     implicit def configValue2stringList(value: ConfigValue): List[String] = {
-      if (value != null && value.value != null && value.value != None) any2stringList(value.value) else null
+      if (value != null && value.value != null && value.value != None) any2stringList(value.value)
+      else throw new IllegalStateException("Value does not exist")
     }
 
     /**
@@ -462,7 +469,8 @@ object ConfigUtils extends Logging {
      * @return
      */
     implicit def configValue2stringSet(value: ConfigValue): Set[String] = {
-      if (value != null && value.value != null && value.value != None) any2stringList(value.value).toSet else null
+      if (value != null && value.value != null && value.value != None) any2stringList(value.value).toSet
+      else throw new IllegalStateException("Value does not exist")
     }
 
     /**
@@ -471,7 +479,8 @@ object ConfigUtils extends Logging {
      * @return
      */
     implicit def configValue2map(value: ConfigValue): Map[String, Any] = {
-      if (value != null && value.value != null && value.value != None) any2map(value.value) else null
+      if (value != null && value.value != null && value.value != None) any2map(value.value)
+      else throw new IllegalStateException("Value does not exist")
     }
   }
 }

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala

@@ -169,17 +169,20 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
   @Test def testImplicits: Unit = {
     val index = ConfigValueIndex("test", Nil, "test")
     new ImplicitConversions {
-      var map: Map[String, Any] = ConfigValue(index, index, Map())
-      map = ConfigValue(index, index, null)
-
       configValue2list(ConfigValue(index, index, List(""))) shouldBe List("")
-      configValue2list(ConfigValue(index, index, null)) shouldBe null
+      intercept[IllegalStateException] {
+        configValue2list(ConfigValue(index, index, null))
+      }
 
       configValue2stringList(ConfigValue(index, index, List(""))) shouldBe List("")
-      configValue2stringList(ConfigValue(index, index, null)) shouldBe null
+      intercept[IllegalStateException] {
+        configValue2stringList(ConfigValue(index, index, null))
+      }
 
       configValue2stringSet(ConfigValue(index, index, List(""))) shouldBe Set("")
-      configValue2stringSet(ConfigValue(index, index, null)) shouldBe null
+      intercept[IllegalStateException] {
+        configValue2stringSet(ConfigValue(index, index, null))
+      }
 
       var int: Int = ConfigValue(index, index, 1)
       intercept[IllegalStateException] {