Fix code style warnings

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala

@@ -24,7 +24,7 @@ import org.testng.annotations.{ DataProvider, Test }
  * Created by pjvan_thof on 1/8/15.
  */
 class ConfigTest extends TestNGSuite with Matchers with ConfigUtils.ImplicitConversions {
-  @Test def testLoadConfigFile: Unit = {
+  @Test def testLoadConfigFile(): Unit = {
     val config = new Config
     config.loadConfigFile(ConfigTest.file)
     config.map shouldBe ConfigTest.map
@@ -32,7 +32,7 @@ class ConfigTest extends TestNGSuite with Matchers with ConfigUtils.ImplicitConv
     config.map shouldBe ConfigTest.map
   }
 
-  @Test def testContains: Unit = {
+  @Test def testContains(): Unit = {
     ConfigTest.config.contains("m1") shouldBe true
     ConfigTest.config.contains("notexist") shouldBe false
     ConfigTest.config.contains(new ConfigValueIndex("m1", Nil, "k1")) shouldBe true
@@ -40,23 +40,23 @@ class ConfigTest extends TestNGSuite with Matchers with ConfigUtils.ImplicitConv
     ConfigTest.config.contains(new ConfigValueIndex("notexist", Nil, "k1", false)) shouldBe false
   }
 
-  @Test def testApply: Unit = {
+  @Test def testApply(): Unit = {
     ConfigTest.config("m1", Nil, "k1").asString shouldBe "v2"
     ConfigTest.config("m1", Nil, "notexist", default = "default").asString shouldBe "default"
   }
 
-  @Test def testMergeConfigs: Unit = {
+  @Test def testMergeConfigs(): Unit = {
     val map1 = Map("1" -> 1)
     val map2 = Map("2" -> 2)
     Config.mergeConfigs(new Config(map1), new Config(map2)).map shouldBe ConfigUtils.mergeMaps(map1, map2)
   }
 
-  @Test def testToString: Unit = {
+  @Test def testToString(): Unit = {
     val map1 = Map("1" -> 1)
     new Config(map1).toString() shouldBe map1.toString()
   }
 
-  @Test def testSkipNested: Unit = {
+  @Test def testSkipNested(): Unit = {
     val map = Map("1" -> Map("2" -> Map("4" -> Map("5" -> Map("k1" -> "v1")))))
     Config.getValueFromMap(map, new ConfigValueIndex("5", List("1", "2", "4", "5"), "k1")).get.asString shouldBe "v1"
     Config.getValueFromMap(map, new ConfigValueIndex("5", List("1", "2", "3", "4", "5"), "k1")).get.asString shouldBe "v1"

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigValueTest.scala

@@ -26,7 +26,7 @@ import org.testng.annotations.Test
  */
 class ConfigValueTest extends TestNGSuite with Matchers {
   val index = ConfigValueIndex("", Nil, "")
-  @Test def testAs: Unit = {
+  @Test def testAs(): Unit = {
     ConfigValue(index, index, "bla").asString shouldBe "bla"
     ConfigValue(index, index, 1).asInt shouldBe 1
     ConfigValue(index, index, 1.0).asDouble shouldBe 1.0
@@ -37,7 +37,7 @@ class ConfigValueTest extends TestNGSuite with Matchers {
     ConfigValue(index, index, List("bla")).asFileList shouldBe List(new File("bla"))
   }
 
-  @Test def testToString: Unit = {
-    ConfigValue(index, index, "bla", true).toString.getClass.getSimpleName shouldBe "String"
+  @Test def testToString(): Unit = {
+    ConfigValue(index, index, "bla", default = true).toString.getClass.getSimpleName shouldBe "String"
   }
 }

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala

@@ -23,7 +23,7 @@ import org.testng.annotations.Test
  * Created by pjvan_thof on 1/8/15.
  */
 class ConfigurableTest extends TestNGSuite with Matchers {
-  @Test def testConfigurable: Unit = {
+  @Test def testConfigurable(): Unit = {
     val classC = new ClassC {
       override def configName = "classc"
       override val globalConfig = new Config(ConfigurableTest.map)

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala

@@ -26,7 +26,7 @@ import scala.sys.process.{ Process, ProcessLogger }
 class GsnapTest extends TestNGSuite with Matchers {
 
   private def setConfig(key: String, value: String): Map[String, Any] = {
-    val oldMap: Map[String, Any] = Config.global.map.toMap
+    val oldMap: Map[String, Any] = Config.global.map
     Config.global.map += (key -> value)
     oldMap
   }

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala

@@ -28,7 +28,7 @@ import org.testng.annotations.Test
 class CollectAlignmentSummaryMetricsTest extends TestNGSuite with Matchers {
 
   @Test
-  def summaryData: Unit = {
+  def summaryData(): Unit = {
     val file = new File(Paths.get(getClass.getResource("/picard.alignmentMetrics").toURI).toString)
     val job = new CollectAlignmentSummaryMetrics(null)
     job.output = file

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala

@@ -28,7 +28,7 @@ import org.testng.annotations.Test
 class CollectInsertSizeMetricsTest extends TestNGSuite with Matchers {
 
   @Test
-  def summaryData: Unit = {
+  def summaryData(): Unit = {
     val file = new File(Paths.get(getClass.getResource("/picard.insertsizemetrics").toURI).toString)
     val job = new CollectInsertSizeMetrics(null)
     job.output = file

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala

@@ -28,7 +28,7 @@ import org.testng.annotations.Test
 class MarkDuplicatesTest extends TestNGSuite with Matchers {
 
   @Test
-  def summaryData: Unit = {
+  def summaryData(): Unit = {
     val file = new File(Paths.get(getClass.getResource("/picard.dedup.metrics").toURI).toString)
     val job = new MarkDuplicates(null)
     job.outputMetrics = file

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala

@@ -61,8 +61,8 @@ class FastqSyncTest extends TestNGSuite with MockitoSugar with Matchers {
 
     val (numDiscard1, numDiscard2, numKept) = syncFastq(refMock, aMock, bMock, aOutMock, bOutMock)
 
-    obs.verify(aOutMock).write(exp(0))
-    obs.verify(bOutMock).write(exp(0))
+    obs.verify(aOutMock).write(exp.head)
+    obs.verify(bOutMock).write(exp.head)
 
     obs.verify(aOutMock).write(exp(1))
     obs.verify(bOutMock).write(exp(1))
@@ -156,8 +156,8 @@ class FastqSyncTest extends TestNGSuite with MockitoSugar with Matchers {
     val (numDiscard1, numDiscard2, numKept) = syncFastq(refMock, aMock, bMock, aOutMock, bOutMock)
 
     // exp(1) is discarded by syncFastq
-    obs.verify(aOutMock).write(exp(0))
-    obs.verify(bOutMock).write(exp(0))
+    obs.verify(aOutMock).write(exp.head)
+    obs.verify(bOutMock).write(exp.head)
 
     obs.verify(aOutMock).write(exp(2))
     obs.verify(bOutMock).write(exp(2))

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala

@@ -92,7 +92,7 @@ class SeqStatTest extends TestNGSuite with MockitoSugar with Matchers {
     baseHistogram(39) shouldEqual 5
     baseHistogram(34) shouldEqual 5
     baseHistogram(33) shouldEqual 5
-    baseHistogram(0) shouldEqual 5
+    baseHistogram.head shouldEqual 5
   }
 
   @Test def testArgsMinimum() = {

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala

@@ -29,7 +29,7 @@ import scala.collection.mutable
 class VcfStatsTest extends TestNGSuite with Matchers {
 
   @Test
-  def testSampleToSampleStats: Unit = {
+  def testSampleToSampleStats(): Unit = {
     val s1 = SampleToSampleStats()
     val s2 = SampleToSampleStats()
     s1.alleleOverlap shouldBe 0
@@ -60,7 +60,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testSampleStats: Unit = {
+  def testSampleStats(): Unit = {
     val s1 = SampleStats()
     val s2 = SampleStats()
 
@@ -94,7 +94,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testAlleleOverlap: Unit = {
+  def testAlleleOverlap(): Unit = {
 
     val a1 = Allele.create("G")
     val a2 = Allele.create("A")

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala

@@ -92,21 +92,21 @@ class VepNormalizerTest extends TestNGSuite with MockitoSugar with Matchers {
     val reader = new VCFFileReader(vepped, false)
     val header = reader.getFileHeader
     val new_infos = parseCsq(header)
-    explodeTranscripts(reader.iterator().next(), new_infos, true).length should be(11)
+    explodeTranscripts(reader.iterator().next(), new_infos, removeCsq = true).length should be(11)
   }
 
   @Test def testStandardVEPLength() = {
     val reader = new VCFFileReader(vepped, false)
     val header = reader.getFileHeader
     val new_infos = parseCsq(header)
-    Array(standardTranscripts(reader.iterator().next(), new_infos, true)).length should be(1)
+    Array(standardTranscripts(reader.iterator().next(), new_infos, removeCsq = true)).length should be(1)
   }
 
   @Test def testStandardVEPAttributeLength() = {
     val reader = new VCFFileReader(vepped, false)
     val header = reader.getFileHeader
     val new_infos = parseCsq(header)
-    val record = standardTranscripts(reader.iterator().next(), new_infos, true)
+    val record = standardTranscripts(reader.iterator().next(), new_infos, removeCsq = true)
     def checkItems(items: Array[String]) = {
       items.foreach { check }
     }

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala

@@ -195,7 +195,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
     //       and only filling the filter with a few items
     val filterNotFunc = makeFilterNotFunction(intervals, sBamFile1, bloomSize = bloomSize, bloomFp = bloomFp)
     // by default, set elements are SAM record read names
-    filterNotFunc(sBamRecs1(0)) shouldBe false
+    filterNotFunc(sBamRecs1.head) shouldBe false
     filterNotFunc(sBamRecs1(1)) shouldBe true
     filterNotFunc(sBamRecs1(2)) shouldBe true
     filterNotFunc(sBamRecs1(3)) shouldBe true
@@ -211,7 +211,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
       new Interval("P", 191, 480)
     )
     val filterNotFunc = makeFilterNotFunction(intervals, sBamFile1, bloomSize = bloomSize, bloomFp = bloomFp)
-    filterNotFunc(sBamRecs1(0)) shouldBe false
+    filterNotFunc(sBamRecs1.head) shouldBe false
     filterNotFunc(sBamRecs1(1)) shouldBe true
     filterNotFunc(sBamRecs1(2)) shouldBe true
     filterNotFunc(sBamRecs1(3)) shouldBe true
@@ -225,7 +225,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
       new Interval("chrQ", 881, 1000) // overlaps first exon of r05
     )
     val filterNotFunc = makeFilterNotFunction(intervals, sBamFile1, bloomSize = bloomSize, bloomFp = bloomFp)
-    filterNotFunc(sBamRecs1(0)) shouldBe false
+    filterNotFunc(sBamRecs1.head) shouldBe false
     filterNotFunc(sBamRecs1(1)) shouldBe false
     filterNotFunc(sBamRecs1(2)) shouldBe false
     filterNotFunc(sBamRecs1(3)) shouldBe false
@@ -240,7 +240,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
       new Interval("chrQ", 900, 920)
     )
     val filterNotFunc = makeFilterNotFunction(intervals, sBamFile1, bloomSize = bloomSize, bloomFp = bloomFp)
-    filterNotFunc(sBamRecs1(0)) shouldBe false
+    filterNotFunc(sBamRecs1.head) shouldBe false
     filterNotFunc(sBamRecs1(1)) shouldBe false
     filterNotFunc(sBamRecs1(2)) shouldBe false
     filterNotFunc(sBamRecs1(3)) shouldBe false
@@ -256,7 +256,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
       new Interval("chrR", 500, 505)
     )
     val filterNotFunc = makeFilterNotFunction(intervals, sBamFile5, bloomSize = bloomSize, bloomFp = bloomFp)
-    filterNotFunc(sBamRecs5(0)) shouldBe true
+    filterNotFunc(sBamRecs5.head) shouldBe true
     filterNotFunc(sBamRecs5(1)) shouldBe false
     filterNotFunc(sBamRecs5(2)) shouldBe false
     filterNotFunc(sBamRecs5(3)) shouldBe true
@@ -271,7 +271,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
     )
     val filterNotFunc = makeFilterNotFunction(intervals, sBamFile1, bloomSize = bloomSize, bloomFp = bloomFp,
       filterOutMulti = false)
-    filterNotFunc(sBamRecs1(0)) shouldBe false
+    filterNotFunc(sBamRecs1.head) shouldBe false
     filterNotFunc(sBamRecs1(1)) shouldBe false
     filterNotFunc(sBamRecs1(2)) shouldBe true
     filterNotFunc(sBamRecs1(3)) shouldBe true
@@ -287,7 +287,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
     )
     val filterNotFunc = makeFilterNotFunction(intervals, sBamFile2, bloomSize = bloomSize, bloomFp = bloomFp,
       minMapQ = 60)
-    filterNotFunc(sBamRecs2(0)) shouldBe false
+    filterNotFunc(sBamRecs2.head) shouldBe false
     // r01 is not in since it is below the MAPQ threshold
     filterNotFunc(sBamRecs2(1)) shouldBe false
     filterNotFunc(sBamRecs2(2)) shouldBe false
@@ -305,7 +305,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
     )
     val filterNotFunc = makeFilterNotFunction(intervals, sBamFile2, bloomSize = bloomSize, bloomFp = bloomFp,
       minMapQ = 60, filterOutMulti = false)
-    filterNotFunc(sBamRecs2(0)) shouldBe false
+    filterNotFunc(sBamRecs2.head) shouldBe false
     filterNotFunc(sBamRecs2(1)) shouldBe false
     // this r01 is not in since it is below the MAPQ threshold
     filterNotFunc(sBamRecs2(2)) shouldBe false
@@ -324,7 +324,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
     )
     val filterNotFunc = makeFilterNotFunction(intervals, sBamFile2, bloomSize = bloomSize, bloomFp = bloomFp,
       readGroupIds = Set("002", "003"))
-    filterNotFunc(sBamRecs2(0)) shouldBe false
+    filterNotFunc(sBamRecs2.head) shouldBe false
     // only r01 is in the set since it is RG 002
     filterNotFunc(sBamRecs2(1)) shouldBe true
     filterNotFunc(sBamRecs2(2)) shouldBe true
@@ -342,7 +342,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
       new Interval("chrQ", 991, 1000) // overlaps nothing; lies in the spliced region of r05
     )
     val filterNotFunc = makeFilterNotFunction(intervals, pBamFile1, bloomSize = bloomSize, bloomFp = bloomFp)
-    filterNotFunc(pBamRecs1(0)) shouldBe false
+    filterNotFunc(pBamRecs1.head) shouldBe false
     filterNotFunc(pBamRecs1(1)) shouldBe false
     filterNotFunc(pBamRecs1(2)) shouldBe true
     filterNotFunc(pBamRecs1(3)) shouldBe true
@@ -363,7 +363,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
       new Interval("chrQ", 891, 1000)
     )
     val filterNotFunc = makeFilterNotFunction(intervals, pBamFile1, bloomSize = bloomSize, bloomFp = bloomFp)
-    filterNotFunc(pBamRecs1(0)) shouldBe false
+    filterNotFunc(pBamRecs1.head) shouldBe false
     filterNotFunc(pBamRecs1(1)) shouldBe false
     filterNotFunc(pBamRecs1(2)) shouldBe false
     filterNotFunc(pBamRecs1(3)) shouldBe false
@@ -387,7 +387,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
     )
     val filterNotFunc = makeFilterNotFunction(intervals, pBamFile1, bloomSize = bloomSize, bloomFp = bloomFp,
       filterOutMulti = false)
-    filterNotFunc(pBamRecs1(0)) shouldBe false
+    filterNotFunc(pBamRecs1.head) shouldBe false
     filterNotFunc(pBamRecs1(1)) shouldBe false
     filterNotFunc(pBamRecs1(2)) shouldBe false
     filterNotFunc(pBamRecs1(3)) shouldBe false
@@ -411,7 +411,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
     val filterNotFunc = makeFilterNotFunction(intervals, pBamFile2, bloomSize = bloomSize, bloomFp = bloomFp,
       minMapQ = 60)
     // r01 is not in since it is below the MAPQ threshold
-    filterNotFunc(pBamRecs2(0)) shouldBe false
+    filterNotFunc(pBamRecs2.head) shouldBe false
     filterNotFunc(pBamRecs2(1)) shouldBe false
     filterNotFunc(pBamRecs2(2)) shouldBe false
     filterNotFunc(pBamRecs2(3)) shouldBe false
@@ -431,7 +431,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
     val filterNotFunc = makeFilterNotFunction(intervals, pBamFile2, bloomSize = bloomSize, bloomFp = bloomFp,
       readGroupIds = Set("002", "003"))
     // only r01 is in the set since it is RG 002
-    filterNotFunc(pBamRecs2(0)) shouldBe false
+    filterNotFunc(pBamRecs2.head) shouldBe false
     filterNotFunc(pBamRecs2(1)) shouldBe false
     filterNotFunc(pBamRecs2(2)) shouldBe true
     filterNotFunc(pBamRecs2(3)) shouldBe true

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

@@ -31,7 +31,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
   import ConfigUtils._
   import ConfigUtilsTest._
 
-  @Test def testGetValueFromPath: Unit = {
+  @Test def testGetValueFromPath(): Unit = {
     getValueFromPath(map1, List("dummy")) shouldBe Some(Map("dummy" -> 1))
     getValueFromPath(map1, List("dummy", "dummy")) shouldBe Some(1)
     getValueFromPath(map1, List("nested3", "nested2", "nested1")) shouldBe Some(Map("dummy" -> 1))
@@ -39,7 +39,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
     getValueFromPath(map1, List("dummy", "notexist")) shouldBe None
   }
 
-  @Test def testGetMapFromPath: Unit = {
+  @Test def testGetMapFromPath(): Unit = {
     getMapFromPath(map1, List("dummy")) shouldBe Some(Map("dummy" -> 1))
     getMapFromPath(map1, List("nested3", "nested2", "nested1")) shouldBe Some(Map("dummy" -> 1))
     intercept[IllegalStateException] {
@@ -48,7 +48,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
   }
 
   // Merge maps
-  @Test def testMergeMaps: Unit = {
+  @Test def testMergeMaps(): Unit = {
     val mergedMap = mergeMaps(map1, map2)
     getValueFromPath(mergedMap, List("nested", "1")) shouldBe Some(1)
     getValueFromPath(mergedMap, List("nested", "2")) shouldBe Some(1)
@@ -56,7 +56,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
   }
 
   // Json to scala values
-  @Test def testFileToJson: Unit = {
+  @Test def testFileToJson(): Unit = {
     fileToJson(file1) shouldBe json1
     fileToJson(file2) shouldBe json2
     intercept[IllegalStateException] {
@@ -64,7 +64,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
     }
   }
 
-  @Test def testJsonToMap: Unit = {
+  @Test def testJsonToMap(): Unit = {
     jsonToMap(json1) shouldBe map1
     jsonToMap(json2) shouldBe map2
     intercept[IllegalStateException] {
@@ -72,13 +72,13 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
     }
   }
 
-  @Test def testFileToConfigMap: Unit = {
+  @Test def testFileToConfigMap(): Unit = {
     fileToConfigMap(file1) shouldBe map1
     fileToConfigMap(file2) shouldBe map2
   }
 
   // Any/scala values to Json objects
-  @Test def testAnyToJson: Unit = {
+  @Test def testAnyToJson(): Unit = {
     anyToJson("bla") shouldBe jString("bla")
     anyToJson(1337) shouldBe Json.jNumberOrString(1337)
     anyToJson(13.37) shouldBe Json.jNumberOrString(13.37)
@@ -90,7 +90,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
     anyToJson(Map("bla" -> 1337)) shouldBe ("bla" := 1337) ->: jEmptyObject
   }
 
-  @Test def testMapToJson: Unit = {
+  @Test def testMapToJson(): Unit = {
     mapToJson(Map()) shouldBe jEmptyObject
     mapToJson(Map("bla" -> 1337)) shouldBe ("bla" := 1337) ->: jEmptyObject
     mapToJson(Map("bla" -> Map())) shouldBe ("bla" := jEmptyObject) ->: jEmptyObject
@@ -98,14 +98,14 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
   }
 
   // Any to scala values
-  @Test def testAny2string: Unit = {
+  @Test def testAny2string(): Unit = {
     any2string("bla") shouldBe "bla"
     any2string(1337) shouldBe "1337"
     any2string(true) shouldBe "true"
     any2string(13.37) shouldBe "13.37"
   }
 
-  @Test def testAny2int: Unit = {
+  @Test def testAny2int(): Unit = {
     any2int(1337) shouldBe 1337
     any2int("1337") shouldBe 1337
     any2int(13.37) shouldBe 13
@@ -114,7 +114,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
     }
   }
 
-  @Test def testAny2long: Unit = {
+  @Test def testAny2long(): Unit = {
     any2long(1337L) shouldBe 1337L
     any2long(1337) shouldBe 1337L
     any2long("1337") shouldBe 1337L
@@ -124,7 +124,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
     }
   }
 
-  @Test def testAny2double: Unit = {
+  @Test def testAny2double(): Unit = {
     any2double(13.37) shouldBe 13.37d
     any2double("1337") shouldBe 1337d
     any2double(1337) shouldBe 1337d
@@ -135,7 +135,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
     }
   }
 
-  @Test def testAny2float: Unit = {
+  @Test def testAny2float(): Unit = {
     any2float(1337d) shouldBe 1337f
     any2float("1337") shouldBe 1337f
     any2float(1337) shouldBe 1337f
@@ -146,7 +146,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
     }
   }
 
-  @Test def testAny2boolean: Unit = {
+  @Test def testAny2boolean(): Unit = {
     any2boolean(true) shouldBe true
     any2boolean("false") shouldBe false
     any2boolean("true") shouldBe true
@@ -157,21 +157,21 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
     }
   }
 
-  @Test def testAny2list: Unit = {
+  @Test def testAny2list(): Unit = {
     any2list(Nil) shouldBe Nil
     any2list(List(1, 2, 3, 4)) shouldBe List(1, 2, 3, 4)
     any2list(List(1337)) shouldBe List(1337)
     any2list(1337) shouldBe List(1337)
   }
 
-  @Test def testAny2stringList: Unit = {
+  @Test def testAny2stringList(): Unit = {
     any2stringList(Nil) shouldBe Nil
     any2stringList(List("1337")) shouldBe List("1337")
     any2stringList(List(1337)) shouldBe List("1337")
     any2stringList(1337) shouldBe List("1337")
   }
 
-  @Test def testAny2map: Unit = {
+  @Test def testAny2map(): Unit = {
     any2map(Map()) shouldBe Map()
     any2map(Map("bla" -> 1337)) shouldBe Map("bla" -> 1337)
     any2map(null) shouldBe null
@@ -180,7 +180,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
     }
   }
 
-  @Test def testImplicits: Unit = {
+  @Test def testImplicits(): Unit = {
     val index = ConfigValueIndex("test", Nil, "test")
     new ImplicitConversions {
       configValue2list(ConfigValue(index, index, List(""))) shouldBe List("")
@@ -210,7 +210,7 @@ object ConfigUtilsTest {
     val w = new PrintWriter(file)
     w.write(text)
     w.close()
-    return file
+    file
   }
 
   val jsonText1 =

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

@@ -11,13 +11,13 @@ import scala.util.Try
  */
 class PackageTest extends TestNGSuite with Matchers {
 
-  @Test def testConvert: Unit = {
+  @Test def testConvert(): Unit = {
     tryToParseNumber("4") shouldBe Try(4)
     tryToParseNumber("13.37") shouldBe Try(13.37)
     tryToParseNumber("I'm not a number") should not be Try("I'm not a number")
 
-    tryToParseNumber("4", true) shouldBe Try(4)
-    tryToParseNumber("13.37", true) shouldBe Try(13.37)
-    tryToParseNumber("I'm not a number", true) shouldBe Try("I'm not a number")
+    tryToParseNumber("4", fallBack = true) shouldBe Try(4)
+    tryToParseNumber("13.37", fallBack = true) shouldBe Try(13.37)
+    tryToParseNumber("I'm not a number", fallBack = true) shouldBe Try("I'm not a number")
   }
 }