Biopet core code inspection round

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PedigreeQScriptTest.scala

@@ -73,7 +73,7 @@ class PedigreeQScriptTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testIsMother() = {
+  def testIsMother(): Unit = {
     val script = PedigreeQScriptTest(trioPed :: Nil)
     script.init()
     script.biopetScript()
@@ -82,7 +82,7 @@ class PedigreeQScriptTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testIsFather() = {
+  def testIsFather(): Unit = {
     val script = PedigreeQScriptTest(trioPed :: Nil)
     script.init()
     script.biopetScript()
@@ -91,7 +91,7 @@ class PedigreeQScriptTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testIsTrio() = {
+  def testIsTrio(): Unit = {
     val script = PedigreeQScriptTest(trioPed :: Nil)
     script.init()
     script.biopetScript()
@@ -106,7 +106,7 @@ class PedigreeQScriptTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testConcatenation() = {
+  def testConcatenation(): Unit = {
     val script = PedigreeQScriptTest(sample1 :: sample2 :: sample3 :: trioPed :: Nil)
     script.init()
     script.biopetScript()
@@ -171,13 +171,18 @@ object PedigreeQScriptTest {
 
   val trioPed = Map("ped_file" -> resourcePath("/trio.ped"))
 
-  def apply(configs: List[Map[String, Any]], only: List[String] = Nil) = {
+  def apply(configs: List[Map[String, Any]], only: List[String] = Nil): QScript with PedigreeQscript {
+    def init(): Unit
+
+    def biopetScript(): Unit
+
+  } = {
     new QScript with PedigreeQscript { qscript =>
 
       qSettings = new QSettings()
       qSettings.runName = "test"
 
-      override val onlySamples = only
+      override val onlySamples: List[String] = only
 
       var buffer = new ListBuffer[String]()
 

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineCommandTest.scala

@@ -26,10 +26,10 @@ import scala.language.reflectiveCalls
   */
 class PipelineCommandTest extends TestNGSuite with Matchers {
   @Test
-  def testPipelineCommand: Unit = {
+  def testPipelineCommand(): Unit = {
     val pipeline = new PipelineCommand {
       override val globalConfig = new Config(Map())
-      def getConfig = globalConfig
+      def getConfig: Config = globalConfig
     }
 
     pipeline.pipelineName shouldBe this.getClass.getSimpleName.toLowerCase

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala

@@ -32,7 +32,7 @@ class ReferenceTest extends TestNGSuite with Matchers {
   import ReferenceTest._
 
   @Test
-  def testDefault: Unit = {
+  def testDefault(): Unit = {
     Logging.errors.clear()
     make(config :: testReferenceNoIndex :: Nil).referenceFasta()
     Logging.checkErrors(true)
@@ -42,7 +42,7 @@ class ReferenceTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testIndexes: Unit = {
+  def testIndexes(): Unit = {
     make(config :: testReferenceNoIndex :: Nil, fai = true, dict = true).referenceFasta()
 
     intercept[IllegalStateException] {
@@ -60,7 +60,7 @@ class ReferenceTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testDbpsnp: Unit = {
+  def testDbpsnp(): Unit = {
     val a = make(config :: Map("dbsnp_version" -> 1) :: testReferenceNoIndex :: Nil,
                  fai = true,
                  dict = true)
@@ -111,12 +111,12 @@ object ReferenceTest {
            r: Configurable = null,
            fai: Boolean = false,
            dict: Boolean = false) = new Reference {
-    val parent = r
+    val parent: Configurable = r
     override def globalConfig =
       new Config(
         configs
           .foldLeft(Map[String, Any]()) { case (a, b) => ConfigUtils.mergeMaps(a, b) })
-    override def dictRequired = if (dict) true else super.dictRequired
-    override def faiRequired = if (fai) true else super.faiRequired
+    override def dictRequired: Boolean = if (dict) true else super.dictRequired
+    override def faiRequired: Boolean = if (fai) true else super.faiRequired
   }
 }

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/SampleLibraryTagTest.scala

@@ -24,7 +24,7 @@ import org.testng.annotations.Test
   */
 class SampleLibraryTagTest extends TestNGSuite with Matchers {
   @Test
-  def testDefault: Unit = {
+  def testDefault(): Unit = {
     val o = new SampleLibraryTag {
       override def parent: Configurable = null
       override def globalConfig = new Config(Map())
@@ -34,7 +34,7 @@ class SampleLibraryTagTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testInherit: Unit = {
+  def testInherit(): Unit = {
     val o1 = new SampleLibraryTag {
       override def parent: Configurable = null
       override def globalConfig = new Config(Map())

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala

@@ -24,7 +24,7 @@ import nl.lumc.sasc.biopet.FullVersion
   */
 class ToolCommandTest extends TestNGSuite with Matchers {
   @Test
-  def testToolCommand: Unit = {
+  def testToolCommand(): Unit = {
     val tool = new ToolCommandFunction {
       def parent = null
       def toolObject = ToolCommandTest
@@ -33,7 +33,7 @@ class ToolCommandTest extends TestNGSuite with Matchers {
     tool.versionCommand shouldBe empty
     tool.versionRegex.toString() shouldBe empty
     tool.getVersion shouldBe Some("Biopet " + FullVersion)
-    tool.beforeGraph
+    tool.beforeGraph()
 
     tool.javaMainClass shouldBe ToolCommandTest.getClass.getName.takeWhile(_ != '$')
   }

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala

@@ -31,10 +31,10 @@ class WriteDependenciesTest extends TestNGSuite with Matchers {
   import WriteDependenciesTest._
 
   case class Qfunc(in: Seq[File], out: Seq[File]) extends QFunction {
-    override def inputs = in
-    override def outputs = out
-    override def doneOutputs = out.map(x => new File(x.getParentFile, s".${x.getName}.done"))
-    override def failOutputs = out.map(x => new File(x.getParentFile, s".${x.getName}.fail"))
+    override def inputs: Seq[File] = in
+    override def outputs: Seq[File] = out
+    override def doneOutputs: Seq[File] = out.map(x => new File(x.getParentFile, s".${x.getName}.done"))
+    override def failOutputs: Seq[File] = out.map(x => new File(x.getParentFile, s".${x.getName}.fail"))
     jobOutputFile = new File(out.head + ".out")
   }
 
@@ -60,19 +60,19 @@ class WriteDependenciesTest extends TestNGSuite with Matchers {
     assert(paths.contains(file3.toString))
 
     files
-      .find(_.get("path") == Some(file1.toString))
+      .find(_.get("path").contains(file1.toString))
       .flatMap(_.get("pipeline_input")) shouldBe Some(true)
     files
-      .find(_.get("path") == Some(file2.toString))
+      .find(_.get("path").contains(file2.toString))
       .flatMap(_.get("pipeline_input")) shouldBe Some(false)
     files
-      .find(_.get("path") == Some(file3.toString))
+      .find(_.get("path").contains(file3.toString))
       .flatMap(_.get("pipeline_input")) shouldBe Some(false)
   }
 }
 
 object WriteDependenciesTest {
-  val tempDir = Files.createTempDir()
+  val tempDir: File = Files.createTempDir()
   tempDir.deleteOnExit()
   val file1 = new File(tempDir, "file1.txt")
   val file2 = new File(tempDir, "file2.txt")

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/annotation/AnnotationTest.scala

@@ -30,7 +30,7 @@ import org.testng.annotations.Test
   */
 class AnnotationTest extends TestNGSuite with Matchers {
   @Test
-  def testAnnotationGtf: Unit = {
+  def testAnnotationGtf(): Unit = {
     val s1 = new AnnotationTest.Script(AnnotationTest.config) with AnnotationGtf
     s1.annotationGtf shouldBe new File("")
     an[IllegalStateException] shouldBe thrownBy(Logging.checkErrors())
@@ -38,18 +38,18 @@ class AnnotationTest extends TestNGSuite with Matchers {
     val s2 = new AnnotationTest.Script(
       AnnotationTest.config ++ Map("species" -> "s1", "reference_name" -> "g1")) with AnnotationGtf
     s2.annotationGtf shouldBe new File("no_set.gtf")
-    noException should be thrownBy (Logging.checkErrors())
+    noException should be thrownBy Logging.checkErrors()
 
     val s3 = new AnnotationTest.Script(
       AnnotationTest.config ++ Map("species" -> "s1",
                                    "reference_name" -> "g1",
                                    "gene_annotation_name" -> "set1")) with AnnotationGtf
     s3.annotationGtf shouldBe new File("set1.gtf")
-    noException should be thrownBy (Logging.checkErrors())
+    noException should be thrownBy Logging.checkErrors()
   }
 
   @Test
-  def testAnnotationGff: Unit = {
+  def testAnnotationGff(): Unit = {
     val s1 = new AnnotationTest.Script(AnnotationTest.config) with AnnotationGff
     s1.annotationGff shouldBe new File("")
     an[IllegalStateException] shouldBe thrownBy(Logging.checkErrors())
@@ -57,18 +57,18 @@ class AnnotationTest extends TestNGSuite with Matchers {
     val s2 = new AnnotationTest.Script(
       AnnotationTest.config ++ Map("species" -> "s1", "reference_name" -> "g1")) with AnnotationGff
     s2.annotationGff shouldBe new File("no_set.gff")
-    noException should be thrownBy (Logging.checkErrors())
+    noException should be thrownBy Logging.checkErrors()
 
     val s3 = new AnnotationTest.Script(
       AnnotationTest.config ++ Map("species" -> "s1",
                                    "reference_name" -> "g1",
                                    "gene_annotation_name" -> "set1")) with AnnotationGff
     s3.annotationGff shouldBe new File("set1.gff")
-    noException should be thrownBy (Logging.checkErrors())
+    noException should be thrownBy Logging.checkErrors()
   }
 
   @Test
-  def testAnnotationRefFlat: Unit = {
+  def testAnnotationRefFlat(): Unit = {
     val s1 = new AnnotationTest.Script(AnnotationTest.config) with AnnotationRefFlat
     s1.annotationRefFlat.get shouldBe new File("")
     an[IllegalStateException] shouldBe thrownBy(Logging.checkErrors())
@@ -77,14 +77,14 @@ class AnnotationTest extends TestNGSuite with Matchers {
       AnnotationTest.config ++ Map("species" -> "s1", "reference_name" -> "g1"))
     with AnnotationRefFlat
     s2.annotationRefFlat.get shouldBe new File("no_set.refFlat")
-    noException should be thrownBy (Logging.checkErrors())
+    noException should be thrownBy Logging.checkErrors()
 
     val s3 = new AnnotationTest.Script(
       AnnotationTest.config ++ Map("species" -> "s1",
                                    "reference_name" -> "g1",
                                    "gene_annotation_name" -> "set1")) with AnnotationRefFlat
     s3.annotationRefFlat.get shouldBe new File("set1.refFlat")
-    noException should be thrownBy (Logging.checkErrors())
+    noException should be thrownBy Logging.checkErrors()
   }
 }
 

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilderTest.scala

@@ -31,9 +31,6 @@ import scala.concurrent.duration.Duration
   * Created by pjvanthof on 24/02/16.
   */
 class MultisampleReportBuilderTest extends TestNGSuite with Matchers {
-  private def resourcePath(p: String): String = {
-    Paths.get(getClass.getResource(p).toURI).toString
-  }
 
   @Test
   def testGeneratePages(): Unit = {

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala

@@ -15,7 +15,6 @@
 package nl.lumc.sasc.biopet.core.report
 
 import java.io.File
-import java.nio.file.Paths
 import java.sql.Date
 
 import com.google.common.io.Files
@@ -32,16 +31,12 @@ import scala.concurrent.duration.Duration
   */
 class ReportBuilderTest extends TestNGSuite with Matchers {
 
-  private def resourcePath(p: String): String = {
-    Paths.get(getClass.getResource(p).toURI).toString
-  }
-
   @DataProvider(name = "testGeneratePages")
-  def generatePageProvider = {
+  def generatePageProvider: Array[Array[Any]] = {
     val sample = Array(Some("sampleName"), None)
     val lib = Array(Some("libName"), None)
     val nested = Array(false, true)
-    for (s <- sample; l <- lib; n <- nested if (!(l.isDefined && s.isEmpty))) yield Array(s, l, n)
+    for (s <- sample; l <- lib; n <- nested if !(l.isDefined && s.isEmpty)) yield Array(s, l, n)
   }
 
   @Test(dataProvider = "testGeneratePages")
@@ -51,7 +46,7 @@ class ReportBuilderTest extends TestNGSuite with Matchers {
       def reportName: String = "test"
       def indexPage: Future[ReportPage] =
         Future(
-          ReportPage((if (nested) "p1" -> Future(ReportPage(Nil, Nil, Map())) :: Nil else Nil),
+          ReportPage(if (nested) "p1" -> Future(ReportPage(Nil, Nil, Map())) :: Nil else Nil,
                      Nil,
                      Map()))
     }
@@ -107,7 +102,7 @@ class ReportBuilderTest extends TestNGSuite with Matchers {
   //  }
 
   @Test
-  def testRenderTemplate: Unit = {
+  def testRenderTemplate(): Unit = {
     ReportBuilder.renderTemplate("/template.ssp", Map("arg" -> "test")) shouldBe "test"
     ReportBuilder.renderTemplate("/template.ssp", Map("arg" -> "bla")) shouldBe "bla"
   }

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportSectionTest.scala

@@ -24,7 +24,7 @@ import org.testng.annotations.Test
 class ReportSectionTest extends TestNGSuite with Matchers {
 
   @Test
-  def testSectionRender: Unit = {
+  def testSectionRender(): Unit = {
     ReportSection("/template.ssp", Map("arg" -> "test")).render() shouldBe "test"
     ReportSection("/template.ssp").render(Map("arg" -> "test")) shouldBe "test"
   }

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala

@@ -25,7 +25,7 @@ import org.testng.annotations.Test
   */
 class SummarizableTest extends TestNGSuite with Matchers {
   @Test
-  def testDefaultMerge: Unit = {
+  def testDefaultMerge(): Unit = {
     val summarizable = new Summarizable {
       def summaryFiles: Map[String, File] = ???
       def summaryStats: Any = ???
@@ -35,11 +35,11 @@ class SummarizableTest extends TestNGSuite with Matchers {
     }
   }
 
-  def testOverrideMerge: Unit = {
+  def testOverrideMerge(): Unit = {
     val summarizable = new Summarizable {
       def summaryFiles: Map[String, File] = ???
       def summaryStats: Any = ???
-      override def resolveSummaryConflict(v1: Any, v2: Any, key: String) = v1
+      override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = v1
     }
     summarizable.resolveSummaryConflict("1", "1", "key") shouldBe "1"
   }

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala

@@ -30,7 +30,7 @@ import SummaryQScriptTest._
   */
 class SummaryQScriptTest extends TestNGSuite with Matchers {
   @Test
-  def testNoJobs: Unit = {
+  def testNoJobs(): Unit = {
     SummaryQScript.md5sumCache.clear()
     val script = makeQscript()
     script.addSummaryJobs()
@@ -38,7 +38,7 @@ class SummaryQScriptTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testFiles: Unit = {
+  def testFiles(): Unit = {
     SummaryQScript.md5sumCache.clear()
     val file = new File(s".${File.separator}bla")
     val script = makeQscript(files = Map("file" -> file))
@@ -55,7 +55,7 @@ class SummaryQScriptTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testDuplicateFiles: Unit = {
+  def testDuplicateFiles(): Unit = {
     SummaryQScript.md5sumCache.clear()
     val file = new File(s".${File.separator}bla")
     val script = makeQscript(files = Map("file" -> file, "file2" -> file))
@@ -72,7 +72,7 @@ class SummaryQScriptTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testAddSummarizable: Unit = {
+  def testAddSummarizable(): Unit = {
     SummaryQScript.md5sumCache.clear()
     val file = new File(s".${File.separator}bla")
     val script = makeQscript()
@@ -91,7 +91,7 @@ class SummaryQScriptTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testInputFile: Unit = {
+  def testInputFile(): Unit = {
     SummaryQScript.md5sumCache.clear()
     val file = new File(s".${File.separator}bla")
     val script = makeQscript()
@@ -112,7 +112,7 @@ class SummaryQScriptTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testAddQscript: Unit = {
+  def testAddQscript(): Unit = {
     SummaryQScript.md5sumCache.clear()
     val script = makeQscript()
     script.addSummaryQScript(script)
@@ -129,7 +129,7 @@ object SummaryQScriptTest {
       override def globalConfig = new Config(c)
       def summarySettings: Map[String, Any] = settings
       def summaryFiles: Map[String, File] = files
-      val tempFile = File.createTempFile("summary", ".json")
+      val tempFile: File = File.createTempFile("summary", ".json")
       tempFile.deleteOnExit()
       def summaryFile: File = tempFile
       def init(): Unit = ???

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala

@@ -41,7 +41,7 @@ import scala.util.matching.Regex
 class WriteSummaryTest extends TestNGSuite with Matchers {
 
   @Test
-  def testCreateFile: Unit = {
+  def testCreateFile(): Unit = {
     val dbFile = File.createTempFile("summary.", ".db")
     dbFile.deleteOnExit()
     val db = SummaryDb.openSqliteSummary(dbFile)
@@ -295,7 +295,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
   }
 
   @AfterClass
-  def removeDirs: Unit = {
+  def removeDirs(): Unit = {
     dirs.foreach(FileUtils.deleteDirectory)
   }
 }
@@ -325,7 +325,7 @@ object WriteSummaryTest {
       override def globalConfig = new Config(c)
       def summarySettings: Map[String, Any] = settings
       def summaryFiles: Map[String, File] = files
-      val tempFile = File.createTempFile("summary", ".json")
+      val tempFile: File = File.createTempFile("summary", ".json")
       tempFile.deleteOnExit()
       def summaryFile: File = tempFile
       def init(): Unit = {}
@@ -348,7 +348,7 @@ object WriteSummaryTest {
       override def globalConfig = new Config(c + ("exe" -> "test"))
       def summarySettings: Map[String, Any] = settings
       def summaryFiles: Map[String, File] = files
-      val tempFile = File.createTempFile("summary", ".json")
+      val tempFile: File = File.createTempFile("summary", ".json")
       tempFile.deleteOnExit()
       def summaryFile: File = tempFile
       def init(): Unit = {}
@@ -367,7 +367,7 @@ object WriteSummaryTest {
       override def globalConfig = new Config(c + ("exe" -> "test"))
       def summarySettings: Map[String, Any] = settings
       def summaryFiles: Map[String, File] = files
-      val tempFile = File.createTempFile("summary", ".json")
+      val tempFile: File = File.createTempFile("summary", ".json")
       tempFile.deleteOnExit()
       def summaryFile: File = tempFile
       def init(): Unit = {}

biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilterTest.scala

@@ -25,12 +25,12 @@ import org.testng.annotations.Test
   */
 class VcfFilterTest extends TestNGSuite with Matchers {
 
-  def cmd(s: String) = {
+  def cmd(s: String): String = {
     s.replace("'", "").replace("  ", " ").trim
   }
 
   @Test
-  def testBeforeGraph() = {
+  def testBeforeGraph(): Unit = {
     val filterer = new VcfFilter(null)
     val iVcf = File.createTempFile("vcfFilter", ".vcf.gz")
     val oVcf = File.createTempFile("vcfFilter", ".vcf.gz")
@@ -43,29 +43,29 @@ class VcfFilterTest extends TestNGSuite with Matchers {
     filterer.outputVcfIndex.getAbsolutePath shouldBe oVcf.getAbsolutePath + ".tbi"
   }
 
-  @Test def testMinSampleDepth() = testCommand(minSampleDepth = Some(2))
-  @Test def testMinTotalDepth() = testCommand(minTotalDepth = Some(2))
-  @Test def testMinAlternateDepth() = testCommand(minAlternateDepth = Some(2))
-  @Test def testMinSamplesPass() = testCommand(minSamplesPass = Some(2))
-  @Test def testMinGenomeQuality() = testCommand(minGenomeQuality = Some(50))
-  @Test def testFilterRefCalls() = testCommand(filterRefCalls = true)
-  @Test def testInvertedOutputVcf() =
+  @Test def testMinSampleDepth(): Unit = testCommand(minSampleDepth = Some(2))
+  @Test def testMinTotalDepth(): Unit = testCommand(minTotalDepth = Some(2))
+  @Test def testMinAlternateDepth(): Unit = testCommand(minAlternateDepth = Some(2))
+  @Test def testMinSamplesPass(): Unit = testCommand(minSamplesPass = Some(2))
+  @Test def testMinGenomeQuality(): Unit = testCommand(minGenomeQuality = Some(50))
+  @Test def testFilterRefCalls(): Unit = testCommand(filterRefCalls = true)
+  @Test def testInvertedOutputVcf(): Unit =
     testCommand(invertedOutputVcf = Some(File.createTempFile("vcfFilter", ".vcf")))
-  @Test def testResToDom() = testCommand(resToDom = Some("dummy"))
-  @Test def testTrioCompound() = testCommand(trioCompound = Some("dummy"))
-  @Test def testDeNovoInSample() = testCommand(deNovoInSample = Some("dummy"))
-  @Test def testDeNovoTrio() = testCommand(deNovoTrio = Some("dummy"))
-  @Test def testTrioLossOfHet() = testCommand(trioLossOfHet = Some("dummy"))
-  @Test def testMustHaveVariant() = testCommand(mustHaveVariant = List("sample1", "sample2"))
-  @Test def testCalledIn() = testCommand(calledIn = List("sample1", "sample2"))
-  @Test def testMustHaveGenotype() =
+  @Test def testResToDom(): Unit = testCommand(resToDom = Some("dummy"))
+  @Test def testTrioCompound(): Unit = testCommand(trioCompound = Some("dummy"))
+  @Test def testDeNovoInSample(): Unit = testCommand(deNovoInSample = Some("dummy"))
+  @Test def testDeNovoTrio(): Unit = testCommand(deNovoTrio = Some("dummy"))
+  @Test def testTrioLossOfHet(): Unit = testCommand(trioLossOfHet = Some("dummy"))
+  @Test def testMustHaveVariant(): Unit = testCommand(mustHaveVariant = List("sample1", "sample2"))
+  @Test def testCalledIn(): Unit = testCommand(calledIn = List("sample1", "sample2"))
+  @Test def testMustHaveGenotype(): Unit =
     testCommand(mustHaveGenotype = List("sample1:HET", "sample2:HET"))
-  @Test def testDiffGenotype() =
+  @Test def testDiffGenotype(): Unit =
     testCommand(diffGenotype = List("sample1:sample2", "sample2:sample3"))
-  @Test def testMinQualScore() = testCommand(minQualScore = Some(50.0))
-  @Test def testFilterHetVarToHomVar() = testCommand(filterHetVarToHomVar = List("dummy"))
-  @Test def testId() = testCommand(id = List("rs01", "rs02"))
-  @Test def testIdFile() = testCommand(idFile = Some(File.createTempFile("vcfFilter", ".txt")))
+  @Test def testMinQualScore(): Unit = testCommand(minQualScore = Some(50.0))
+  @Test def testFilterHetVarToHomVar(): Unit = testCommand(filterHetVarToHomVar = List("dummy"))
+  @Test def testId(): Unit = testCommand(id = List("rs01", "rs02"))
+  @Test def testIdFile(): Unit = testCommand(idFile = Some(File.createTempFile("vcfFilter", ".txt")))
 
   protected def testCommand(minSampleDepth: Option[Int] = None,
                             minTotalDepth: Option[Int] = None,