VcfFilter tests. See #188.

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

@@ -56,7 +56,7 @@ class VcfFilter(val root: Configurable) extends ToolCommandFuntion {
 
 object VcfFilter extends ToolCommand {
   /** Container class for a trio */
-  protected case class Trio(child: String, father: String, mother: String) {
+  protected[tools] case class Trio(child: String, father: String, mother: String) {
     def this(arg: String) = {
       this(arg.split(":")(0), arg.split(":")(1), arg.split(":")(2))
     }

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

@@ -50,7 +50,7 @@ class VepNormalizer(val root: Configurable) extends ToolCommandFuntion {
   var mode: String = config("mode", default = "explode")
   var doNotRemove: Boolean = config("donotremove", default = false)
 
-  override def defaultCoreMemory = 1.0
+  override def defaultCoreMemory = 4.0
 
   override def commandLine = super.commandLine +
     required("-I", inputVCF) +

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

@@ -147,4 +147,63 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
     mustHaveVariant(record, List("Child_7006504", "Father_7006506", "Mother_7006508")) shouldBe false
   }
 
+  @Test def testSameGenotype() = {
+    val reader = new VCFFileReader(vepped, false)
+    val record = reader.iterator().next()
+
+    notSameGenotype(record, "Child_7006504", "Father_7006506") shouldBe false
+    notSameGenotype(record, "Child_7006504", "Mother_7006508") shouldBe true
+    notSameGenotype(record, "Father_7006506", "Mother_7006508") shouldBe true
+  }
+
+  @Test def testfilterHetVarToHomVar() = {
+    val reader = new VCFFileReader(vepped, false)
+    val record = reader.iterator().next()
+
+    filterHetVarToHomVar(record, "Child_7006504", "Father_7006506") shouldBe true
+    filterHetVarToHomVar(record, "Child_7006504", "Mother_7006508") shouldBe true
+    filterHetVarToHomVar(record, "Father_7006506", "Mother_7006508") shouldBe true
+  }
+
+  @Test def testDeNovo() = {
+    val reader = new VCFFileReader(vepped, false)
+    val record = reader.iterator().next()
+
+    denovoInSample(record, "Child_7006504") shouldBe false
+    denovoInSample(record, "Father_7006506") shouldBe false
+    denovoInSample(record, "Mother_7006508") shouldBe false
+  }
+
+  @Test def testResToDom() = {
+    val reader = new VCFFileReader(vepped, false)
+    val record = reader.iterator().next()
+    val trio = new Trio("Child_7006504", "Father_7006506", "Mother_7006508")
+
+    resToDom(record, List(trio)) shouldBe false
+  }
+
+  @Test def testTrioCompound = {
+    val reader = new VCFFileReader(vepped, false)
+    val record = reader.iterator().next()
+    val trio = new Trio("Child_7006504", "Father_7006506", "Mother_7006508")
+
+    trioCompound(record, List(trio))
+  }
+
+  @Test def testDeNovoTrio = {
+    val reader = new VCFFileReader(vepped, false)
+    val record = reader.iterator().next()
+    val trio = new Trio("Child_7006504", "Father_7006506", "Mother_7006508")
+
+    denovoTrio(record, List(trio))
+  }
+
+  @Test def testInIDSet() = {
+    val reader = new VCFFileReader(vepped, false)
+    val record = reader.iterator().next()
+
+    inIdSet(record, Set("rs199537431")) shouldBe true
+    inIdSet(record, Set("dummy")) shouldBe false
+  }
+
 }