diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala index f5fb9f3a6a4101f66f35735c8a8e11108474e4c5..24cfab400aa77e20c5b95556681327797ab30e68 100644 --- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala +++ b/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)) } diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala index 8543b7706670ef40d9a877f27a0bf1b1ed3d77a9..1b7af776ee186acb2573539eeda86afbc05e07be 100644 --- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala +++ b/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) + diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala index 840abf9043982badfcf8dc7e4d4b35838f098de5..80fe1980eccad9932e0472ae28242ae93e6b6420 100644 --- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala +++ b/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 + } + }