From 5f0512b57ae59c87fa07213f23cf135f54d0aee2 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Thu, 13 Aug 2015 17:44:36 +0200
Subject: [PATCH] VcfFilter tests. See #188.
---
.../nl/lumc/sasc/biopet/tools/VcfFilter.scala | 2 +-
.../sasc/biopet/tools/VepNormalizer.scala | 2 +-
.../sasc/biopet/tools/VcfFilterTest.scala | 59 +++++++++++++++++++
3 files changed, 61 insertions(+), 2 deletions(-)
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 f5fb9f3a6..24cfab400 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 8543b7706..1b7af776e 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 840abf904..80fe1980e 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
+ }
+
}
--
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