From 02e5f5ec552edeb6447297a88956bab473d63297 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Wed, 12 Aug 2015 18:17:40 +0200
Subject: [PATCH] Partial VcfFilter tests. See #180
---
.../nl/lumc/sasc/biopet/tools/VcfFilter.scala | 2 +-
.../sasc/biopet/tools/VcfFilterTest.scala | 66 +++++++++++++++++++
2 files changed, 67 insertions(+), 1 deletion(-)
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 981203de4..f5fb9f3a6 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
@@ -278,7 +278,7 @@ object VcfFilter extends ToolCommand {
}
/**
- * Checks if AD genotype field have a minimal value
+ * Checks if non-ref AD genotype field have a minimal value
* @param record VCF record
* @param minAlternateDepth minimal depth
* @param minSamplesPass Minimal number of samples to pass filter
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 2b47405a4..840abf904 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
@@ -81,4 +81,70 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
hasGenotype(record, List(("Mother_7006508", GenotypeType.HET), ("Child_7006504", GenotypeType.HOM_REF))) shouldBe false
}
+ @Test def testMinQualScore() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ minQualscore(record, 2000) shouldBe false
+ minQualscore(record, 1000) shouldBe true
+
+ }
+
+ @Test def testHasNonRefCalls() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ hasNonRefCalls(record) shouldBe true
+ }
+
+ @Test def testHasCalls() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ hasCalls(record) shouldBe true
+ }
+
+ @Test def testHasMinDP() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ hasMinTotalDepth(record, 100) shouldBe true
+ hasMinTotalDepth(record, 200) shouldBe false
+ }
+
+ @Test def testHasMinSampleDP() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ hasMinSampleDepth(record, 30, 1) shouldBe true
+ hasMinSampleDepth(record, 30, 2) shouldBe true
+ hasMinSampleDepth(record, 30, 3) shouldBe true
+ hasMinSampleDepth(record, 40, 1) shouldBe true
+ hasMinSampleDepth(record, 40, 2) shouldBe true
+ hasMinSampleDepth(record, 40, 3) shouldBe false
+ hasMinSampleDepth(record, 50, 1) shouldBe false
+ hasMinSampleDepth(record, 50, 2) shouldBe false
+ hasMinSampleDepth(record, 50, 3) shouldBe false
+ }
+
+ @Test def testHasMinSampleAD() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ minAlternateDepth(record, 0, 3) shouldBe true
+ minAlternateDepth(record, 10, 2) shouldBe true
+ minAlternateDepth(record, 10, 3) shouldBe false
+ minAlternateDepth(record, 20, 1) shouldBe true
+ minAlternateDepth(record, 20, 2) shouldBe false
+ }
+
+ @Test def testMustHaveVariant() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ mustHaveVariant(record, List("Child_7006504")) shouldBe true
+ mustHaveVariant(record, List("Child_7006504", "Father_7006506")) shouldBe true
+ mustHaveVariant(record, List("Child_7006504", "Father_7006506", "Mother_7006508")) shouldBe false
+ }
+
}
--
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