From 7fceac90c2dbc3c88486d01427eee9a603d057f0 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 15 May 2016 16:34:28 +0200
Subject: [PATCH] Added test for referenceVcf
---
.../pipelines/shiva/ShivaVariantcallingTest.scala | 11 ++++++++---
1 file changed, 8 insertions(+), 3 deletions(-)
diff --git a/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala b/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
index b7ac20b05..6541eb843 100644
--- a/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+++ b/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
@@ -11,7 +11,7 @@ import com.google.common.io.Files
import nl.lumc.sasc.biopet.core.BiopetPipe
import nl.lumc.sasc.biopet.extensions.Freebayes
import nl.lumc.sasc.biopet.extensions.bcftools.{BcftoolsCall, BcftoolsMerge}
-import nl.lumc.sasc.biopet.extensions.gatk.{CombineVariants, HaplotypeCaller, UnifiedGenotyper}
+import nl.lumc.sasc.biopet.extensions.gatk.{CombineVariants, GenotypeConcordance, HaplotypeCaller, UnifiedGenotyper}
import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.tools.{MpileupToVcf, VcfFilter, VcfStats}
import nl.lumc.sasc.biopet.extensions.vt.{VtDecompose, VtNormalize}
@@ -48,6 +48,7 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
def haplotypeCaller: Boolean = false
def freebayes: Boolean = false
def varscanCnsSinglesample: Boolean = false
+ def referenceVcf: Option[File] = None
def normalize = false
def decompose = false
@@ -87,7 +88,7 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
"variantcallers" -> callers.toList,
"execute_vt_normalize" -> normalize,
"execute_vt_decompose" -> decompose
- )
+ ) ++ referenceVcf.map("reference_vcf" -> _)
val pipeline = initPipeline(map)
pipeline.inputBams = (for (n <- 1 to bams) yield n.toString -> ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toMap
@@ -116,6 +117,7 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (1 + callers.size)
pipeline.functions.count(_.isInstanceOf[VtNormalize]) shouldBe (if (normalize) callers.size else 0)
pipeline.functions.count(_.isInstanceOf[VtDecompose]) shouldBe (if (decompose) callers.size else 0)
+ pipeline.functions.count(_.isInstanceOf[GenotypeConcordance]) shouldBe (if (referenceVcf.isDefined) 1 else 0)
}
}
}
@@ -176,7 +178,10 @@ class ShivaVariantcallingNormalizeDecomposeTest extends ShivaVariantcallingTestT
override def normalize = true
override def decompose = true
}
-
+class ShivaVariantcallingUReferenceVcfTest extends ShivaVariantcallingTestTrait {
+ override def unifiedGenotyper: Boolean = true
+ override def referenceVcf = Some(new File("ref.vcf"))
+}
object ShivaVariantcallingTest {
val outputDir = Files.createTempDir()
--
GitLab