From 30696cabc25d1250de1e07b11bef6a8c24c78510 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 19 Jan 2016 14:00:57 +0100
Subject: [PATCH] Fixed unit tests
---
.../sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
index 2cf338385..dda3fb8c1 100644
--- a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+++ b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
@@ -77,7 +77,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
pipeline.inputBams = (for (n <- 1 to bams) yield n.toString -> ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toMap
- val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools && !bcftoolsSinglesample && !freebayes)
+ val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools && !bcftoolsSinglesample && !freebayes && !varscanCnsSinglesample)
if (illegalArgumentException) intercept[IllegalArgumentException] {
pipeline.script()
@@ -86,7 +86,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
if (!illegalArgumentException) {
pipeline.script()
- pipeline.functions.count(_.isInstanceOf[CombineVariants]) shouldBe 1 + (if (raw) 1 else 0)
+ pipeline.functions.count(_.isInstanceOf[CombineVariants]) shouldBe (1 + (if (raw) 1 else 0) + (if (varscanCnsSinglesample) 1 else 0))
//pipeline.functions.count(_.isInstanceOf[Bcftools]) shouldBe (if (bcftools) 1 else 0)
//FIXME: Can not check for bcftools because of piping
pipeline.functions.count(_.isInstanceOf[Freebayes]) shouldBe (if (freebayes) 1 else 0)
--
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