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Commit 30696cab authored by Peter van 't Hof's avatar Peter van 't Hof
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Fixed unit tests

parent dd9a7060
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public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
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......@@ -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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