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biopet.biopet
Commit e9a7187e authored by Peter van 't Hof's avatar Peter van 't Hof
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fixing unit tests

parent 1d22fa44
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basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
View file @ e9a7187e
......@@ -102,7 +102,7 @@ class BastyTest extends TestNGSuite with Matchers {
// Gatk preprocess
pipeline.functions.count(_.isInstanceOf[IndelRealigner]) shouldBe (if (realign) numberSamples else 0)
pipeline.functions.count(_.isInstanceOf[RealignerTargetCreator]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))
pipeline.functions.count(_.isInstanceOf[RealignerTargetCreator]) shouldBe (if (realign) numberSamples else 0)
pipeline.functions.count(_.isInstanceOf[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration) (numberLibs * 2) else 0)
pipeline.functions.count(_.isInstanceOf[PrintReads]) shouldBe (if (dbsnp && baseRecalibration) numberLibs else 0)
......
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @ e9a7187e
......@@ -105,7 +105,7 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
// Gatk preprocess
pipeline.functions.count(_.isInstanceOf[IndelRealigner]) shouldBe (if (realign) numberSamples else 0)
pipeline.functions.count(_.isInstanceOf[RealignerTargetCreator]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))
pipeline.functions.count(_.isInstanceOf[RealignerTargetCreator]) shouldBe (if (realign) numberSamples else 0)
pipeline.functions.count(_.isInstanceOf[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration) (numberLibs * 2) else 0)
pipeline.functions.count(_.isInstanceOf[PrintReads]) shouldBe (if (dbsnp && baseRecalibration && usePrintReads) numberLibs else 0)
......
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