Commit af816bfa authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing unit tests

parent 8b2b1732
......@@ -101,7 +101,7 @@ class BastyTest extends TestNGSuite with Matchers {
pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberLibs + numberSamples)
// Gatk preprocess
pipeline.functions.count(_.isInstanceOf[IndelRealigner]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))
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[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration) (numberLibs * 2) else 0)
pipeline.functions.count(_.isInstanceOf[PrintReads]) shouldBe (if (dbsnp && baseRecalibration) numberLibs else 0)
......
......@@ -104,7 +104,7 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberLibs + numberSamples)
// Gatk preprocess
pipeline.functions.count(_.isInstanceOf[IndelRealigner]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))
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[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration) (numberLibs * 2) else 0)
pipeline.functions.count(_.isInstanceOf[PrintReads]) shouldBe (if (dbsnp && baseRecalibration && usePrintReads) numberLibs else 0)
......@@ -120,7 +120,7 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
sample.libraries.foreach {
case (libId, lib) =>
lib.summarySettings.get("library_variantcalling") shouldBe Some(libraryCalling)
lib.summarySettings.get("use_indel_realigner") shouldBe Some(realign)
lib.summarySettings.get("use_indel_realigner") shouldBe None // Should not exist anymore
lib.summarySettings.get("use_base_recalibration") shouldBe Some(baseRecalibration && dbsnp)
}
}
......
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