Commit 4e87ca4c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix unit testing

parent bf6c2be4
...@@ -19,7 +19,7 @@ import java.io.File ...@@ -19,7 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{BiopetFifoPipe, PipelineCommand, SampleLibraryTag} import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, PipelineCommand, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect } import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
import nl.lumc.sasc.biopet.extensions.picard._ import nl.lumc.sasc.biopet.extensions.picard._
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
......
...@@ -81,12 +81,7 @@ class BamMetricsTest extends TestNGSuite with Matchers { ...@@ -81,12 +81,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
bammetrics.functions.count(_.isInstanceOf[CollectMultipleMetrics]) shouldBe 1 bammetrics.functions.count(_.isInstanceOf[CollectMultipleMetrics]) shouldBe 1
bammetrics.functions.count(_.isInstanceOf[CalculateHsMetrics]) shouldBe (if (amplicon) 1 else 0) bammetrics.functions.count(_.isInstanceOf[CalculateHsMetrics]) shouldBe (if (amplicon) 1 else 0)
bammetrics.functions.count(_.isInstanceOf[CollectTargetedPcrMetrics]) shouldBe (if (amplicon) 1 else 0) bammetrics.functions.count(_.isInstanceOf[CollectTargetedPcrMetrics]) shouldBe (if (amplicon) 1 else 0)
bammetrics.functions.count(_.isInstanceOf[BiopetFlagstat]) shouldBe (1 + (regions * 2)) bammetrics.functions.count(_.isInstanceOf[BiopetFlagstat]) shouldBe 1
bammetrics.functions.count(_.isInstanceOf[SamtoolsFlagstat]) shouldBe (1 + (regions * 2))
bammetrics.functions.count(_.isInstanceOf[BedtoolsIntersect]) shouldBe (regions * 2)
bammetrics.functions.count(_.isInstanceOf[BedtoolsCoverage]) shouldBe regions
bammetrics.functions.count(_.isInstanceOf[CoverageStats]) shouldBe regions
} }
// remove temporary run directory all tests in the class have been run // remove temporary run directory all tests in the class have been run
......
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