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biopet.biopet
Commit b88623c3 authored by Peter van 't Hof's avatar Peter van 't Hof
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Fixed unit tests

parent f418cc1a
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bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
View file @ b88623c3
......@@ -18,7 +18,7 @@ import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
import nl.lumc.sasc.biopet.extensions.picard._
import nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
import nl.lumc.sasc.biopet.extensions.tools.BamStats
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils
......@@ -77,7 +77,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
bammetrics.functions.count(_.isInstanceOf[CollectMultipleMetrics]) shouldBe 1
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[BiopetFlagstat]) shouldBe 1
bammetrics.functions.count(_.isInstanceOf[BamStats]) shouldBe 1
}
// remove temporary run directory all tests in the class have been run
......
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