Fix unit testing

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -19,7 +19,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 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.picard._
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat

public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

@@ -81,12 +81,7 @@ 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 + (regions * 2))
-    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
+    bammetrics.functions.count(_.isInstanceOf[BiopetFlagstat]) shouldBe 1
   }
 
   // remove temporary run directory all tests in the class have been run