Commit b55361cd authored by Wai Yi Leung's avatar Wai Yi Leung

add test for WipeReads, check on instance in Gentrap

parent c7be8c6d
......@@ -14,20 +14,20 @@
*/
package nl.lumc.sasc.biopet.pipelines.gentrap
import java.io.{ File, FileOutputStream }
import java.io.{File, FileOutputStream}
import com.google.common.io.Files
import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, BiopetPipe }
import nl.lumc.sasc.biopet.core.{BiopetFifoPipe, BiopetPipe}
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
import nl.lumc.sasc.biopet.extensions.tools.BaseCounter
import nl.lumc.sasc.biopet.extensions.tools.{BaseCounter, WipeReads}
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Config
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{ DataProvider, Test }
import org.testng.annotations.{DataProvider, Test}
abstract class GentrapTestAbstract(val expressionMeasure: String, val aligner: Option[String]) extends TestNGSuite with Matchers {
......@@ -146,6 +146,10 @@ abstract class GentrapTestAbstract(val expressionMeasure: String, val aligner: O
assert(gentrap.functions.exists(_.isInstanceOf[Ln]))
}
if (gentrap.removeRibosomalReads) {
assert(gentrap.functions.exists(_.isInstanceOf[WipeReads]))
}
val classMap = Map(
"gsnap" -> classOf[Gsnap],
"tophat" -> classOf[Tophat],
......
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