Commit 81e75fbd authored by Peter van 't Hof's avatar Peter van 't Hof

Format fix

parent 1aea2582
package nl.lumc.sasc.biopet.pipelines.basty
import java.io.{File, FileOutputStream}
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
import nl.lumc.sasc.biopet.extensions.{Raxml, RunGubbins}
import nl.lumc.sasc.biopet.extensions.gatk.{BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator}
import nl.lumc.sasc.biopet.extensions.{ Raxml, RunGubbins }
import nl.lumc.sasc.biopet.extensions.gatk.{ BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator }
import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import nl.lumc.sasc.biopet.extensions.tools.{BastyGenerateFasta, VcfStats}
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import nl.lumc.sasc.biopet.extensions.tools.{ BastyGenerateFasta, VcfStats }
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
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 }
/**
* Created by pjvanthof on 27/09/16.
*/
* Created by pjvanthof on 27/09/16.
*/
class BastyTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): Basty = {
new Basty() {
......@@ -27,7 +27,6 @@ class BastyTest extends TestNGSuite with Matchers {
}
}
@DataProvider(name = "bastyOptions")
def bastyOptions = {
for (
......@@ -110,8 +109,8 @@ class BastyTest extends TestNGSuite with Matchers {
pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (
(if (multisampleCalling) 2 else 0) +
(if (sampleCalling) numberSamples * 2 else 0) +
(if (libraryCalling) numberLibs * 2 else 0))
(if (sampleCalling) numberSamples * 2 else 0) +
(if (libraryCalling) numberLibs * 2 else 0))
pipeline.functions.count(_.isInstanceOf[BastyGenerateFasta]) shouldBe 2 + (2 * numberSamples)
pipeline.functions.count(_.isInstanceOf[Raxml]) shouldBe (2 * (2 + bootRuns.getOrElse(100)))
......
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