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

Format fix

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