Commit 25f487cc authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed style

parent 8c75f931
......@@ -22,14 +22,13 @@ import com.google.common.io.Files
import nl.lumc.sasc.biopet.extensions.breakdancer.{ BreakdancerCaller, BreakdancerConfig, BreakdancerVCF }
import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
import nl.lumc.sasc.biopet.extensions.pindel.{ PindelVCF, PindelConfig, PindelCaller }
import nl.lumc.sasc.biopet.extensions.pindel.{ PindelCaller, PindelConfig, PindelVCF }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{ AfterClass, DataProvider, Test }
import org.testng.annotations.{ DataProvider, Test }
import scala.collection.mutable.ListBuffer
......@@ -106,7 +105,7 @@ class ShivaSvCallingTest extends TestNGSuite with Matchers {
pipeline.functions.count(_.isInstanceOf[PindelVCF]) shouldBe (if (pindel) bams else 0)
pipeline.functions.count(_.isInstanceOf[CleverCaller]) shouldBe (if (clever) bams else 0)
pipeline.functions.count(_.isInstanceOf[DellyCaller]) shouldBe (if (delly) (bams * 4) else 0)
pipeline.functions.count(_.isInstanceOf[DellyCaller]) shouldBe (if (delly) bams * 4 else 0)
}
}
......@@ -114,12 +113,12 @@ class ShivaSvCallingTest extends TestNGSuite with Matchers {
@DataProvider(name = "dellyOptions")
def dellyOptions = {
val bool = Array(true, false)
(for (
for (
del <- bool;
dup <- bool;
inv <- bool;
tra <- bool
) yield Array(1, del, dup, inv, tra)).toArray
) yield Array(1, del, dup, inv, tra)
}
@Test(dataProvider = "dellyOptions")
......@@ -176,14 +175,11 @@ class ShivaSvCallingTest extends TestNGSuite with Matchers {
assert(summaryCallers.contains("clever"))
assert(summaryCallers.contains("breakdancer"))
}
@AfterClass def removeTempOutputDir() = {
FileUtils.deleteDirectory(ShivaSvCallingTest.outputDir)
}
}
object ShivaSvCallingTest {
val outputDir = Files.createTempDir()
outputDir.deleteOnExit()
new File(outputDir, "input").mkdirs()
def inputTouch(name: String): File = {
val file = new File(outputDir, "input" + File.separator + name).getAbsoluteFile
......
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