diff --git a/public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala b/public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala index 54e5ef6733edd578653940eaa92eb77e7ea0f3c0..3fc8da5077ca45b25bdf5404a827203538eb6b92 100644 --- a/public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala +++ b/public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala @@ -8,11 +8,10 @@ import org.scalatest.testng.TestNGSuite import org.testng.annotations.Test /** - * Created by ahbbollen on 3-3-16. - */ + * Created by ahbbollen on 3-3-16. + */ class VariantEffectPredictorTest extends TestNGSuite with Matchers { - @Test def testSummaryStats = { val file = new File(Paths.get(getClass.getResource("/vep.metrics").toURI).toString) @@ -31,7 +30,6 @@ class VariantEffectPredictorTest extends TestNGSuite with Matchers { stats.contains("Distribution_of_variants_on_chromosome_1") shouldBe true stats.contains("Position_in_protein") shouldBe true - } } diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala index 3de20d5fde7310fb1a3f84536f27d235e22794f5..27b17496f28a58fec370deb04eb226c2cedcfe37 100644 --- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala +++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala @@ -130,7 +130,7 @@ object SeqStat extends ToolCommand { baseStats ++= mutable.ArrayBuffer.fill(record.length - baseStats.length)(BaseStat()) } - if (readStats.lengths.length <= record.length) { + if (readStats.lengths.length <= record.length) readStats.lengths ++= mutable.ArrayBuffer.fill(record.length - readStats.lengths.length + 1)(0) val readQuality = record.getBaseQualityString diff --git a/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala b/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala index 7f49fcb1c2aa681264ebb429d65f4981d44f8054..81e97ab6a22aa7ea93e7dec4769219540ef60dff 100644 --- a/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala +++ b/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala @@ -15,7 +15,7 @@ */ 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.extensions._ @@ -25,7 +25,7 @@ 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) extends TestNGSuite with Matchers {