Commit ab5e1c96 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Code style fix

parent 8b7765a4
......@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.{Reference, BiopetCommandLineFunction}
import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
......
......@@ -19,7 +19,7 @@ import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import nl.lumc.sasc.biopet.core.{Reference, BiopetCommandLineFunction}
import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.core.config.Configurable
/**
......
......@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.{Reference, BiopetCommandLineFunction}
import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
......
......@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.{Reference, BiopetCommandLineFunction}
import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
......
......@@ -45,9 +45,9 @@ import nl.lumc.sasc.biopet.tools.{ MergeTables, WipeReads }
* @author Wibowo Arindrarto <w.arindrarto@lumc.nl>
*/
class Gentrap(val root: Configurable) extends QScript
with MultiSampleQScript
with SummaryQScript
with Reference { qscript =>
with MultiSampleQScript
with SummaryQScript
with Reference { qscript =>
import Gentrap._
import Gentrap.ExpMeasures._
......
......@@ -109,9 +109,9 @@ class MappingTest extends TestNGSuite with Matchers {
// Sort sam or replace readgroup
val sort = aligner match {
case "bwa" | "bwa-aln" | "stampy" => "sortsam"
case "bwa" | "bwa-aln" | "stampy" => "sortsam"
case "star" | "star-2pass" | "bowtie" | "gsnap" | "tophat" => "replacereadgroups"
case _ => throw new IllegalArgumentException("aligner: " + aligner + " does not exist")
case _ => throw new IllegalArgumentException("aligner: " + aligner + " does not exist")
}
mapping.functions.count(_.isInstanceOf[SortSam]) shouldBe ((if (sort == "sortsam") 1 else 0) * chunks)
......
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