Style

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala

@@ -4,12 +4,12 @@ package nl.lumc.sasc.biopet.extensions.clever
  * Created by wyleung on 4-4-16.
  */
 
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
 
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
 import nl.lumc.sasc.biopet.utils.ToolCommand
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 import scala.io.Source
 
@@ -125,9 +125,9 @@ object CleverFixVCF extends ToolCommand {
 
     val inputVCF = Source.fromFile(input)
     val writer = new PrintWriter(output)
-      inputVCF.getLines().foreach(x =>
-        writer.write(replaceHeaderLine(x, vcfColHeader, vcfColReplacementHeader + commandArgs.sampleLabel, extraHeader))
-      )
+    inputVCF.getLines().foreach(x =>
+      writer.write(replaceHeaderLine(x, vcfColHeader, vcfColReplacementHeader + commandArgs.sampleLabel, extraHeader))
+    )
     writer.close()
     inputVCF.close()
   }

biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCFTest.scala

@@ -5,8 +5,8 @@ import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
 /**
-  * Created by wyleung on 13-5-16.
-  */
+ * Created by wyleung on 13-5-16.
+ */
 class CleverFixVCFTest extends TestNGSuite with Matchers {
 
   @Test
@@ -16,10 +16,9 @@ class CleverFixVCFTest extends TestNGSuite with Matchers {
       CleverFixVCF.vcfColHeader,
       CleverFixVCF.vcfColReplacementHeader + "testsample",
       CleverFixVCF.extraHeader
-    ) should equal(CleverFixVCF.extraHeader + "\n" + CleverFixVCF.vcfColReplacementHeader + "testsample"+ "\n")
+    ) should equal(CleverFixVCF.extraHeader + "\n" + CleverFixVCF.vcfColReplacementHeader + "testsample" + "\n")
   }
 
-
   @Test
   def replacementOther = {
     val vcfRecord = "chrM\t312\tL743020\t.\t<DEL>\t.\tPASS\tBPWINDOW=313,16189;CILEN=15866,15888;IMPRECISE;SVLEN=-15877;SVTYPE=DEL\tGT:DP\t1/.:103"
@@ -29,7 +28,7 @@ class CleverFixVCFTest extends TestNGSuite with Matchers {
       CleverFixVCF.vcfColHeader,
       CleverFixVCF.vcfColReplacementHeader + "testsample",
       CleverFixVCF.extraHeader
-    ) should equal(vcfRecordExpected+ "\n")
+    ) should equal(vcfRecordExpected + "\n")
   }
 
 }

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala

@@ -15,7 +15,7 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
 
-import nl.lumc.sasc.biopet.extensions.breakdancer.{BreakdancerCaller, BreakdancerConfig, BreakdancerVCF}
+import nl.lumc.sasc.biopet.extensions.breakdancer.{ BreakdancerCaller, BreakdancerConfig, BreakdancerVCF }
 import nl.lumc.sasc.biopet.extensions.picard.SortVcf
 import nl.lumc.sasc.biopet.utils.config.Configurable
 

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala

@@ -15,7 +15,7 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
 
-import nl.lumc.sasc.biopet.extensions.clever.{CleverCaller, CleverFixVCF}
+import nl.lumc.sasc.biopet.extensions.clever.{ CleverCaller, CleverFixVCF }
 import nl.lumc.sasc.biopet.extensions.picard.SortVcf
 import nl.lumc.sasc.biopet.utils.config.Configurable
 

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/SvCaller.scala

@@ -30,7 +30,7 @@ trait SvCaller extends QScript with BiopetQScript with Reference {
 
   var inputBams: Map[String, File] = Map.empty
 
-  val sampleNameSuffix: String = config("samplename_suffix", default="")
+  val sampleNameSuffix: String = config("samplename_suffix", default = "")
 
   def outputVCF(sample: String): Option[File] = {
     outputVCFs.get(sample) match {