Format

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SnptestToVcf.scala

@@ -48,7 +48,7 @@ object SnptestToVcf extends ToolCommand {
 
     infoHeader match {
       case Some(header) => parseLines(header, infoIt, cmdArgs)
-      case _            =>
+      case _ =>
         writeEmptyVcf(cmdArgs.outputVcf, cmdArgs.referenceFasta)
         logger.info("No header and records found in file")
     }

public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala

@@ -94,9 +94,9 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
     val snpTests = BedRecordList.fromReference(referenceFasta())
       .scatter(config("bin_size", default = 1000000))
       .allRecords.map { region =>
-      val name = s"${region.chr}-${region.start + 1}-${region.end}"
+        val name = s"${region.chr}-${region.start + 1}-${region.end}"
 
-      val regionDir = new File(outputDir, ".queue" + File.separator + "regions" + File.separator + region.chr)
+        val regionDir = new File(outputDir, ".queue" + File.separator + "regions" + File.separator + region.chr)
         regionDir.mkdirs()
         val bedFile = new File(regionDir, s"${name}.bed")
         BedRecordList.fromList(List(region)).writeToFile(bedFile)