Style fixes

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * Extension for CombineVariants from GATK

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

@@ -17,10 +17,10 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Reference, ToolCommandFunction}
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFunction }
 import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
 /**
  *

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

@@ -14,8 +14,8 @@ import scala.collection.JavaConversions._
 import scala.io.Source
 
 /**
-  * Created by pjvanthof on 15/03/16.
-  */
+ * Created by pjvanthof on 15/03/16.
+ */
 object GensToVcf extends ToolCommand {
 
   case class Args(inputGenotypes: File = null,
@@ -79,23 +79,24 @@ object GensToVcf extends ToolCommand {
       val alt = Allele.create(genotypeValues(4))
       val start = genotypeValues(2).toInt
       val end = ref.length - 1 + start
-      val genotypes = samples.toList.zipWithIndex.map { case (sampleName, index) =>
-        val gps = Array(
-          genotypeValues(5 + (index * 3)),
-          genotypeValues(5 + (index * 3) + 1),
-          genotypeValues(5 + (index * 3) + 2)
-        ).map(_.toDouble)
-        val alleles = gps.indexOf(gps.max) match {
-          case 0 => List(ref, ref)
-          case 1 => List(ref, alt)
-          case 2 => List(alt, alt)
-        }
-        new GenotypeBuilder()
-          .name(sampleName)
-          .alleles(alleles)
-          .attribute("GP", gps)
-          .PL(gps)
-          .make()
+      val genotypes = samples.toList.zipWithIndex.map {
+        case (sampleName, index) =>
+          val gps = Array(
+            genotypeValues(5 + (index * 3)),
+            genotypeValues(5 + (index * 3) + 1),
+            genotypeValues(5 + (index * 3) + 2)
+          ).map(_.toDouble)
+          val alleles = gps.indexOf(gps.max) match {
+            case 0 => List(ref, ref)
+            case 1 => List(ref, alt)
+            case 2 => List(alt, alt)
+          }
+          new GenotypeBuilder()
+            .name(sampleName)
+            .alleles(alleles)
+            .attribute("GP", gps)
+            .PL(gps)
+            .make()
       }
 
       val builder = (new VariantContextBuilder)

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

@@ -2,16 +2,16 @@ package nl.lumc.sasc.biopet.pipelines.gwastest
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference, BiopetQScript}
-import nl.lumc.sasc.biopet.extensions.gatk.{SelectVariants, CombineVariants}
+import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, BiopetQScript }
+import nl.lumc.sasc.biopet.extensions.gatk.{ SelectVariants, CombineVariants }
 import nl.lumc.sasc.biopet.extensions.tools.GensToVcf
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
 import org.broadinstitute.gatk.queue.QScript
 
 /**
-  * Created by pjvanthof on 16/03/16.
-  */
+ * Created by pjvanthof on 16/03/16.
+ */
 class GwasTest(val root: Configurable) extends QScript with BiopetQScript with Reference {
   def this() = this(null)
 
@@ -24,10 +24,11 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
   else {
     if (config.contains("input_gens")) {
       val gens: List[Any] = configValue2list(config("input_gens"))
-      Some(gens.map{ case value: Map[String, Any] =>
-        GensInput(new File(value("genotypes").toString),
-          value.get("info").map(x => new File(x.toString)),
-          value("contig").toString)
+      Some(gens.map {
+        case value: Map[String, Any] =>
+          GensInput(new File(value("genotypes").toString),
+            value.get("info").map(x => new File(x.toString)),
+            value("contig").toString)
       })
     } else None
   }
@@ -60,24 +61,24 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
     }
 
     val snpTests = BedRecordList.fromReference(referenceFasta())
-      .scatter(config("bin_size", default = 10^6))
+      .scatter(config("bin_size", default = 10 ^ 6))
       .allRecords.map { region =>
-      val regionDir = new File(outputDir, "snptest"  + File.separator + region.chr)
-      regionDir.mkdirs()
-      val bedFile = new File(regionDir, s"${region.chr}-${region.start + 1}-${region.end}.bed")
-      BedRecordList.fromList(List(region)).writeToFile(bedFile)
-      bedFile.deleteOnExit()
+        val regionDir = new File(outputDir, "snptest" + File.separator + region.chr)
+        regionDir.mkdirs()
+        val bedFile = new File(regionDir, s"${region.chr}-${region.start + 1}-${region.end}.bed")
+        BedRecordList.fromList(List(region)).writeToFile(bedFile)
+        bedFile.deleteOnExit()
 
-      val sv = new SelectVariants(this)
-      sv.inputFiles :+= vcfFile
-      sv.outputFile = new File(regionDir, s"${region.chr}-${region.start + 1}-${region.end}.vcf.gz")
-      sv.intervals :+= bedFile
-      sv.isIntermediate = true
-      add(sv)
+        val sv = new SelectVariants(this)
+        sv.inputFiles :+= vcfFile
+        sv.outputFile = new File(regionDir, s"${region.chr}-${region.start + 1}-${region.end}.vcf.gz")
+        sv.intervals :+= bedFile
+        sv.isIntermediate = true
+        add(sv)
 
-      //TODO: snptest
-      (region -> "")
-    }
+        //TODO: snptest
+        (region -> "")
+      }
   }
 }