Style fixes

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala

@@ -18,10 +18,10 @@ package nl.lumc.sasc.biopet.extensions
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.summary.Summarizable
-import nl.lumc.sasc.biopet.utils.{Logging, VcfUtils, tryToParseNumber}
+import nl.lumc.sasc.biopet.utils.{ Logging, VcfUtils, tryToParseNumber }
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Reference, Version}
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 import scala.io.Source
 
@@ -285,7 +285,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
     else {
       (v1, v2) match {
         case (x1: Int, x2: Int) => x1 + x2
-        case _ => throw new IllegalStateException(s"Value are not Int's, unable to sum them up, key: $key, v1: $v1, v2: $v2")
+        case _                  => throw new IllegalStateException(s"Value are not Int's, unable to sum them up, key: $key, v1: $v1, v2: $v2")
       }
     }
   }

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

@@ -2,9 +2,9 @@ package nl.lumc.sasc.biopet.extensions.gatk
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{BiopetJavaCommandLineFunction, Reference}
+import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Reference }
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, Output }
 
 class CatVariants(val root: Configurable) extends BiopetJavaCommandLineFunction with Reference {
   analysisName = "CatVariants"

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala

@@ -24,7 +24,6 @@ import htsjdk.variant.vcf._
 import nl.lumc.sasc.biopet.utils.ToolCommand
 
 import scala.collection.JavaConversions._
-import scala.collection.mutable.{ Map => MMap }
 
 /**
  * This tool parses a VEP annotated VCF into a standard VCF file.
@@ -59,7 +58,7 @@ object VepNormalizer extends ToolCommand {
     val header = reader.getFileHeader
     val writer = new AsyncVariantContextWriter(new VariantContextWriterBuilder().
       setOutputFile(output).setReferenceDictionary(header.getSequenceDictionary)
-      build())
+      build ())
 
     if (reader.iterator().hasNext) {
       logger.debug("Checking for CSQ tag")
@@ -97,8 +96,8 @@ object VepNormalizer extends ToolCommand {
 
   /**
    * Normalizer
-    *
-    * @param reader input VCF VCFFileReader
+   *
+   * @param reader input VCF VCFFileReader
    * @param writer output VCF AsyncVariantContextWriter
    * @param newInfos array of string containing names of new info fields
    * @param mode normalizer mode (explode or standard)
@@ -125,8 +124,8 @@ object VepNormalizer extends ToolCommand {
 
   /**
    * Checks whether header has a CSQ tag
-    *
-    * @param header VCF header
+   *
+   * @param header VCF header
    */
   def csqCheck(header: VCFHeader) = {
     if (!header.hasInfoLine("CSQ")) {
@@ -139,8 +138,8 @@ object VepNormalizer extends ToolCommand {
    * Checks whether version of input VCF is at least 4.0
    * VEP is known to cause issues below 4.0
    * Throws exception if not
-    *
-    * @param header VCFHeader of input VCF
+   *
+   * @param header VCFHeader of input VCF
    */
   def versionCheck(header: VCFHeader) = {
     var format = ""
@@ -158,8 +157,8 @@ object VepNormalizer extends ToolCommand {
 
   /**
    * Parses the CSQ tag in the header
-    *
-    * @param header the VCF header
+   *
+   * @param header the VCF header
    * @return list of strings with new info fields
    */
   def parseCsq(header: VCFHeader): Array[String] = {
@@ -170,8 +169,8 @@ object VepNormalizer extends ToolCommand {
   /**
    * Explode a single VEP-annotated record to multiple normal records
    * Based on the number of annotated transcripts in the CSQ tag
-    *
-    * @param record the record as a VariantContext object
+   *
+   * @param record the record as a VariantContext object
    * @param csqInfos An array with names of new info tags
    * @return An array with the new records
    */

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala

@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.utils
 
 import java.io.File
 
-import htsjdk.samtools.{SAMSequenceDictionary, SamReader, SamReaderFactory}
-import nl.lumc.sasc.biopet.utils.intervals.{BedRecord, BedRecordList}
+import htsjdk.samtools.{ SAMSequenceDictionary, SamReader, SamReaderFactory }
+import nl.lumc.sasc.biopet.utils.intervals.{ BedRecord, BedRecordList }
 
 import scala.collection.JavaConversions._
 import scala.collection.mutable
@@ -146,12 +146,12 @@ object BamUtils {
   /** This class will add functionality to [[SAMSequenceDictionary]] */
   implicit class SamDictCheck(samDics: SAMSequenceDictionary) {
     /**
-      * This method will check if all contig and sizes are the same without looking at the order of the contigs
-      *
-      * @throws AssertionError
-      * @param that Dict to compare to
-      * @param ignoreOrder When true the order of the contig does not matter
-      */
+     * This method will check if all contig and sizes are the same without looking at the order of the contigs
+     *
+     * @throws AssertionError
+     * @param that Dict to compare to
+     * @param ignoreOrder When true the order of the contig does not matter
+     */
     def assertSameDictionary(that: SAMSequenceDictionary, ignoreOrder: Boolean): Unit = {
       if (ignoreOrder) {
         assert(samDics.getReferenceLength == that.getReferenceLength)

toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala

@@ -21,11 +21,11 @@ import htsjdk.samtools.reference.FastaSequenceFile
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsView
-import nl.lumc.sasc.biopet.extensions.bedtools.{BedtoolsIntersect, BedtoolsMerge}
-import nl.lumc.sasc.biopet.extensions.gatk.{CatVariants, SelectVariants}
-import nl.lumc.sasc.biopet.extensions.manwe.{ManweAnnotateVcf, ManweSamplesImport}
-import nl.lumc.sasc.biopet.extensions.tools.{GvcfToBed, VcfWithVcf, VepNormalizer}
-import nl.lumc.sasc.biopet.extensions.{Bgzip, Ln, VariantEffectPredictor}
+import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsIntersect, BedtoolsMerge }
+import nl.lumc.sasc.biopet.extensions.gatk.{ CatVariants, SelectVariants }
+import nl.lumc.sasc.biopet.extensions.manwe.{ ManweAnnotateVcf, ManweSamplesImport }
+import nl.lumc.sasc.biopet.extensions.tools.{ GvcfToBed, VcfWithVcf, VepNormalizer }
+import nl.lumc.sasc.biopet.extensions.{ Bgzip, Ln, VariantEffectPredictor }
 import nl.lumc.sasc.biopet.utils.VcfUtils
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
@@ -47,9 +47,9 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
 
   def outputVcf: File = (gonlVcfFile, exacVcfFile) match {
     case (Some(_), Some(_)) => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.gonl.exac.vcf.gz")
-    case (Some(_), _) => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.gonl.vcf.gz")
-    case (_, Some(_)) => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.exac.vcf.gz")
-    case _ => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.vcf.gz")
+    case (Some(_), _)       => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.gonl.vcf.gz")
+    case (_, Some(_))       => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.exac.vcf.gz")
+    case _                  => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.vcf.gz")
   }
 
   lazy val minScatterGenomeSize: Long = config("min_scatter_genome_size", default = 75000000)