Inspection round biopet utils

bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala

@@ -31,7 +31,7 @@ class Bam2Wig(val parent: Configurable) extends QScript with BiopetQScript {
   def this() = this(null)
 
   @Input(doc = "Input bam file", required = true)
-  var bamFile: File = null
+  var bamFile: File = _
 
   def init(): Unit = {
     inputFiles :+= new InputFile(bamFile)

bam2wig/src/test/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala

@@ -32,7 +32,7 @@ class BamToChromSizesTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testChromSizes: Unit = {
+  def testChromSizes(): Unit = {
     val bamFile = new File(resourcePath("/empty.bam"))
     val bamToChromSizes = new BamToChromSizes(null)
     bamToChromSizes.bamFile = bamFile

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp

@@ -13,8 +13,8 @@
     <tr><th>Version</th><td>${run.version}</td></tr>
     <tr><th>Last commit hash</th><td>${run.commitHash}</td></tr>
     <tr><th>Output directory</th><td>${run.outputDir}</td></tr>
-    <tr><th>Sample</th><td>${allSamples.filter(_.id == sampleId.get).headOption.map(_.name)}</td></tr>
-    <tr><th>Library</th><td>${allLibraries.filter(_.id == libId.get).headOption.map(_.name)}</td></tr>
+    <tr><th>Sample</th><td>${allSamples.find(_.id == sampleId.get).map(_.name)}</td></tr>
+    <tr><th>Library</th><td>${allLibraries.find(_.id == libId.get).map(_.name)}</td></tr>
 </tbody>
 </table>
 <br/>

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -48,7 +48,7 @@ class BamMetrics(val parent: Configurable)
   override def defaults = Map("bedtoolscoverage" -> Map("sorted" -> true))
 
   /** returns files to store in summary */
-  def summaryFiles =
+  def summaryFiles: Map[String, File] =
     Map("reference" -> referenceFasta(), "input_bam" -> inputBam) ++
       ampliconBedFile.map("amplicon" -> _).toMap ++
       ampliconBedFile.map(x => "roi_" + x.getName.stripSuffix(".bed") -> x).toMap
@@ -58,7 +58,7 @@ class BamMetrics(val parent: Configurable)
     Map("amplicon_name" -> ampliconBedFile.collect { case x => x.getName.stripSuffix(".bed") },
         "roi_name" -> roiBedFiles.map(_.getName.stripSuffix(".bed")))
 
-  override def reportClass = {
+  override def reportClass: Some[BammetricsReport] = {
     val bammetricsReport = new BammetricsReport(this)
     bammetricsReport.outputDir = new File(outputDir, "report")
     bammetricsReport.summaryDbFile = summaryDbFile

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -487,7 +487,7 @@ object BammetricsReport extends ReportBuilder {
   }
 
   def writeTableToTsv(tsvFile: File, table: Map[String, Array[Any]], firstColumn: String): Unit = {
-    require(table.map(_._2.size).toList.distinct.size == 1,
+    require(table.map(_._2.length).toList.distinct.size == 1,
             "Not all values has the same number or rows")
     val keys = table.keys.filterNot(_ == firstColumn).toList.sorted
     val writer = new PrintWriter(tsvFile)

bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

@@ -44,7 +44,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
   }
 
   @DataProvider(name = "bammetricsOptions")
-  def bammetricsOptions = {
+  def bammetricsOptions: Array[Array[AnyVal]] = {
     val rois = Array(0, 1, 2, 3)
     val bool = Array(true, false)
 
@@ -57,7 +57,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
   private var dirs: List[File] = Nil
 
   @Test(dataProvider = "bammetricsOptions")
-  def testBamMetrics(rois: Int, amplicon: Boolean, rna: Boolean, wgs: Boolean) = {
+  def testBamMetrics(rois: Int, amplicon: Boolean, rna: Boolean, wgs: Boolean): Unit = {
     val outputDir = Files.createTempDir()
     dirs :+= outputDir
     val map = ConfigUtils.mergeMaps(Map("output_dir" -> outputDir,
@@ -74,8 +74,6 @@ class BamMetricsTest extends TestNGSuite with Matchers {
     bammetrics.libId = Some("1")
     bammetrics.script()
 
-    var regions: Int = rois + (if (amplicon) 1 else 0)
-
     bammetrics.functions.count(_.isInstanceOf[CollectRnaSeqMetrics]) shouldBe (if (rna) 1 else 0)
     bammetrics.functions.count(_.isInstanceOf[CollectWgsMetrics]) shouldBe (if (wgs) 1 else 0)
     bammetrics.functions.count(_.isInstanceOf[CollectMultipleMetrics]) shouldBe 1
@@ -86,13 +84,13 @@ class BamMetricsTest extends TestNGSuite with Matchers {
   }
 
   // remove temporary run directory all tests in the class have been run
-  @AfterClass def removeTempOutputDir() = {
+  @AfterClass def removeTempOutputDir(): Unit = {
     dirs.foreach(FileUtils.deleteDirectory)
   }
 }
 
 object BamMetricsTest {
-  val inputDir = Files.createTempDir()
+  val inputDir: File = Files.createTempDir()
 
   val bam = new File(inputDir, "bla.bam")
   Files.touch(bam)
@@ -100,7 +98,7 @@ object BamMetricsTest {
   Files.touch(ampliconBed)
 
   def roi(i: Int): File = {
-    val roi = new File(inputDir, s"roi${i}.bed")
+    val roi = new File(inputDir, s"roi$i.bed")
     Files.touch(roi)
     roi
   }

basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

@@ -42,7 +42,7 @@ class Basty(val parent: Configurable) extends QScript with MultiSampleQScript {
 
   def variantcallers = List("unifiedgenotyper")
 
-  val numBoot = config("boot_runs", default = 100, namespace = "raxml").asInt
+  val numBoot: Int = config("boot_runs", default = 100, namespace = "raxml").asInt
 
   override def defaults = Map(
     "ploidy" -> 1,

basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala

@@ -48,7 +48,7 @@ class BastyTest extends TestNGSuite with Matchers {
   }
 
   @DataProvider(name = "bastyOptions")
-  def bastyOptions = {
+  def bastyOptions: Array[Array[Any]] = {
     for (s1 <- sample1; s2 <- sample2) yield Array("", s1, s2)
   }
 
@@ -114,7 +114,7 @@ class BastyTest extends TestNGSuite with Matchers {
                                                                                    numberSamples
                                                                                  else 0)
       pipeline.functions.count(_.isInstanceOf[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration)
-                                                                             (numberLibs * 2)
+                                                                             numberLibs * 2
                                                                            else 0)
       pipeline.functions.count(_.isInstanceOf[PrintReads]) shouldBe (if (dbsnp && baseRecalibration)
                                                                        numberLibs
@@ -125,7 +125,7 @@ class BastyTest extends TestNGSuite with Matchers {
       pipeline.summaryFiles shouldBe Map()
 
       pipeline.samples foreach {
-        case (sampleId, sample) =>
+        case (_, sample) =>
           sample.summarySettings shouldBe Map()
           sample.summaryFiles.get("variants_fasta") should not be None
           sample.summaryFiles.get("consensus_fasta") should not be None
@@ -135,7 +135,7 @@ class BastyTest extends TestNGSuite with Matchers {
           sample.summaryFiles.get("snps_only_consensus_variants_fasta") should not be None
           sample.summaryStats shouldBe Map()
           sample.libraries.foreach {
-            case (libId, lib) =>
+            case (_, lib) =>
               lib.summarySettings shouldBe Map()
               lib.summaryFiles shouldBe Map()
               lib.summaryStats shouldBe Map()
@@ -154,14 +154,14 @@ class BastyTest extends TestNGSuite with Matchers {
   }
 
   // remove temporary run directory all tests in the class have been run
-  @AfterClass def removeTempOutputDir() = {
+  @AfterClass def removeTempOutputDir(): Unit = {
     dirs.foreach(FileUtils.deleteDirectory)
   }
 }
 
 object BastyTest {
-  def outputDir = Files.createTempDir()
-  val inputDir = Files.createTempDir()
+  def outputDir: File = Files.createTempDir()
+  val inputDir: File = Files.createTempDir()
 
   def inputTouch(name: String): String = {
     val file = new File(inputDir, name)

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

@@ -35,7 +35,7 @@ object BamUtils {
     *
     * @throws IllegalArgumentException
     * @param bamFiles input bam files
-    * @return
+    * @return Map of sample bam files
     */
   def sampleBamMap(bamFiles: List[File]): Map[String, File] = {
     val temp = bamFiles.map { file =>
@@ -59,7 +59,7 @@ object BamUtils {
     *
     * @param inputBam input bam file
     * @param contig contig to scan for
-    * @param end postion to stop scanning
+    * @param end position to stop scanning
     * @return Int with insertsize for this contig
     */
   def contigInsertSize(inputBam: File,
@@ -82,7 +82,7 @@ object BamUtils {
 
         val counts: mutable.Map[Int, Int] = mutable.Map()
 
-        for (i <- 0 until samplingSize if samIterator.hasNext) {
+        for (_ <- 0 until samplingSize if samIterator.hasNext) {
           val rec = samIterator.next()
           val isPaired = rec.getReadPairedFlag
           val minQ10 = rec.getMappingQuality >= 10
@@ -97,27 +97,24 @@ object BamUtils {
         counts.keys.size match {
           case 1 => Some(counts.keys.head)
           case 0 => None
-          case _ => {
+          case _ =>
             Some(counts.foldLeft(0)((old, observation) => {
               observation match {
-                case (insertSize: Int, observations: Int) => {
+                case (insertSize: Int, observations: Int) =>
                   (old + (insertSize * observations)) / (observations + 1)
-                }
                 case _ => 0
               }
             }))
-          }
         }
       })
 
     insertSizesOnAllFragments.size match {
       case 1 => Some(insertSizesOnAllFragments.head)
       case 0 => None
-      case _ => {
+      case _ =>
         Some(insertSizesOnAllFragments.foldLeft(0)((old, observation) => {
           (old + observation) / 2
         }))
-      }
 
     }
   }
@@ -140,10 +137,10 @@ object BamUtils {
                                   binSize)
       })
       .toList
-    val counts = bamInsertSizes.flatMap(x => x)
+    val counts = bamInsertSizes.flatten
 
     // avoid division by zero
-    if (counts.size != 0) counts.sum / counts.size
+    if (counts.nonEmpty) counts.sum / counts.size
     else 0
   }
 
@@ -161,7 +158,7 @@ object BamUtils {
     }.toMap
 
   /** This class will add functionality to [[SAMSequenceDictionary]] */
-  implicit class SamDictCheck(samDics: SAMSequenceDictionary) {
+  implicit class SamDictCheck(samDicts: SAMSequenceDictionary) {
 
     /**
       * This method will check if all contig and sizes are the same without looking at the order of the contigs
@@ -172,15 +169,15 @@ object BamUtils {
       */
     def assertSameDictionary(that: SAMSequenceDictionary, ignoreOrder: Boolean): Unit = {
       if (ignoreOrder) {
-        assert(samDics.getReferenceLength == that.getReferenceLength)
+        assert(samDicts.getReferenceLength == that.getReferenceLength)
         val thisContigNames =
-          samDics.getSequences.map(x => (x.getSequenceName, x.getSequenceLength)).sorted.toSet
+          samDicts.getSequences.map(x => (x.getSequenceName, x.getSequenceLength)).sorted.toSet
         assert(
           thisContigNames == that.getSequences
             .map(x => (x.getSequenceName, x.getSequenceLength))
             .sorted
             .toSet)
-      } else samDics.assertSameDictionary(that)
+      } else samDicts.assertSameDictionary(that)
     }
   }
 }

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

@@ -35,7 +35,7 @@ object ConfigUtils extends Logging {
     *
     * @param map1 input map
     * @param map2 input map
-    * @return Uniqe map1
+    * @return Unique map1
     */
   def uniqueKeys(map1: Map[String, Any], map2: Map[String, Any]): Map[String, Any] = {
     filterEmtpyMapValues(
@@ -57,32 +57,34 @@ object ConfigUtils extends Logging {
     */
   def filterEmtpyMapValues(map: Map[String, Any]): Map[String, Any] = {
     map.filter {
-      case (key, value: Map[_, _]) => value.nonEmpty
+      case (_, value: Map[_, _]) => value.nonEmpty
       case _ => true
     }
   }
 
   /**
     * Merge 2 maps, when value is in a map in map1 and map2 the value calls recursively this function
+    *
     * @param map1 Prio over map2
     * @param map2 Backup for map1
     * @return merged map
     */
+  //noinspection ScalaUnnecessaryParentheses,ScalaUnnecessaryParentheses,ScalaUnnecessaryParentheses,ScalaUnnecessaryParentheses,ScalaUnnecessaryParentheses
   def mergeMaps(
       map1: Map[String, Any],
       map2: Map[String, Any],
-      resolveConflict: (Any, Any, String) => Any = (m1, m2, key) => m1): Map[String, Any] = {
+      resolveConflict: (Any, Any, String) => Any = (m1, _, _) => m1): Map[String, Any] = {
     (for (key <- map1.keySet.++(map2.keySet)) yield {
-      if (!map2.contains(key)) (key -> map1(key))
-      else if (!map1.contains(key)) (key -> map2(key))
+      if (!map2.contains(key)) key -> map1(key)
+      else if (!map1.contains(key)) key -> map2(key)
       else {
         map1(key) match {
           case m1: Map[_, _] =>
             map2(key) match {
-              case m2: Map[_, _] => (key -> mergeMaps(any2map(m1), any2map(m2), resolveConflict))
-              case _ => (key -> map1(key))
+              case m2: Map[_, _] => key -> mergeMaps(any2map(m1), any2map(m2), resolveConflict)
+              case _ => key -> map1(key)
             }
-          case _ => (key -> resolveConflict(map1(key), map2(key), key))
+          case _ => key -> resolveConflict(map1(key), map2(key), key)
         }
       }
     }).toMap
@@ -122,7 +124,7 @@ object ConfigUtils extends Logging {
     } else Some(map)
   }
 
-  /** Make json aboject from a file */
+  /** Make json object from a file */
   def fileToJson(configFile: File): Json = {
     logger.debug("Jsonfile: " + configFile)
     val jsonText = scala.io.Source.fromFile(configFile).mkString
@@ -172,15 +174,16 @@ object ConfigUtils extends Logging {
 
   lazy val yaml = new Yaml()
 
-  def mapToYaml(map: Map[String, Any]) = yaml.dump(yaml.load(ConfigUtils.mapToJson(map).nospaces))
+  def mapToYaml(map: Map[String, Any]): JsonField =
+    yaml.dump(yaml.load(ConfigUtils.mapToJson(map).nospaces))
 
-  def mapToYamlFile(map: Map[String, Any], outputFile: File) = {
+  def mapToYamlFile(map: Map[String, Any], outputFile: File): Unit = {
     val writer = new PrintWriter(outputFile)
     writer.println(mapToYaml(map))
     writer.close()
   }
 
-  def mapToJsonFile(map: Map[String, Any], outputFile: File) = {
+  def mapToJsonFile(map: Map[String, Any], outputFile: File): Unit = {
     val writer = new PrintWriter(outputFile)
     writer.println(anyToJson(map).toString())
     writer.close()
@@ -531,13 +534,13 @@ object ConfigUtils extends Logging {
 
     /** Convert ConfigValue to List[Double] */
     implicit def configValue2doubleList(value: ConfigValue): List[Double] = {
-      if (requiredValue(value)) any2list(value.value).map(any2double(_))
+      if (requiredValue(value)) any2list(value.value).map(any2double)
       else Nil
     }
 
     /** Convert ConfigValue to List[Int] */
     implicit def configValue2intList(value: ConfigValue): List[Int] = {
-      if (requiredValue(value)) any2list(value.value).map(any2int(_))
+      if (requiredValue(value)) any2list(value.value).map(any2int)
       else Nil
     }
 

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

@@ -43,7 +43,7 @@ object FastaUtils {
   private var dictCache: Map[File, SAMSequenceDictionary] = Map()
 
   /** This will clear the dict cache */
-  def clearCache() = {
+  def clearCache(): Unit = {
     dictCache = Map()
   }
 
@@ -84,8 +84,8 @@ object FastaUtils {
       .map { line =>
         val columns = line.split("\t")
         val refContig = columns(0)
-        val alterniveNames = columns(1).split(";").toSet
-        refContig -> alterniveNames
+        val alternativeNames = columns(1).split(";").toSet
+        refContig -> alternativeNames
       }
       .toMap
     reader.close()

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

@@ -72,12 +72,7 @@ object IoUtils {
       else fname
     }
 
-  /**
-    * This return the contends of a file as a List[String]
-    *
-    * @param file
-    * @return
-    */
+  /** This return the contends of a file as a List[String] */
   def getLinesFromFile(file: File): List[String] = {
     val reader = Source.fromFile(file)
     val lines = reader.getLines().toList
@@ -87,16 +82,15 @@ object IoUtils {
 
   def executableExist(exe: String): Boolean = {
     try {
-      val process = Process(Seq(exe)).run()
       true
     } catch {
-      case e: IOException => false
+      case _: IOException => false
     }
   }
 
   def writeLinesToFile(output: File, lines: List[String]): Unit = {
     val writer = new PrintWriter(output)
-    lines.foreach(writer.println(_))
+    lines.foreach(writer.println)
     writer.close()
   }
 }

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

@@ -19,12 +19,12 @@ package nl.lumc.sasc.biopet.utils
   */
 class LazyCheck[T](function: => T) {
   private var _isSet = false
-  def isSet = _isSet
-  lazy val value = {
+  def isSet: Boolean = _isSet
+  lazy val value: T = {
     val cache = function
     _isSet = true
     cache
   }
-  def apply() = value
-  def get = value
+  def apply(): T = value
+  def get: T = value
 }

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

@@ -19,7 +19,7 @@ package nl.lumc.sasc.biopet.utils
   */
 trait MainCommand {
 
-  lazy val commandName = this.getClass.getSimpleName
+  lazy val commandName: String = this.getClass.getSimpleName
     .split("\\$")
     .last
 

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

@@ -22,24 +22,24 @@ object Question {
   def string(name: String,
              default: Option[String] = None,
              description: Option[String] = None,
-             posibleValues: List[String] = Nil,
+             possibleValues: List[String] = Nil,
              validation: List[(String) => Boolean] = Nil): String = {
     description.foreach(println)
-    if (posibleValues.nonEmpty) println(s"possible values: ${posibleValues.mkString(", ")}")
+    if (possibleValues.nonEmpty) println(s"possible values: ${possibleValues.mkString(", ")}")
     default.foreach(x => println(s"Default value: $x"))
     print(s"$name > ")
     (scala.io.StdIn.readLine.trim, default) match {
       case (a, Some(d)) if a.isEmpty => d
       case (a, None) if a.isEmpty =>
         println("ERROR: Value is required")
-        string(name, default, description, posibleValues, validation)
+        string(name, default, description, possibleValues, validation)
       case (a, _) =>
         if (!validation.forall(_(a))) {
           println("ERROR: Validation of failed")
-          string(name, default, description, posibleValues, validation)
-        } else if (posibleValues.nonEmpty && !posibleValues.contains(a)) {
+          string(name, default, description, possibleValues, validation)
+        } else if (possibleValues.nonEmpty && !possibleValues.contains(a)) {
           println("ERROR: Value not allowed")
-          string(name, default, description, posibleValues, validation)
+          string(name, default, description, possibleValues, validation)
         } else a
     }
   }
@@ -69,24 +69,24 @@ object Question {
   def list(name: String,
            default: Option[List[String]] = None,
            description: Option[String] = None,
-           posibleValues: List[String] = Nil,
-           validation: (String) => Boolean = String => true): List[String] = {
+           possibleValues: List[String] = Nil,
+           validation: (String) => Boolean = _ => true): List[String] = {
     description.foreach(println)
-    if (posibleValues.nonEmpty) println(s"possible values: ${posibleValues.mkString(", ")}")
+    if (possibleValues.nonEmpty) println(s"possible values: ${possibleValues.mkString(", ")}")
     default.foreach(x => println(s"Default value: $x"))
     print(s"$name > ")
     (scala.io.StdIn.readLine.split(",").toList.map(_.trim), default) match {
       case (List(""), Some(d)) => d
       case (List(""), None) =>
         println("ERROR: Value is required")
-        list(name, default, description, posibleValues, validation)
+        list(name, default, description, possibleValues, validation)
       case (a, _) =>
         if (!a.forall(validation)) {
           println("ERROR: Validation of failed")
-          list(name, default, description, posibleValues, validation)
-        } else if (posibleValues.nonEmpty && !a.forall(posibleValues.contains)) {
+          list(name, default, description, possibleValues, validation)
+        } else if (possibleValues.nonEmpty && !a.forall(possibleValues.contains)) {
           println("ERROR: Value not allowed")
-          list(name, default, description, posibleValues, validation)
+          list(name, default, description, possibleValues, validation)
         } else a
     }
   }

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

 package nl.lumc.sasc.biopet.utils
+import scala.util.matching.Regex
 
 /**
   * Created by pjvanthof on 29/04/2017.
@@ -34,7 +35,7 @@ case class SemanticVersion(major: Int, minor: Int, patch: Int, build: Option[Str
 }
 
 object SemanticVersion {
-  val semanticVersionRegex = "[vV]?(\\d+)\\.(\\d+)\\.(\\d+)(-.*)?".r
+  val semanticVersionRegex: Regex = "[vV]?(\\d+)\\.(\\d+)\\.(\\d+)(-.*)?".r
 
   /**
     * Check whether a version string is a semantic version.

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

@@ -25,7 +25,7 @@ trait ToolCommand extends MainCommand with Logging {
   protected abstract class AbstractArgs {}
 
   /**
-    * Abstract opt parser to add efault args to each biopet tool
+    * Abstract opt parser to add default args to each biopet tool
     */
   protected abstract class AbstractOptParser extends scopt.OptionParser[Args](commandName) {
     opt[String]('l', "log_level") foreach { x =>

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

@@ -31,7 +31,7 @@ object VcfUtils {
     * @param vcfRecord record to check
     * @return allele with most nucleotides
     */
-  def getLongestAllele(vcfRecord: VariantContext) = {
+  def getLongestAllele(vcfRecord: VariantContext): Allele = {
     val alleles = vcfRecord.getAlleles
     val longestAlleleId = alleles.map(_.getBases.length).zipWithIndex.maxBy(_._1)._2
     alleles(longestAlleleId)

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/annotation/Feature.scala

@@ -52,8 +52,8 @@ case class Feature(contig: String,
       attributes.map(x => x._1 + s"=${x._2}").mkString(";")
     ).mkString("\t")
 
-  def minPosition = if (start < end) start else end
-  def maxPosition = if (start > end) start else end
+  def minPosition: Int = if (start < end) start else end
+  def maxPosition: Int = if (start > end) start else end
 }
 
 object Feature {
@@ -72,11 +72,11 @@ object Feature {
           s"strand only allows '+' or '-', not ${values(6)}, gtf line: $line")
     }
 
-    val artibutes = values.lift(8).map(_.split(";")).getOrElse(Array()).map {
-      case artibutesGtfRegex(key, value) => key -> value
-      case artibutesGffRegex(key, value) => key -> value
+    val attributes = values.lift(8).map(_.split(";")).getOrElse(Array()).map {
+      case attributesGtfRegex(key, value) => key -> value
+      case attributesGffRegex(key, value) => key -> value
       case _ =>
-        throw new IllegalArgumentException(s"Atribute it not correct formatted, gtf line: $line")
+        throw new IllegalArgumentException(s"Attribute it not correct formatted, gtf line: $line")
     } toMap
 
     val score = values(5) match {
@@ -99,9 +99,9 @@ object Feature {
             score,
             strand,
             frame,
-            artibutes)
+            attributes)
   }
 
-  lazy val artibutesGtfRegex: Regex = """\s*(\S*) "(.*)"$""".r
-  lazy val artibutesGffRegex: Regex = """\s*(\S*)=(.*)$""".r
+  lazy val attributesGtfRegex: Regex = """\s*(\S*) "(.*)"$""".r
+  lazy val attributesGffRegex: Regex = """\s*(\S*)=(.*)$""".r
 }

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala

@@ -38,8 +38,8 @@ class Config(protected var _map: Map[String, Any],
     loadDefaultConfig()
   }
 
-  def map = _map
-  def defaults = _defaults
+  def map: Map[String, Any] = _map
+  def defaults: Map[String, Any] = _defaults
 
   /**
     * Loading a environmental variable as location of config files to merge into the config
@@ -85,7 +85,7 @@ class Config(protected var _map: Map[String, Any],
   }
 
   /**
-    * Add a single vallue to the config
+    * Add a single value to the config
     * @param key key of value
     * @param value value itself
     * @param path Path to value
@@ -231,7 +231,7 @@ class Config(protected var _map: Map[String, Any],
       map.foreach {
         case (key, value: Map[_, _]) =>
           reportUnused(value.asInstanceOf[Map[String, Any]], path :+ key)
-        case (key, value) =>
+        case (key, _) =>
           logger.warn(
             s"config key in user config is never used, key: $key" +
               (if (path.nonEmpty) s", path: ${path.mkString(" -> ")}" else ""))
@@ -303,7 +303,7 @@ object Config extends Logging {
         if (p.isDefined)
           Option(
             ConfigValue(startIndex,
-                        ConfigValueIndex(startIndex.module, path, startIndex.key, freeVar = true),
+                        ConfigValueIndex(startIndex.module, path, startIndex.key),
                         p.get))
         else None
       } else None

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/ConfigValue.scala

@@ -24,19 +24,19 @@ class ConfigValue(val requestIndex: ConfigValueIndex,
                   val default: Boolean) {
 
   /** Get value as String */
-  def asString = any2string(value)
+  def asString: String = any2string(value)
 
   /** Get value as File */
   def asFile = new File(any2string(value))
 
   /** Get value as Int */
-  def asInt = any2int(value)
+  def asInt: Int = any2int(value)
 
   /** Get value as Double */
-  def asDouble = any2double(value)
+  def asDouble: Double = any2double(value)
 
   /** Get value as List[Any] */
-  def asList = any2list(value)
+  def asList: List[Any] = any2list(value)
 
   /** Get value as List[File] */
   def asFileList: List[File] = for (file <- any2stringList(value)) yield new File(file)
@@ -45,10 +45,10 @@ class ConfigValue(val requestIndex: ConfigValueIndex,
   def asStringList: List[String] = any2stringList(value)
 
   /** Get value as Map */
-  def asMap = any2map(value)
+  def asMap: Map[String, Any] = any2map(value)