Code warning found biopet tools

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

@@ -22,6 +22,7 @@ import nl.lumc.sasc.biopet.utils.intervals.{BedRecord, BedRecordList}
 import picard.annotation.{Gene, GeneAnnotationReader}
 
 import scala.collection.JavaConversions._
+import scala.collection.immutable
 
 /**
   * This tool will generate Base count based on a bam file and a refflat file
@@ -277,7 +278,7 @@ object BaseCounter extends ToolCommand {
       val intronSense = geneCount.intronCounts.map(_.counts.senseBases).sum
       val intronAntiSense = geneCount.intronCounts.map(_.counts.antiSenseBases).sum
       geneIntronSenseCounts += intronSense
-      geneExonicAntiSenseCounts += intronAntiSense
+      geneIntronAntiSenseCounts += intronAntiSense
       geneIntronicWriter.println(geneCount.gene.getName + "\t" + (intronSense + intronAntiSense))
       geneIntronicSenseWriter.println(geneCount.gene.getName + "\t" + intronSense)
       geneIntronicAntiSenseWriter.println(geneCount.gene.getName + "\t" + intronAntiSense)
@@ -451,7 +452,7 @@ object BaseCounter extends ToolCommand {
 
     bamReader.close()
     counter += 1
-    if (counter % 1000 == 0) logger.info(s"${counter} chunks done")
+    if (counter % 1000 == 0) logger.info(s"$counter chunks done")
     ThreadOutput(counts.values.toList, metaExons, plusMetaExons ::: minMetaExons)
   }
 
@@ -512,7 +513,7 @@ object BaseCounter extends ToolCommand {
     overlap
   }
 
-  def groupGenesOnOverlap(genes: Iterable[Gene]) = {
+  def groupGenesOnOverlap(genes: Iterable[Gene]): Map[String, List[List[Gene]]] = {
     genes
       .groupBy(_.getContig)
       .map {
@@ -531,13 +532,13 @@ object BaseCounter extends ToolCommand {
   class Counts {
     var senseBases = 0L
     var antiSenseBases = 0L
-    def totalBases = senseBases + antiSenseBases
+    def totalBases: Long = senseBases + antiSenseBases
     var senseReads = 0L
     var antiSenseReads = 0L
-    def totalReads = senseReads + antiSenseReads
+    def totalReads: Long = senseReads + antiSenseReads
   }
 
-  def generateMergedExonRegions(gene: Gene) =
+  def generateMergedExonRegions(gene: Gene): BedRecordList =
     BedRecordList
       .fromList(
         gene
@@ -548,17 +549,18 @@ object BaseCounter extends ToolCommand {
 
   class GeneCount(val gene: Gene) {
     val counts = new Counts
-    val transcripts = gene.iterator().map(new TranscriptCount(_)).toList
-    def intronRegions =
+    val transcripts: List[TranscriptCount] = gene.iterator().map(new TranscriptCount(_)).toList
+    def intronRegions: BedRecordList =
       BedRecordList
         .fromList(
           BedRecord(gene.getContig, gene.getStart - 1, gene.getEnd) :: generateMergedExonRegions(
             gene).allRecords.toList)
         .squishBed(strandSensitive = false, nameSensitive = false)
 
-    val exonCounts =
+    val exonCounts: immutable.Iterable[RegionCount] =
       generateMergedExonRegions(gene).allRecords.map(e => new RegionCount(e.start + 1, e.end))
-    val intronCounts = intronRegions.allRecords.map(e => new RegionCount(e.start + 1, e.end))
+    val intronCounts: immutable.Iterable[RegionCount] =
+      intronRegions.allRecords.map(e => new RegionCount(e.start + 1, e.end))
 
     def addRecord(samRecord: SAMRecord, sense: Boolean): Unit = {
       bamRecordBasesOverlap(samRecord, gene.getStart, gene.getEnd, counts, sense)
@@ -570,7 +572,7 @@ object BaseCounter extends ToolCommand {
 
   class TranscriptCount(val transcript: Gene#Transcript) {
     val counts = new Counts
-    def intronRegions =
+    def intronRegions: BedRecordList =
       BedRecordList
         .fromList(
           BedRecord(transcript.getGene.getContig, transcript.start() - 1, transcript.end()) ::
@@ -579,9 +581,9 @@ object BaseCounter extends ToolCommand {
             .toList)
         .squishBed(strandSensitive = false, nameSensitive = false)
 
-    val exonCounts = transcript.exons.map(new RegionCount(_))
-    val intronCounts =
-      if (transcript.exons.size > 1)
+    val exonCounts: Array[RegionCount] = transcript.exons.map(new RegionCount(_))
+    val intronCounts: List[RegionCount] =
+      if (transcript.exons.length > 1)
         intronRegions.allRecords.map(e => new RegionCount(e.start + 1, e.end)).toList
       else Nil
     def addRecord(samRecord: SAMRecord, sense: Boolean): Unit = {

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

@@ -61,7 +61,7 @@ object BastyGenerateFasta extends ToolCommand {
       (x, c) =>
         c.copy(outputConsensusVariants = x)
     } text "Consensus fasta from bam with variants from vcf file, always reference bases else 'N'"
-    opt[Unit]("snpsOnly") unbounded () action { (x, c) =>
+    opt[Unit]("snpsOnly") unbounded () action { (_, c) =>
       c.copy(snpsOnly = true)
     } text "Only use snps from vcf file"
     opt[String]("sampleName") unbounded () action { (x, c) =>
@@ -87,7 +87,7 @@ object BastyGenerateFasta extends ToolCommand {
         val err: ListBuffer[String] = ListBuffer()
         if (c.outputConsensus != null || c.outputConsensusVariants != null) {
           if (c.reference == null)
-            err.add("No reference suplied")
+            err.add("No reference supplied")
           else {
             val index = new File(c.reference.getAbsolutePath + ".fai")
             if (!index.exists) err.add("Reference does not have index")
@@ -178,10 +178,10 @@ object BastyGenerateFasta extends ToolCommand {
             if (variant.isDefined) {
               logger.info(variant.get._2)
               val stripPrefix = if (variant.get._1._1 < begin) begin - variant.get._1._1 else 0
-              val stripSufix = if (variant.get._1._2 > end) variant.get._1._2 - end else 0
+              val stripSuffix = if (variant.get._1._2 > end) variant.get._1._2 - end else 0
               val allele = getMaxAllele(variant.get._2)
               consensusPos += variant.get._2.getReference.getBases.length
-              buffer.append(allele.substring(stripPrefix, allele.length - stripSufix))
+              buffer.append(allele.substring(stripPrefix, allele.length - stripSuffix))
             } else {
               buffer.append(consensus(consensusPos))
               consensusPos += 1

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

@@ -64,7 +64,7 @@ object CheckAllelesVcfInBam extends ToolCommand {
     opt[File]('b', "bam") unbounded () minOccurs 1 action { (x, c) =>
       c.copy(bamFiles = x :: c.bamFiles)
     } text "bam file, from which the variants (VCF files) were called"
-    opt[Int]('m', "min_mapping_quality") maxOccurs 1 action { (x, c) =>
+    opt[Int]('m', "min_mapping_quality") maxOccurs 1 action { (_, c) =>
       c.copy(minMapQual = c.minMapQual)
     } text "minimum mapping quality score for a read to be taken into account"
   }
@@ -120,28 +120,6 @@ object CheckAllelesVcfInBam extends ToolCommand {
           vcfRecord.getStart + refAllele.length - 1)
         val bamIter = bamReader.query(Array(queryInterval), false)
 
-        def filterRead(samRecord: SAMRecord): Boolean = {
-          if (samRecord.getDuplicateReadFlag) {
-            countReports(sample).duplicateReads += 1
-            return true
-          }
-          if (samRecord.getSupplementaryAlignmentFlag) return true
-          if (samRecord.getNotPrimaryAlignmentFlag) return true
-          if (samRecord.getMappingQuality < commandArgs.minMapQual) {
-            countReports(sample).lowMapQualReads += 1
-            return true
-          }
-          false
-        }
-
-        val counts = for (samRecord <- bamIter if !filterRead(samRecord)) {
-          checkAlleles(samRecord, vcfRecord) match {
-            case Some(a) =>
-              if (countReports(sample).aCounts.contains(a)) countReports(sample).aCounts(a) += 1
-              else countReports(sample).aCounts += (a -> 1)
-            case _ => countReports(sample).notFound += 1
-          }
-        }
         bamIter.close()
       }
 

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

@@ -68,14 +68,14 @@ object DownloadNcbiAssembly extends ToolCommand {
     */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val cmdargs
+    val cmdArgs
       : Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
-    logger.info(s"Reading ${cmdargs.assemblyReport}")
-    val reader = Source.fromFile(cmdargs.assemblyReport)
+    logger.info(s"Reading ${cmdArgs.assemblyReport}")
+    val reader = Source.fromFile(cmdArgs.assemblyReport)
     val assamblyReport = reader.getLines().toList
     reader.close()
-    cmdargs.reportFile.foreach { file =>
+    cmdArgs.reportFile.foreach { file =>
       val writer = new PrintWriter(file)
       assamblyReport.foreach(writer.println)
       writer.close()
@@ -88,12 +88,12 @@ object DownloadNcbiAssembly extends ToolCommand {
       .split("\t")
       .zipWithIndex
       .toMap
-    val nameId = cmdargs.contigNameHeader.map(x => headers(x))
+    val nameId = cmdArgs.contigNameHeader.map(x => headers(x))
     val lengthId = headers.get("Sequence-Length")
 
     val baseUrlEutils = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"
 
-    val fastaWriter = new PrintWriter(cmdargs.outputFile)
+    val fastaWriter = new PrintWriter(cmdArgs.outputFile)
 
     val allContigs = assamblyReport
       .filter(!_.startsWith("#"))
@@ -101,23 +101,23 @@ object DownloadNcbiAssembly extends ToolCommand {
     val totalLength = lengthId.map(id => allContigs.map(_.apply(id).toLong).sum)
 
     logger.info(s"${allContigs.size} contigs found")
-    totalLength.foreach(l => logger.info(s"Total length: ${l}"))
+    totalLength.foreach(l => logger.info(s"Total length: $l"))
 
     val filterContigs = allContigs
-      .filter(values => cmdargs.mustNotHave.forall(x => values(headers(x._1)) != x._2))
+      .filter(values => cmdArgs.mustNotHave.forall(x => values(headers(x._1)) != x._2))
       .filter(values =>
-        cmdargs.mustHaveOne
-          .exists(x => values(headers(x._1)) == x._2) || cmdargs.mustHaveOne.isEmpty)
+        cmdArgs.mustHaveOne
+          .exists(x => values(headers(x._1)) == x._2) || cmdArgs.mustHaveOne.isEmpty)
     val filterLength = lengthId.map(id => filterContigs.map(_.apply(id).toLong).sum)
 
     logger.info(s"${filterContigs.size} contigs left after filtering")
-    filterLength.foreach(l => logger.info(s"Filtered length: ${l}"))
+    filterLength.foreach(l => logger.info(s"Filtered length: $l"))
 
     filterContigs.foreach { values =>
       val id = if (values(6) == "na") values(4) else values(6)
-      logger.info(s"Start download ${id}")
-      val fastaReader = Source.fromURL(
-        s"${baseUrlEutils}/efetch.fcgi?db=nuccore&id=${id}&retmode=text&rettype=fasta")
+      logger.info(s"Start download $id")
+      val fastaReader =
+        Source.fromURL(s"$baseUrlEutils/efetch.fcgi?db=nuccore&id=$id&retmode=text&rettype=fasta")
       fastaReader
         .getLines()
         .map(x => nameId.map(y => x.replace(">", s">${values(y)} ")).getOrElse(x))

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

@@ -30,7 +30,7 @@ object ExtractAlignedFastq extends ToolCommand {
   type FastqInput = (FastqRecord, Option[FastqRecord])
 
   /** Get the FastqRecord ID */
-  def fastqId(rec: FastqRecord) = rec.getReadHeader.split(" ")(0)
+  def fastqId(rec: FastqRecord): String = rec.getReadHeader.split(" ")(0)
 
   /**
     * Function to create iterator over Interval given input interval string
@@ -97,7 +97,7 @@ object ExtractAlignedFastq extends ToolCommand {
       inAlnReader.getFileHeader.getSequenceIndex(name) match {
         case x if x >= 0 =>
           x
-        case otherwise =>
+        case _ =>
           throw new IllegalArgumentException(
             "Chromosome " + name + " is not found in the alignment file")
       }

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

@@ -8,7 +8,7 @@ import nl.lumc.sasc.biopet.utils.annotation.Feature
 import scala.io.Source
 
 /**
-  * Created by pjvan_thof on 8-6-17.
+  * Created by pjvanthof on 8-6-17.
   */
 object ExtractTagsFromGtf extends ToolCommand {
   case class Args(outputFile: File = null,

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

@@ -60,9 +60,8 @@ object FastqFilter extends ToolCommand {
     var total = 0
     var kept = 0
     for (record <- reader.iterator()) {
-      if (cmdArgs.idRegex
-            .map(_.findFirstIn(record.getReadHeader.takeWhile(_ != ' ')).isDefined)
-            .getOrElse(true)) {
+      if (cmdArgs.idRegex.forall(
+            _.findFirstIn(record.getReadHeader.takeWhile(_ != ' ')).isDefined)) {
         writer.write(record)
         kept += 1
       }

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

@@ -58,7 +58,7 @@ object FastqSplitter extends ToolCommand {
     var counter: Long = 0
     while (reader.hasNext) {
       for (writer <- output) {
-        for (t <- 1 to groupSize if reader.hasNext) {
+        for (_ <- 1 to groupSize if reader.hasNext) {
           writer.write(reader.next())
           counter += 1
           if (counter % 1000000 == 0) logger.info(counter + " reads processed")

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

@@ -29,7 +29,7 @@ object FastqSync extends ToolCommand {
 
   /** Implicit class to allow for lazy retrieval of FastqRecord ID without any read pair mark */
   private implicit class FastqPair(fq: FastqRecord) {
-    lazy val fragId = idRegex.split(fq.getReadHeader.split(" ")(0))(0)
+    lazy val fragId: String = idRegex.split(fq.getReadHeader.split(" ")(0))(0)
   }
 
   /**

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

@@ -47,7 +47,7 @@ object FindOverlapMatch extends ToolCommand {
     opt[Double]('c', "cutoff") required () unbounded () valueName "<value>" action { (x, c) =>
       c.copy(cutoff = x)
     } text "minimum value to report it as pair"
-    opt[Unit]("use_same_names") unbounded () valueName "<value>" action { (x, c) =>
+    opt[Unit]("use_same_names") unbounded () valueName "<value>" action { (_, c) =>
       c.copy(filterSameNames = false)
     } text "Do not compare samples with the same name"
     opt[String]("rowSampleRegex") unbounded () valueName "<regex>" action { (x, c) =>
@@ -82,12 +82,11 @@ object FindOverlapMatch extends ToolCommand {
       case _ => sys.process.stdout
     }
 
-    for (columnSample <- samplesColumnHeader if cmdArgs.columnSampleRegex
-           .map(_.findFirstIn(columnSample._1).isDefined)
-           .getOrElse(true)) {
+    for (columnSample <- samplesColumnHeader
+         if cmdArgs.columnSampleRegex.forall(_.findFirstIn(columnSample._1).isDefined)) {
       val buffer = ListBuffer[(String, Double)]()
       for (rowSample <- samplesRowHeader
-           if cmdArgs.rowSampleRegex.map(_.findFirstIn(rowSample._1).isDefined).getOrElse(true)) {
+           if cmdArgs.rowSampleRegex.forall(_.findFirstIn(rowSample._1).isDefined)) {
         val value = data(columnSample._2)(rowSample._2).toDouble
         if (value >= cmdArgs.cutoff && (!cmdArgs.filterSameNames || columnSample._2 != rowSample._2)) {
           buffer.+=((rowSample._1, value))

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

@@ -100,7 +100,7 @@ object FindRepeatsPacBio extends ToolCommand {
       }
       bamIter.close()
       commandArgs.outputFile match {
-        case Some(file) => {
+        case Some(file) =>
           val writer = new PrintWriter(file)
           writer.println(header.mkString("\t"))
           writer.println(
@@ -119,8 +119,7 @@ object FindRepeatsPacBio extends ToolCommand {
               notSpan
             ).mkString("\t"))
           writer.close()
-        }
-        case _ => {
+        case _ =>
           println(header.mkString("\t"))
           println(
             List(
@@ -137,7 +136,6 @@ object FindRepeatsPacBio extends ToolCommand {
               deletions.mkString("/"),
               notSpan
             ).mkString("\t"))
-        }
       }
     }
   }
@@ -152,7 +150,7 @@ object FindRepeatsPacBio extends ToolCommand {
     var ins: List[Ins] = Nil
     var samRecord: SAMRecord = _
 
-    override def toString = {
+    override def toString: String = {
       "id: " + samRecord.getReadName + "  beginDel: " + beginDel + "  endDel: " + endDel + "  dels: " + dels + "  ins: " + ins
     }
   }

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

@@ -62,7 +62,7 @@ object GensToVcf extends ToolCommand {
     opt[String]('c', "contig") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(contig = x)
     } text "contig of impute file"
-    opt[Unit]("sortInput") maxOccurs 1 action { (x, c) =>
+    opt[Unit]("sortInput") maxOccurs 1 action { (_, c) =>
       c.copy(sortInput = true)
     } text "In memory sorting"
   }

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

@@ -174,7 +174,7 @@ object GtfToRefflat extends ToolCommand {
     val writer = new PrintWriter(refflatFile)
 
     for {
-      (contig, genes) <- genesBuffer.values.toList.groupBy(_.contig).toList.sortBy(_._1)
+      (_, genes) <- genesBuffer.values.toList.groupBy(_.contig).toList.sortBy(_._1)
       gene <- genes.sortBy(_.start)
       transcript <- gene.transcripts
     } {

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

@@ -25,6 +25,7 @@ import nl.lumc.sasc.biopet.utils.ToolCommand
 import scala.collection.mutable
 import scala.collection.mutable.ListBuffer
 import scala.io.Source
+import scala.util.matching.Regex
 
 object KrakenReportToJson extends ToolCommand {
 
@@ -53,7 +54,7 @@ object KrakenReportToJson extends ToolCommand {
   }
 
   var cladeIDs: mutable.ArrayBuffer[Long] = mutable.ArrayBuffer.fill(32)(0)
-  val spacePattern = "^( +)".r
+  val spacePattern: Regex = "^( +)".r
   private var lines: Map[Long, KrakenHit] = Map.empty
 
   case class Args(krakenreport: File = null,
@@ -118,7 +119,7 @@ object KrakenReportToJson extends ToolCommand {
 
     cladeIDs(cladeLevel + 1) = values(4).toLong
     Map(
-      values(4).toLong -> new KrakenHit(
+      values(4).toLong -> KrakenHit(
         taxonomyID = values(4).toLong,
         taxonomyName = if (skipNames) "" else scientificName.trim,
         cladeCount = values(2).toLong,
@@ -168,7 +169,7 @@ object KrakenReportToJson extends ToolCommand {
       }
     })
 
-    val result = Map("unclassified" -> lines(0).toJSON(withChildren = false),
+    val result = Map("unclassified" -> lines(0).toJSON(),
                      "classified" -> lines(1).toJSON(withChildren = true))
     mapToJson(result).spaces2
 

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

@@ -86,7 +86,7 @@ object MergeAlleles extends ToolCommand {
         else output += variant.getStart -> List(variant)
       }
 
-      for ((k, v) <- SortedMap(output.toSeq: _*)) {
+      for ((_, v) <- SortedMap(output.toSeq: _*)) {
         writer.add(mergeAlleles(v))
       }
     }

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

@@ -101,12 +101,11 @@ object MergeTables extends ToolCommand {
       .sorted
 
     output.write((featureName +: samples).mkString("\t") + "\n")
-    features.foreach {
-      case feature =>
-        // get feature values for each sample (order == order of samples in header)
-        val line = feature +: samples
-          .map(results(_).getOrElse(feature, fallback))
-        output.write(line.mkString("\t") + "\n")
+    features.foreach { feature =>
+      // get feature values for each sample (order == order of samples in header)
+      val line = feature +: samples
+        .map(results(_).getOrElse(feature, fallback))
+      output.write(line.mkString("\t") + "\n")
     }
     output.flush()
   }

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

@@ -62,7 +62,7 @@ object MpileupToVcf extends ToolCommand {
     opt[Double]("seqError") action { (x, c) =>
       c.copy(seqError = x)
     }
-    opt[Unit]("refCalls") action { (x, c) =>
+    opt[Unit]("refCalls") action { (_, c) =>
       c.copy(refCalls = true)
     }
   }
@@ -204,9 +204,9 @@ object MpileupToVcf extends ToolCommand {
           for (a <- ad.indices if ad(a) > (if (max >= 0) ad(max) else -1) && !gt.contains(a))
             max = a
           val f = ad(max).toDouble / left
-          for (a <- 0 to floor(f).toInt if gt.size < commandArgs.ploidy) gt.append(max)
+          for (_ <- 0 to floor(f).toInt if gt.size < commandArgs.ploidy) gt.append(max)
           if (f - floor(f) >= commandArgs.homoFraction) {
-            for (b <- p to commandArgs.ploidy if gt.size < commandArgs.ploidy) gt.append(max)
+            for (_ <- p to commandArgs.ploidy if gt.size < commandArgs.ploidy) gt.append(max)
           }
           left -= ad(max)
         }

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

@@ -33,7 +33,7 @@ object MultiCoverage extends ToolCommand {
       (x, c) =>
         c.copy(outputFile = x)
     } text "output file"
-    opt[Unit]("mean") unbounded () valueName "<file>" action { (x, c) =>
+    opt[Unit]("mean") unbounded () valueName "<file>" action { (_, c) =>
       c.copy(mean = true)
     } text "By default total bases is outputed, enable this option make the output relative to region length"
   }

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

@@ -67,10 +67,6 @@ object NcbiReportToContigMap extends ToolCommand {
       .zipWithIndex
       .toMap
 
-    val allContigs = assamblyReport
-      .filter(!_.startsWith("#"))
-      .map(_.split("\t"))
-
     val altNameIds = cmdargs.names.filter(_ != cmdargs.contigNameHeader).map(headers)
     val nameId = headers(cmdargs.contigNameHeader)
 

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

@@ -43,7 +43,7 @@ object RegionAfCount extends ToolCommand {
       (x, c) =>
         c.copy(outputPrefix = x)
     }
-    opt[Unit]('s', "scatterPlot") unbounded () action { (x, c) =>
+    opt[Unit]('s', "scatterPlot") unbounded () action { (_, c) =>
       c.copy(scatterpPlot = true)
     }
     opt[File]('V', "vcfFile") unbounded () minOccurs 1 action { (x, c) =>
@@ -116,7 +116,7 @@ object RegionAfCount extends ToolCommand {
           afCounts.toMap
         }).toMap
 
-    logger.info(s"Done reading, ${c} regions")
+    logger.info(s"Done reading, $c regions")
 
     logger.info("Writing output files")
 

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

@@ -58,7 +58,7 @@ object SageCreateLibrary extends ToolCommand {
     }
   }
 
-  val geneRegex = """ENSG[0-9]{11}""".r
+  val geneRegex: Regex = """ENSG[0-9]{11}""".r
 
   val tagGenesMap: mutable.Map[String, TagGenes] = mutable.Map()
 
@@ -143,7 +143,7 @@ object SageCreateLibrary extends ToolCommand {
   }
 
   private def addTagresultToTaglib(name: String, tagResult: TagResult) {
-    val id = name.split(" ").head //.stripPrefix("hg19_ensGene_")
+    //.stripPrefix("hg19_ensGene_")
     val geneID = geneRegex.findFirstIn(name).getOrElse("unknown_gene")
     allGenes.add(geneID)
 

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

@@ -56,11 +56,10 @@ object SamplesTsvToConfig extends ToolCommand {
     cmdArgs.outputFile match {
       case Some(file) if file.getName.endsWith(".yml") || file.getName.endsWith(".yaml") =>
         ConfigUtils.mapToYamlFile(configMap, file)
-      case Some(file) => {
+      case Some(file) =>
         val writer = new PrintWriter(file)
         writer.println(ConfigUtils.mapToJson(configMap).spaces2)
         writer.close()
-      }
       case _ => println(ConfigUtils.mapToYaml(configMap))
     }
   }

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

@@ -111,7 +111,7 @@ object SeqStat extends ToolCommand {
                       lengths: mutable.ArrayBuffer[Int] = mutable.ArrayBuffer())
 
   val baseStats: mutable.ArrayBuffer[BaseStat] = mutable.ArrayBuffer()
-  val readStats: ReadStat = new ReadStat()
+  val readStats: ReadStat = ReadStat()
 
   var readLengthHistogram: mutable.Map[String, Long] = mutable.Map.empty
 
@@ -203,7 +203,7 @@ object SeqStat extends ToolCommand {
       )
       // ensure bases: `ACTGN` is always reported even having a zero count.
       // Other chars might be counted also, these are also reported
-      .retain((nucleotide, count) => (count > 0 || "ACTGN".contains(nucleotide.toString)))
+      .retain((nucleotide, count) => count > 0 || "ACTGN".contains(nucleotide.toString))
 
     baseQualHistogram = quals.slice(phredEncoding.id, quals.size)
     baseQualHistogram ++= mutable.ArrayBuffer.fill(reportValues.max + 1 - baseQualHistogram.size)(
@@ -262,11 +262,10 @@ object SeqStat extends ToolCommand {
     val report = reportMap(commandArgs.fastq)
 
     commandArgs.outputJson match {
-      case Some(file) => {
+      case Some(file) =>
         val writer = new PrintWriter(file)
         writer.println(ConfigUtils.mapToJson(report))
         writer.close()
-      }
       case _ => println(ConfigUtils.mapToJson(report))
     }
   }

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

@@ -34,7 +34,7 @@ object SquishBed extends ToolCommand {
     opt[File]('o', "output") required () unbounded () valueName "<file>" action { (x, c) =>
       c.copy(output = x)
     }
-    opt[Unit]('s', "strandSensitive") unbounded () valueName "<file>" action { (x, c) =>
+    opt[Unit]('s', "strandSensitive") unbounded () valueName "<file>" action { (_, c) =>
       c.copy(strandSensitive = true)
     }
   }

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

@@ -79,25 +79,23 @@ object SummaryToTsv extends ToolCommand {
       fetchValues(summary, paths, sample = cmdArgs.mode == "sample", lib = cmdArgs.mode == "lib")
 
     cmdArgs.outputFile match {
-      case Some(file) => {
+      case Some(file) =>
         val writer = new PrintWriter(file)
         writer.println(createHeader(paths))
         for (lineId <- values.head._2.keys)
           writer.println(createLine(paths, values, lineId))
         writer.close()
-      }
-      case _ => {
+      case _ =>
         println(createHeader(paths))
         for (lineId <- values.head._2.keys)
           println(createLine(paths, values, lineId))
-      }
     }
   }
 
   def fetchValues(summary: Summary,
                   paths: Map[String, Array[String]],
                   sample: Boolean = false,
-                  lib: Boolean = false) = {
+                  lib: Boolean = lib = false): Map[String, Map[String, Option[Any]]] = {
     for ((name, path) <- paths)
       yield
         name -> {
@@ -109,7 +107,7 @@ object SummaryToTsv extends ToolCommand {
   }
 
   def createHeader(paths: Map[String, Array[String]]): String = {
-    paths.map(_._1).mkString("\t", "\t", "")
+    paths.keys.mkString("\t", "\t", "")
   }
 
   def createLine(paths: Map[String, Array[String]],

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

@@ -41,7 +41,7 @@ object ValidateAnnotation extends ToolCommand {
     opt[File]('R', "reference") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(reference = x)
     } text "Reference fasta to check vcf file against"
-    opt[Unit]("disableFail") maxOccurs 1 valueName "<file>" action { (x, c) =>
+    opt[Unit]("disableFail") maxOccurs 1 valueName "<file>" action { (_, c) =>
       c.copy(failOnError = false)
     } text "Do not fail on error. The tool will still exit when encountering an error, but will do so with exit code 0"
   }

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

@@ -16,11 +16,12 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 
-import htsjdk.samtools.fastq.{FastqRecord, FastqReader}
+import htsjdk.samtools.fastq.{FastqReader, FastqRecord}
 import nl.lumc.sasc.biopet.utils.ToolCommand