Fix code style warnings

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/SquishBed.scala

@@ -40,6 +40,6 @@ object SquishBed {
     val squishBed = new SquishBed(root)
     squishBed.input = input
     squishBed.output = new File(outputDir, input.getName.stripSuffix(".bed") + ".squish.bed")
-    return squishBed
+    squishBed
   }
 }

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

@@ -26,13 +26,15 @@ import scala.collection.JavaConversions._
 import scala.collection.mutable
 import scala.io.Source
 
-/**
- * Created by pjvan_thof on 1/10/15.
- */
 class AnnotateVcfWithBed {
   // TODO: Queue wrapper
 }
 
+/**
+ * This a tools to annotate a vcf file with values from a bed file
+ *
+ * Created by pjvan_thof on 1/10/15.
+ */
 object AnnotateVcfWithBed extends ToolCommand {
 
   /**
@@ -52,30 +54,29 @@ object AnnotateVcfWithBed extends ToolCommand {
                   fieldType: String = "String") extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
-    opt[File]('I', "inputFile") required () unbounded () valueName ("<vcf file>") action { (x, c) =>
+    opt[File]('I', "inputFile") required () unbounded () valueName "<vcf file>" action { (x, c) =>
       c.copy(inputFile = x)
-    } text ("Input is a required file property")
-    opt[File]('B', "bedFile") required () unbounded () valueName ("<bed file>") action { (x, c) =>
+    } text "Input is a required file property"
+    opt[File]('B', "bedFile") required () unbounded () valueName "<bed file>" action { (x, c) =>
       c.copy(bedFile = x)
-    } text ("Bedfile is a required file property")
-    opt[File]('o', "output") required () unbounded () valueName ("<vcf file>") action { (x, c) =>
+    } text "Bedfile is a required file property"
+    opt[File]('o', "output") required () unbounded () valueName "<vcf file>" action { (x, c) =>
       c.copy(outputFile = x)
-    } text ("out is a required file property")
-    opt[String]('f', "fieldName") required () unbounded () valueName ("<name of field in vcf file>") action { (x, c) =>
+    } text "out is a required file property"
+    opt[String]('f', "fieldName") required () unbounded () valueName "<name of field in vcf file>" action { (x, c) =>
       c.copy(fieldName = x)
-    } text ("Name of info field in new vcf file")
-    opt[String]('d', "fieldDescription") unbounded () valueName ("<name of field in vcf file>") action { (x, c) =>
+    } text "Name of info field in new vcf file"
+    opt[String]('d', "fieldDescription") unbounded () valueName "<name of field in vcf file>" action { (x, c) =>
       c.copy(fieldDescription = x)
-    } text ("Description of field in new vcf file")
-    opt[String]('t', "fieldType") unbounded () valueName ("<name of field in vcf file>") action { (x, c) =>
+    } text "Description of field in new vcf file"
+    opt[String]('t', "fieldType") unbounded () valueName "<name of field in vcf file>" action { (x, c) =>
       c.copy(fieldType = x)
-    } text ("Description of field in new vcf file")
+    } text "Description of field in new vcf file"
   }
 
   /**
-   * Program will Annotate a vcf file with the overlapping regions of a bed file, 4e column of the bed file we in a info tag in the vcf file
-   *
-   * @param args
+   * Program will Annotate a vcf file with the overlapping regions of a bed file,
+   * 4e column of the bed file we in a info tag in the vcf file
    */
   def main(args: Array[String]): Unit = {
 
@@ -108,7 +109,7 @@ object AnnotateVcfWithBed extends ToolCommand {
       val values = line.split("\t")
       if (values.size >= 4)
         bedRecords(values(0)) = (values(1).toInt, values(2).toInt, values(3)) :: bedRecords.getOrElse(values(0), Nil)
-      else (values.size >= 3 && fieldType == VCFHeaderLineType.Flag)
+      else values.size >= 3 && fieldType == VCFHeaderLineType.Flag
       bedRecords(values(0)) = (values(1).toInt, values(2).toInt, "") :: bedRecords.getOrElse(values(0), Nil)
     }
 
@@ -148,8 +149,8 @@ object AnnotateVcfWithBed extends ToolCommand {
         writer.add(builder.make)
       }
     }
-    reader.close
-    writer.close
+    reader.close()
+    writer.close()
 
     logger.info("Done")
   }

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

@@ -58,8 +58,8 @@ class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion with
 
   override val defaultCoreMemory = 4.0
 
-  override def beforeGraph: Unit = {
-    super.beforeGraph
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
     reference = referenceFasta()
   }
 
@@ -91,43 +91,43 @@ object BastyGenerateFasta extends ToolCommand {
                   reference: File = null) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
-    opt[File]('V', "inputVcf") unbounded () valueName ("<file>") action { (x, c) =>
+    opt[File]('V', "inputVcf") unbounded () valueName "<file>" action { (x, c) =>
       c.copy(inputVcf = x)
-    } text ("vcf file, needed for outputVariants and outputConsensusVariants") validate { x =>
+    } text "vcf file, needed for outputVariants and outputConsensusVariants" validate { x =>
       if (x.exists) success else failure("File does not exist: " + x)
     }
-    opt[File]("bamFile") unbounded () valueName ("<file>") action { (x, c) =>
+    opt[File]("bamFile") unbounded () valueName "<file>" action { (x, c) =>
       c.copy(bamFile = x)
-    } text ("bam file, needed for outputConsensus and outputConsensusVariants") validate { x =>
+    } text "bam file, needed for outputConsensus and outputConsensusVariants" validate { x =>
       if (x.exists) success else failure("File does not exist: " + x)
     }
-    opt[File]("outputVariants") maxOccurs (1) unbounded () valueName ("<file>") action { (x, c) =>
+    opt[File]("outputVariants") maxOccurs 1 unbounded () valueName "<file>" action { (x, c) =>
       c.copy(outputVariants = x)
-    } text ("fasta with only variants from vcf file")
-    opt[File]("outputConsensus") maxOccurs (1) unbounded () valueName ("<file>") action { (x, c) =>
+    } text "fasta with only variants from vcf file"
+    opt[File]("outputConsensus") maxOccurs 1 unbounded () valueName "<file>" action { (x, c) =>
       c.copy(outputConsensus = x)
-    } text ("Consensus fasta from bam, always reference bases else 'N'")
-    opt[File]("outputConsensusVariants") maxOccurs (1) unbounded () valueName ("<file>") action { (x, c) =>
+    } text "Consensus fasta from bam, always reference bases else 'N'"
+    opt[File]("outputConsensusVariants") maxOccurs 1 unbounded () valueName "<file>" action { (x, c) =>
       c.copy(outputConsensusVariants = x)
-    } text ("Consensus fasta from bam with variants from vcf file, always reference bases else 'N'")
+    } text "Consensus fasta from bam with variants from vcf file, always reference bases else 'N'"
     opt[Unit]("snpsOnly") unbounded () action { (x, c) =>
       c.copy(snpsOnly = true)
-    } text ("Only use snps from vcf file")
+    } text "Only use snps from vcf file"
     opt[String]("sampleName") unbounded () action { (x, c) =>
       c.copy(sampleName = x)
-    } text ("Sample name in vcf file")
+    } text "Sample name in vcf file"
     opt[String]("outputName") required () unbounded () action { (x, c) =>
       c.copy(outputName = x)
-    } text ("Output name in fasta file header")
+    } text "Output name in fasta file header"
     opt[Int]("minAD") unbounded () action { (x, c) =>
       c.copy(minAD = x)
-    } text ("min AD value in vcf file for sample. Defaults to: 8")
+    } text "min AD value in vcf file for sample. Defaults to: 8"
     opt[Int]("minDepth") unbounded () action { (x, c) =>
       c.copy(minDepth = x)
-    } text ("min depth in bam file. Defaults to: 8")
+    } text "min depth in bam file. Defaults to: 8"
     opt[File]("reference") unbounded () action { (x, c) =>
       c.copy(reference = x)
-    } text ("Indexed reference fasta file") validate { x =>
+    } text "Indexed reference fasta file" validate { x =>
       if (x.exists) success else failure("File does not exist: " + x)
     }
 
@@ -188,7 +188,7 @@ object BastyGenerateFasta extends ToolCommand {
 
         val variants: Map[(Int, Int), VariantContext] = if (cmdArgs.inputVcf != null) {
           val reader = new VCFFileReader(cmdArgs.inputVcf, true)
-          (for (variant <- reader.query(chrName, begin, end) if (!cmdArgs.snpsOnly || variant.isSNP)) yield {
+          (for (variant <- reader.query(chrName, begin, end) if !cmdArgs.snpsOnly || variant.isSNP) yield {
             (variant.getStart, variant.getEnd) -> variant
           }).toMap
         } else Map()
@@ -202,10 +202,10 @@ object BastyGenerateFasta extends ToolCommand {
             for (t <- s to e) coverage(t - begin) += 1
           }
         } else {
-          for (t <- 0 until coverage.length) coverage(t) = cmdArgs.minDepth
+          for (t <- coverage.indices) coverage(t) = cmdArgs.minDepth
         }
 
-        val consensus = for (t <- 0 until coverage.length) yield {
+        val consensus = for (t <- coverage.indices) yield {
           if (coverage(t) >= cmdArgs.minDepth) referenceSequence.getBases()(t).toChar
           else 'N'
         }
@@ -222,7 +222,7 @@ object BastyGenerateFasta extends ToolCommand {
               val stripSufix = 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.size - stripSufix))
+              buffer.append(allele.substring(stripPrefix, allele.length - stripSufix))
             } else {
               buffer.append(consensus(consensusPos))
               consensusPos += 1
@@ -230,7 +230,7 @@ object BastyGenerateFasta extends ToolCommand {
           }
         }
 
-        (chunk -> (consensus.mkString.toUpperCase, buffer.toString.toUpperCase))
+        chunk -> (consensus.mkString.toUpperCase, buffer.toString().toUpperCase)
       }).toMap
       if (cmdArgs.outputConsensus != null) {
         val writer = new PrintWriter(cmdArgs.outputConsensus)
@@ -239,7 +239,7 @@ object BastyGenerateFasta extends ToolCommand {
           writer.print(chunks(c)._1)
         }
         writer.println()
-        writer.close
+        writer.close()
       }
       if (cmdArgs.outputConsensusVariants != null) {
         val writer = new PrintWriter(cmdArgs.outputConsensusVariants)
@@ -248,7 +248,7 @@ object BastyGenerateFasta extends ToolCommand {
           writer.print(chunks(c)._2)
         }
         writer.println()
-        writer.close
+        writer.close()
       }
     }
   }
@@ -257,12 +257,12 @@ object BastyGenerateFasta extends ToolCommand {
     val writer = new PrintWriter(cmdArgs.outputVariants)
     writer.println(">" + cmdArgs.outputName)
     val vcfReader = new VCFFileReader(cmdArgs.inputVcf, false)
-    for (vcfRecord <- vcfReader if (!cmdArgs.snpsOnly || vcfRecord.isSNP)) yield {
+    for (vcfRecord <- vcfReader if !cmdArgs.snpsOnly || vcfRecord.isSNP) yield {
       writer.print(getMaxAllele(vcfRecord))
     }
     writer.println()
-    writer.close
-    vcfReader.close
+    writer.close()
+    vcfReader.close()
   }
 
   protected def getMaxAllele(vcfRecord: VariantContext): String = {
@@ -276,6 +276,6 @@ object BastyGenerateFasta extends ToolCommand {
     if (AD == null) return fillAllele("", maxSize)
     val maxADid = AD.zipWithIndex.maxBy(_._1)._2
     if (AD(maxADid) < cmdArgs.minAD) return fillAllele("", maxSize)
-    return fillAllele(vcfRecord.getAlleles()(maxADid).getBaseString, maxSize)
+    fillAllele(vcfRecord.getAlleles()(maxADid).getBaseString, maxSize)
   }
 }
\ No newline at end of file

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

@@ -53,19 +53,19 @@ object BedToInterval extends ToolCommand {
     bedToInterval.input = inputBed
     bedToInterval.bamFile = inputBam
     bedToInterval.output = output
-    return bedToInterval
+    bedToInterval
   }
 
   case class Args(inputFile: File = null, outputFile: File = null, bamFile: File = null) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
-    opt[File]('I', "inputFile") required () valueName ("<file>") action { (x, c) =>
+    opt[File]('I', "inputFile") required () valueName "<file>" action { (x, c) =>
       c.copy(inputFile = x)
     }
-    opt[File]('o', "output") required () valueName ("<file>") action { (x, c) =>
+    opt[File]('o', "output") required () valueName "<file>" action { (x, c) =>
       c.copy(outputFile = x)
     }
-    opt[File]('b', "bam") required () valueName ("<file>") action { (x, c) =>
+    opt[File]('b', "bam") required () valueName "<file>" action { (x, c) =>
       c.copy(bamFile = x)
     }
   }
@@ -85,12 +85,12 @@ object BedToInterval extends ToolCommand {
       writer.write("@SQ\tSN:" + record.getSequenceName + "\tLN:" + record.getSequenceLength + "\n")
       record.getSequenceName -> record.getSequenceLength
     }
-    inputSam.close
+    inputSam.close()
     val refsMap = Map(refs: _*)
 
     val bedFile = Source.fromFile(commandArgs.inputFile)
     for (
-      line <- bedFile.getLines;
+      line <- bedFile.getLines();
       split = line.split("\t") if split.size >= 3;
       chr = split(0);
       start = split(1);
@@ -102,7 +102,7 @@ object BedToInterval extends ToolCommand {
       else {
         var strand = "+"
         for (t <- 3 until split.length) {
-          if ((split(t) == "+" || split(t) == "-")) strand = split(t)
+          if (split(t) == "+" || split(t) == "-") strand = split(t)
         }
         writer.write(strand)
       }

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

@@ -21,8 +21,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-import scala.collection.SortedMap
-import scala.collection.mutable.Map
+import scala.collection.{ mutable, SortedMap }
 import scala.io.Source
 
 class BedtoolsCoverageToCounts(val root: Configurable) extends ToolCommandFuntion {
@@ -45,10 +44,10 @@ object BedtoolsCoverageToCounts extends ToolCommand {
   case class Args(input: File = null, output: File = null) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
-    opt[File]('I', "input") required () valueName ("<file>") action { (x, c) =>
+    opt[File]('I', "input") required () valueName "<file>" action { (x, c) =>
       c.copy(input = x)
     }
-    opt[File]('o', "output") required () unbounded () valueName ("<file>") action { (x, c) =>
+    opt[File]('o', "output") required () unbounded () valueName "<file>" action { (x, c) =>
       c.copy(output = x)
     }
   }
@@ -62,8 +61,8 @@ object BedtoolsCoverageToCounts extends ToolCommand {
 
     if (!commandArgs.input.exists) throw new IllegalStateException("Input file not found, file: " + commandArgs.input)
 
-    val counts: Map[String, Long] = Map()
-    for (line <- Source.fromFile(commandArgs.input).getLines) {
+    val counts: mutable.Map[String, Long] = mutable.Map()
+    for (line <- Source.fromFile(commandArgs.input).getLines()) {
       val values = line.split("\t")
       val gene = values(3)
       val count = values(6).toLong
@@ -77,6 +76,6 @@ object BedtoolsCoverageToCounts extends ToolCommand {
     for ((seq, count) <- sortedCounts) {
       if (count > 0) writer.println(seq + "\t" + count)
     }
-    writer.close
+    writer.close()
   }
 }
\ No newline at end of file

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

@@ -25,6 +25,7 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 import scala.collection.JavaConversions._
+import scala.collection.mutable
 
 class BiopetFlagstat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
   javaMainClass = getClass.getName
@@ -63,13 +64,13 @@ object BiopetFlagstat extends ToolCommand {
   case class Args(inputFile: File = null, summaryFile: Option[File] = None, region: Option[String] = None) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
-    opt[File]('I', "inputFile") required () valueName ("<file>") action { (x, c) =>
+    opt[File]('I', "inputFile") required () valueName "<file>" action { (x, c) =>
       c.copy(inputFile = x)
-    } text ("input bam file")
-    opt[File]('s', "summaryFile") valueName ("<file>") action { (x, c) =>
+    } text "input bam file"
+    opt[File]('s', "summaryFile") valueName "<file>" action { (x, c) =>
       c.copy(summaryFile = Some(x))
-    } text ("summary output file")
-    opt[String]('r', "region") valueName ("<chr:start-stop>") action { (x, c) =>
+    } text "summary output file"
+    opt[String]('r', "region") valueName "<chr:start-stop>" action { (x, c) =>
       c.copy(region = Some(x))
     }
   }
@@ -82,7 +83,7 @@ object BiopetFlagstat extends ToolCommand {
     val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
 
     val inputSam = SamReaderFactory.makeDefault.open(commandArgs.inputFile)
-    val iterSam = if (commandArgs.region == None) inputSam.iterator else {
+    val iterSam = if (commandArgs.region.isEmpty) inputSam.iterator else {
       val regionRegex = """(.*):(.*)-(.*)""".r
       commandArgs.region.get match {
         case regionRegex(chr, start, stop) => inputSam.query(chr, start.toInt, stop.toInt, false)
@@ -91,7 +92,7 @@ object BiopetFlagstat extends ToolCommand {
     }
 
     val flagstatCollector = new FlagstatCollector
-    flagstatCollector.loadDefaultFunctions
+    flagstatCollector.loadDefaultFunctions()
     val m = 10
     val max = 60
     for (t <- 0 to (max / m))
@@ -144,11 +145,10 @@ object BiopetFlagstat extends ToolCommand {
     }
 
     commandArgs.summaryFile.foreach {
-      case file => {
+      case file =>
         val writer = new PrintWriter(file)
         writer.println(flagstatCollector.summary)
         writer.close()
-      }
     }
 
     println(flagstatCollector.report)
@@ -157,12 +157,12 @@ object BiopetFlagstat extends ToolCommand {
   class FlagstatCollector {
     private var functionCount = 0
     var readsCount = 0
-    private val names: Map[Int, String] = Map()
+    private val names: mutable.Map[Int, String] = mutable.Map()
     private var functions: Array[SAMRecord => Boolean] = Array()
     private var totalCounts: Array[Long] = Array()
     private var crossCounts = Array.ofDim[Long](1, 1)
 
-    def loadDefaultFunctions {
+    def loadDefaultFunctions() {
       addFunction("All", record => true)
       addFunction("Mapped", record => !record.getReadUnmappedFlag)
       addFunction("Duplicates", record => record.getDuplicateReadFlag)
@@ -207,7 +207,7 @@ object BiopetFlagstat extends ToolCommand {
       crossCounts = Array.ofDim[Long](functionCount, functionCount)
       totalCounts = new Array[Long](functionCount)
       val temp = new Array[SAMRecord => Boolean](functionCount)
-      for (t <- 0 until (temp.size - 1)) temp(t) = functions(t)
+      for (t <- 0 until (temp.length - 1)) temp(t) = functions(t)
       functions = temp
 
       val index = functionCount - 1
@@ -228,7 +228,7 @@ object BiopetFlagstat extends ToolCommand {
       buffer.append(crossReport() + "\n")
       buffer.append(crossReport(fraction = true) + "\n")
 
-      return buffer.toString
+      buffer.toString()
     }
 
     def summary: String = {
@@ -236,7 +236,7 @@ object BiopetFlagstat extends ToolCommand {
         names(t) -> totalCounts(t)
       }).toMap
 
-      return ConfigUtils.mapToJson(map).spaces4
+      ConfigUtils.mapToJson(map).spaces4
     }
 
     def crossReport(fraction: Boolean = false): String = {
@@ -258,7 +258,7 @@ object BiopetFlagstat extends ToolCommand {
           else buffer.append("\t")
         }
       }
-      return buffer.toString
+      buffer.toString()
     }
   } // End of class
 

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

@@ -46,19 +46,19 @@ object CheckAllelesVcfInBam extends ToolCommand {
                   bamFiles: List[File] = Nil, minMapQual: Int = 1) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
-    opt[File]('I', "inputFile") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
+    opt[File]('I', "inputFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(inputFile = x)
     }
-    opt[File]('o', "outputFile") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
+    opt[File]('o', "outputFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(outputFile = x)
     }
-    opt[String]('s', "sample") unbounded () minOccurs (1) action { (x, c) =>
+    opt[String]('s', "sample") unbounded () minOccurs 1 action { (x, c) =>
       c.copy(samples = x :: c.samples)
     }
-    opt[File]('b', "bam") unbounded () minOccurs (1) action { (x, c) =>
+    opt[File]('b', "bam") unbounded () minOccurs 1 action { (x, c) =>
       c.copy(bamFiles = x :: c.bamFiles)
     }
-    opt[Int]('m', "min_mapping_quality") maxOccurs (1) action { (x, c) =>
+    opt[Int]('m', "min_mapping_quality") maxOccurs 1 action { (x, c) =>
       c.copy(minMapQual = c.minMapQual)
     }
   }
@@ -98,7 +98,7 @@ object CheckAllelesVcfInBam extends ToolCommand {
       val refAllele = vcfRecord.getReference.getBaseString
       for ((sample, bamReader) <- bamReaders) {
         val queryInterval = new QueryInterval(bamHeaders(sample).getSequenceIndex(vcfRecord.getChr),
-          vcfRecord.getStart, vcfRecord.getStart + refAllele.size - 1)
+          vcfRecord.getStart, vcfRecord.getStart + refAllele.length - 1)
         val bamIter = bamReader.query(Array(queryInterval), false)
 
         def filterRead(samRecord: SAMRecord): Boolean = {
@@ -112,7 +112,7 @@ object CheckAllelesVcfInBam extends ToolCommand {
             countReports(sample).lowMapQualReads += 1
             return true
           }
-          return false
+          false
         }
 
         val counts = for (samRecord <- bamIter if !filterRead(samRecord)) {
@@ -122,7 +122,7 @@ object CheckAllelesVcfInBam extends ToolCommand {
             case _ => countReports(sample).notFound += 1
           }
         }
-        bamIter.close
+        bamIter.close()
       }
 
       val builder = new VariantContextBuilder(vcfRecord)
@@ -137,49 +137,49 @@ object CheckAllelesVcfInBam extends ToolCommand {
       }
       writer.add(builder.make)
     }
-    for ((_, r) <- bamReaders) r.close
-    reader.close
-    writer.close
+    for ((_, r) <- bamReaders) r.close()
+    reader.close()
+    writer.close()
   }
 
   def checkAlles(samRecord: SAMRecord, vcfRecord: VariantContext): Option[String] = {
     val readStartPos = List.range(0, samRecord.getReadBases.length)
       .find(x => samRecord.getReferencePositionAtReadPosition(x + 1) == vcfRecord.getStart) getOrElse { return None }
-    val readBases = samRecord.getReadBases()
+    val readBases = samRecord.getReadBases
     val alleles = vcfRecord.getAlleles.map(x => x.getBaseString)
     val refAllele = alleles.head
     var maxSize = 1
-    for (allele <- alleles if allele.size > maxSize) maxSize = allele.size
+    for (allele <- alleles if allele.length > maxSize) maxSize = allele.length
     val readC = for (t <- readStartPos until readStartPos + maxSize if t < readBases.length) yield readBases(t).toChar
-    val allelesInRead = mutable.Set(alleles.filter(readC.mkString.startsWith(_)): _*)
+    val allelesInRead = mutable.Set(alleles.filter(readC.mkString.startsWith): _*)
 
     // Removal of insertions that are not really in the cigarstring
-    for (allele <- allelesInRead if allele.size > refAllele.size) {
-      val refPos = for (t <- refAllele.size until allele.size) yield samRecord.getReferencePositionAtReadPosition(readStartPos + t + 1)
+    for (allele <- allelesInRead if allele.length > refAllele.length) {
+      val refPos = for (t <- refAllele.length until allele.length) yield samRecord.getReferencePositionAtReadPosition(readStartPos + t + 1)
       if (refPos.exists(_ > 0)) allelesInRead -= allele
     }
 
     // Removal of alleles that are not really in the cigarstring
     for (allele <- allelesInRead) {
-      val readPosAfterAllele = samRecord.getReferencePositionAtReadPosition(readStartPos + allele.size + 1)
-      val vcfPosAfterAllele = vcfRecord.getStart + refAllele.size
+      val readPosAfterAllele = samRecord.getReferencePositionAtReadPosition(readStartPos + allele.length + 1)
+      val vcfPosAfterAllele = vcfRecord.getStart + refAllele.length
       if (readPosAfterAllele != vcfPosAfterAllele &&
-        (refAllele.size != allele.size || (refAllele.size == allele.size && readPosAfterAllele < 0))) allelesInRead -= allele
+        (refAllele.length != allele.length || (refAllele.length == allele.length && readPosAfterAllele < 0))) allelesInRead -= allele
     }
 
-    for (allele <- allelesInRead if allele.size >= refAllele.size) {
-      if (allelesInRead.exists(_.size > allele.size)) allelesInRead -= allele
+    for (allele <- allelesInRead if allele.length >= refAllele.length) {
+      if (allelesInRead.exists((_.length) > allele.length)) allelesInRead -= allele
     }
-    if (allelesInRead.contains(refAllele) && allelesInRead.exists(_.size < refAllele.size)) allelesInRead -= refAllele
-    if (allelesInRead.isEmpty) return None