Fix code style warnings

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

@@ -5,7 +5,7 @@ import java.io.{ File, PrintWriter }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportBuilder, ReportPage, ReportSection }
 import nl.lumc.sasc.biopet.core.summary.{ Summary, SummaryValue }
-import nl.lumc.sasc.biopet.extensions.rscript.{ StackedBarPlot, XYPlot }
+import nl.lumc.sasc.biopet.extensions.rscript.{ StackedBarPlot, LinePlot }
 
 class BammetricsReport(val root: Configurable) extends ReportBuilderExtension {
   val builder = BammetricsReport
@@ -204,7 +204,7 @@ object BammetricsReport extends ReportBuilder {
 
     tsvWriter.close()
 
-    val plot = new XYPlot(null)
+    val plot = new LinePlot(null)
     plot.input = tsvFile
     plot.output = pngFile
     plot.ylabel = Some("Reads")
@@ -292,7 +292,7 @@ object BammetricsReport extends ReportBuilder {
 
     tsvWriter.close()
 
-    val plot = new XYPlot(null)
+    val plot = new LinePlot(null)
     plot.input = tsvFile
     plot.output = pngFile
     plot.ylabel = Some("Bases")

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala

@@ -59,8 +59,8 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
   var maqerr: Option[Int] = config("maqerr")
   var maxins: Option[Int] = config("maxins")
 
-  override def beforeGraph {
-    super.beforeGraph
+  override def beforeGraph() {
+    super.beforeGraph()
     if (reference == null) reference = referenceFasta()
   }
 
@@ -81,10 +81,9 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
       optional("--maxins", maxins) +
       required(reference) +
       (R2 match {
-        case Some(r2) => {
+        case Some(r2) =>
           required("-1", R1) +
             optional("-2", r2)
-        }
         case _ => required(R1)
       }) +
       " > " + required(output)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala

@@ -52,6 +52,6 @@ object Cat {
     val cat = new Cat(root)
     cat.input = input
     cat.output = output
-    return cat
+    cat
   }
 }
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala

@@ -76,7 +76,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
     val stats: mutable.Map[String, Int] = mutable.Map("trimmed" -> 0, "tooshort" -> 0, "toolong" -> 0)
     val adapter_stats: mutable.Map[String, Int] = mutable.Map()
 
-    if (stats_output.exists) for (line <- Source.fromFile(stats_output).getLines) {
+    if (stats_output.exists) for (line <- Source.fromFile(stats_output).getLines()) {
       line match {
         case trimR(m)                 => stats += ("trimmed" -> m.toInt)
         case tooShortR(m)             => stats += ("tooshort" -> m.toInt)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala

@@ -22,6 +22,8 @@ import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
+ * Extension for freebayes
+ *
  * Created by pjvan_thof on 3/3/15.
  */
 class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with Reference {
@@ -42,8 +44,8 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
   override val versionRegex = """version:  (.*)""".r
   override def versionCommand = executable + " --version"
 
-  override def beforeGraph: Unit = {
-    super.beforeGraph
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
     reference = referenceFasta()
   }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala

@@ -41,6 +41,6 @@ object Gzip {
     val gzip = new Gzip(root)
     gzip.input = input
     gzip.output = output
-    return gzip
+    gzip
   }
 }
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala

@@ -51,11 +51,11 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
   lazy val cmd: String = {
     lazy val inCanonical: String = {
       // need to remove "/~" to correctly expand path with tilde
-      input.getCanonicalPath().replace("/~", "")
+      input.getCanonicalPath.replace("/~", "")
     }
 
     lazy val outCanonical: String = {
-      output.getCanonicalPath().replace("/~", "")
+      output.getCanonicalPath.replace("/~", "")
     }
 
     lazy val inToks: Array[String] = {
@@ -68,8 +68,8 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
 
     lazy val commonPrefixLength: Int = {
       val maxLength = scala.math.min(inToks.length, outToks.length)
-      var i: Int = 0;
-      while (i < maxLength && inToks(i) == outToks(i)) i += 1;
+      var i: Int = 0
+      while (i < maxLength && inToks(i) == outToks(i)) i += 1
       i
     }
 
@@ -108,11 +108,11 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
     }
   }
 
-  override def run {
+  override def run() {
     val stdout = new StringBuffer()
     val stderr = new StringBuffer()
     val process = Process(cmd).run(ProcessLogger(stdout append _ + "\n", stderr append _ + "\n"))
-    val exitcode = process.exitValue
+    val exitcode = process.exitValue()
     if (exitcode != 0) {
       throw new Exception("Error creating symbolic link, this was the original message: \n" + stderr)
     }
@@ -136,6 +136,6 @@ object Ln {
     ln.input = input
     ln.output = output
     ln.relative = relative
-    return ln
+    ln
   }
 }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala

@@ -45,7 +45,7 @@ object Md5sum {
     val md5sum = new Md5sum(root)
     md5sum.input = fastqfile
     md5sum.output = new File(outDir, fastqfile.getName + ".md5")
-    return md5sum
+    md5sum
   }
 
   /** Makes md5sum with md5 file in same dir as input file */
@@ -53,6 +53,6 @@ object Md5sum {
     val md5sum = new Md5sum(root)
     md5sum.input = file
     md5sum.output = new File(file.getParentFile, file.getName + ".md5")
-    return md5sum
+    md5sum
   }
 }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala

@@ -37,8 +37,8 @@ class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
   override val defaultCoreMemory = memory.getOrElse(1000).toDouble / 1000
   override val defaultThreads = 2
 
-  override def beforeCmd {
-    if (!memory.isEmpty) memory = Option(memory.get * threads)
+  override def beforeCmd() {
+    if (memory.isDefined) memory = Option(memory.get * threads)
   }
 
   /** return commandline to execute */
@@ -58,6 +58,6 @@ object Pbzip2 {
     val pbzip2 = new Pbzip2(root)
     pbzip2.input = input
     pbzip2.output = output
-    return pbzip2
+    pbzip2
   }
 }
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala

@@ -57,7 +57,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
   }
 
   /** return basic command to prefix the complete command with */
-  def getPythonCommand(): String = {
+  def getPythonCommand: String = {
     required(executable) + required(python_script)
   }
 }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala

@@ -72,11 +72,11 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
   var executableThreads: Option[String] = config("exe_pthreads")
 
   /** Sets correct output files to job */
-  override def beforeGraph {
+  override def beforeGraph() {
     require(w != null)
     if (threads == 0) threads = getThreads(defaultThreads)
     executable = if (threads > 1 && executableThreads.isDefined) executableThreads.get else executableNonThreads
-    super.beforeGraph
+    super.beforeGraph()
     out :::= List(Some(getInfoFile), getBestTreeFile, getBootstrapFile, getBipartitionsFile).flatten
     f match {
       case "d" if b.isEmpty => for (t <- 0 until N.getOrElse(1)) {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala

@@ -22,6 +22,8 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import scala.sys.process._
 
 /**
+ * General rscript extension
+ *
  * Created by wyleung on 17-2-15.
  */
 trait RscriptCommandLineFunction extends BiopetCommandLineFunction {
@@ -30,7 +32,7 @@ trait RscriptCommandLineFunction extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "Rscript", submodule = "Rscript")
 
-  override def beforeGraph: Unit = {
+  override def beforeGraph(): Unit = {
     checkScript()
   }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala

@@ -53,8 +53,8 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
   var noCleanup: Boolean = config("no_cleanup", default = false)
 
   /** Set correct output files */
-  override def beforeGraph: Unit = {
-    super.beforeGraph
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
     require(outputDirectory != null)
     jobLocalDir = outputDirectory
     if (prefix.isEmpty) prefix = Some(fastafile.getName)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala

@@ -41,6 +41,6 @@ object Sha1sum {
     val sha1sum = new Sha1sum(root)
     sha1sum.input = input
     sha1sum.output = new File(outDir, input.getName + ".sha1")
-    return sha1sum
+    sha1sum
   }
 }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala

@@ -62,7 +62,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
   override def versionCommand = executable + " --version"
 
   /** Sets qualityType is still empty */
-  override def beforeGraph {
+  override def beforeGraph() {
     if (qualityType.isEmpty) qualityType = Some(defaultQualityType)
   }
 
@@ -100,22 +100,20 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
 
     var stats: mutable.Map[String, Int] = mutable.Map()
 
-    if (output_stats.exists) for (line <- Source.fromFile(output_stats).getLines) {
+    if (output_stats.exists) for (line <- Source.fromFile(output_stats).getLines()) {
       line match {
         // single run
         case sKept(num)              => stats += ("num_reads_kept" -> num.toInt)
         case sDiscarded(num)         => stats += ("num_reads_discarded_total" -> num.toInt)
         // paired run
         case pPairKept(reads, pairs) => stats += ("num_reads_kept" -> reads.toInt)
-        case pSingleKept(total, r1, r2) => {
+        case pSingleKept(total, r1, r2) =>
           stats += ("num_reads_kept_R1" -> r1.toInt)
           stats += ("num_reads_kept_R2" -> r2.toInt)
-        }
         case pPairDiscarded(reads, pairs) => stats += ("num_reads_discarded_both" -> reads.toInt)
-        case pSingleDiscarded(total, r1, r2) => {
+        case pSingleDiscarded(total, r1, r2) =>
           stats += ("num_reads_discarded_R1" -> r1.toInt)
           stats += ("num_reads_discarded_R2" -> r2.toInt)
-        }
         case _ =>
       }
     }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala

@@ -70,8 +70,8 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction with Refe
   override def versionCommand = executable + " --help"
 
   /** Sets readgroup when not set yet */
-  override def beforeGraph: Unit = {
-    super.beforeGraph
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
     require(readgroup != null)
     if (reference == null) reference = referenceFasta()
   }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala

@@ -68,7 +68,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
 
   /** Sets output files for the graph */
   override def beforeGraph() {
-    super.beforeGraph
+    super.beforeGraph()
     if (reference == null) reference = referenceFasta()
     genomeDir = config("genomeDir", new File(reference.getAbsoluteFile.getParent, "star"))
     if (outFileNamePrefix != null && !outFileNamePrefix.endsWith(".")) outFileNamePrefix += "."
@@ -111,7 +111,7 @@ object Star {
    * @param R1 R1 fastq file
    * @param R2 R2 fastq file
    * @param outputDir Outputdir for Star
-   * @param isIntermediate
+   * @param isIntermediate When set true jobs are flaged as intermediate
    * @param deps Deps to add to wait on run
    * @return Return Star
    *
@@ -123,8 +123,8 @@ object Star {
     star.outputDir = outputDir
     star.isIntermediate = isIntermediate
     star.deps = deps
-    star.beforeGraph
-    return star
+    star.beforeGraph()
+    star
   }
 
   /**
@@ -133,7 +133,7 @@ object Star {
    * @param R1 R1 fastq file
    * @param R2 R2 fastq file
    * @param outputDir Outputdir for Star
-   * @param isIntermediate
+   * @param isIntermediate When set true jobs are flaged as intermediate
    * @param deps Deps to add to wait on run
    * @return Return Star
    */
@@ -146,21 +146,21 @@ object Star {
     val starCommand_pass1 = Star(configurable, R1, R2, new File(outputDir, "aln-pass1"))
     starCommand_pass1.isIntermediate = isIntermediate
     starCommand_pass1.deps = deps
-    starCommand_pass1.beforeGraph
+    starCommand_pass1.beforeGraph()
 
     val starCommand_reindex = new Star(configurable)
     starCommand_reindex.sjdbFileChrStartEnd = starCommand_pass1.outputTab
     starCommand_reindex.outputDir = new File(outputDir, "re-index")
     starCommand_reindex.runmode = "genomeGenerate"
     starCommand_reindex.isIntermediate = isIntermediate
-    starCommand_reindex.beforeGraph
+    starCommand_reindex.beforeGraph()
 
     val starCommand_pass2 = Star(configurable, R1, R2, new File(outputDir, "aln-pass2"))
     starCommand_pass2.genomeDir = starCommand_reindex.outputDir
     starCommand_pass2.isIntermediate = isIntermediate
     starCommand_pass2.deps = deps
-    starCommand_pass2.beforeGraph
+    starCommand_pass2.beforeGraph()
 
-    return (starCommand_pass2.outputSam, List(starCommand_pass1, starCommand_reindex, starCommand_pass2))
+    (starCommand_pass2.outputSam, List(starCommand_pass1, starCommand_reindex, starCommand_pass2))
   }
 }
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala

@@ -66,7 +66,7 @@ class Tabix(val root: Configurable) extends BiopetCommandLineFunction {
   /** Formats that tabix can handle */
   private val validFormats: Set[String] = Set("gff", "bed", "sam", "vcf", "psltbl")
 
-  override def beforeGraph: Unit = {
+  override def beforeGraph(): Unit = {
     p match {
       case Some(fmt) =>
         require(validFormats.contains(fmt), "-p flag must be one of " + validFormats.mkString(", "))

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

@@ -141,8 +141,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   var db_version: Option[Int] = config("db_version")
   var buffer_size: Option[Int] = config("buffer_size")
 
-  override def beforeGraph: Unit = {
-    super.beforeGraph
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
     if (!cache && !database) {
       throw new IllegalArgumentException("Must supply either cache or database")
     } else if (cache && dir.isEmpty) {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala

@@ -44,6 +44,6 @@ object Zcat {
     val zcat = new Zcat(root)
     zcat.input = input
     zcat.output = output
-    return zcat
+    zcat
   }
 }
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala

@@ -20,10 +20,7 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-/**
- * This extension is based on bcftools 1.1-134
- * @param root
- */
+/** This extension is based on bcftools 1.1-134 */
 class BcftoolsCall(val root: Configurable) extends Bcftools {
   @Input(doc = "Input File")
   var input: File = _
@@ -36,7 +33,7 @@ class BcftoolsCall(val root: Configurable) extends Bcftools {
   var c: Boolean = config("c", default = false)
   var m: Boolean = config("m", default = false)
 
-  override def beforeGraph: Unit = {
+  override def beforeGraph(): Unit = {
     require(c != m)
   }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala

@@ -43,7 +43,7 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
 
   var inputTag = "-a"
 
-  override def beforeCmd {
+  override def beforeCmd() {
     if (input.getName.endsWith(".bam")) inputTag = "-abam"
   }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala

@@ -40,7 +40,7 @@ class BedtoolsIntersect(val root: Configurable) extends Bedtools {
 
   var inputTag = "-a"
 
-  override def beforeCmd {
+  override def beforeCmd() {
     if (input.getName.endsWith(".bam")) inputTag = "-abam"
   }
 
@@ -63,6 +63,6 @@ object BedtoolsIntersect {
     bedtoolsIntersect.output = output
     bedtoolsIntersect.minOverlap = minOverlap
     bedtoolsIntersect.count = count
-    return bedtoolsIntersect
+    bedtoolsIntersect
   }
 }
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala

@@ -77,8 +77,8 @@ object Breakdancer extends PipelineCommand {
     breakdancer.input = input
     breakdancer.reference = reference
     breakdancer.workdir = runDir
-    breakdancer.init
-    breakdancer.biopetScript
-    return breakdancer
+    breakdancer.init()
+    breakdancer.biopetScript()
+    breakdancer
   }
 }
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala

@@ -58,7 +58,7 @@ class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunctio
   var h: Boolean = config("h", default = false)
   var y: Option[Int] = config("y", default = 30)
 
-  override def beforeCmd {
+  override def beforeCmd() {
   }
 
   def cmdLine = required(executable) +
@@ -86,6 +86,6 @@ object BreakdancerCaller {
     val bdcaller = new BreakdancerCaller(root)
     bdcaller.input = input
     bdcaller.output = output
-    return bdcaller
+    bdcaller
   }
 }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala

@@ -43,17 +43,17 @@ object BreakdancerConfig {
     val bdconf = new BreakdancerConfig(root)
     bdconf.input = input
     bdconf.output = output
-    return bdconf
+    bdconf
   }
 
   def apply(root: Configurable, input: File, outputDir: String): BreakdancerConfig = {
     val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
     val outputFile = new File(dir + swapExtension(input.getName))
-    return apply(root, input, outputFile)
+    apply(root, input, outputFile)
   }
 
   def apply(root: Configurable, input: File): BreakdancerConfig = {
-    return apply(root, input, new File(swapExtension(input.getAbsolutePath)))
+    apply(root, input, new File(swapExtension(input.getAbsolutePath)))
   }
 
   private def swapExtension(inputFile: String) = inputFile.substring(0, inputFile.lastIndexOf(".bam")) + ".breakdancer.cfg"

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala

@@ -42,6 +42,6 @@ object BreakdancerVCF {
     val bd = new BreakdancerVCF(root)
     bd.input = input
     bd.output = output
-    return bd
+    bd
   }
 }
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala

@@ -64,8 +64,8 @@ class BwaAln(val root: Configurable) extends Bwa with Reference {
   override val defaultCoreMemory = 4.0
   override val defaultThreads = 8
 
-  override def beforeGraph {
-    super.beforeGraph
+  override def beforeGraph() {
+    super.beforeGraph()
     if (reference == null) reference = referenceFasta()
   }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala

@@ -71,8 +71,8 @@ class BwaMem(val root: Configurable) extends Bwa with Reference {
   override val defaultCoreMemory = 4.0
   override val defaultThreads = 8
 
-  override def beforeGraph {
-    super.beforeGraph
+  override def beforeGraph() {
+    super.beforeGraph()
     if (reference == null) reference = referenceFasta()
   }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala

@@ -57,8 +57,8 @@ class BwaSampe(val root: Configurable) extends Bwa with Reference {
 
   var r: String = _
 
-  override def beforeGraph {
-    super.beforeGraph
+  override def beforeGraph() {
+    super.beforeGraph()
     if (reference == null) reference = referenceFasta()
   }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala

@@ -43,8 +43,8 @@ class BwaSamse(val root: Configurable) extends Bwa with Reference {
   var n: Option[Int] = config("n")
   var r: String = _
 
-  override def beforeGraph {
-    super.beforeGraph
+  override def beforeGraph() {
+    super.beforeGraph()
     if (reference == null) reference = referenceFasta()
   }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/Clever.scala

@@ -57,9 +57,9 @@ object Clever extends PipelineCommand {
     val cleverpipeline = new Clever(root)