Update code style using scalariform

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

@@ -2,63 +2,63 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
 
 import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
 import org.broadinstitute.gatk.queue.QScript
-import nl.lumc.sasc.biopet.core.{BiopetQScript, PipelineCommand}
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import java.io.File
-import nl.lumc.sasc.biopet.core.apps.{BedToInterval, BiopetFlagstat}
+import nl.lumc.sasc.biopet.core.apps.{ BedToInterval, BiopetFlagstat }
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.function.bedtools.{BedtoolsCoverage, BedtoolsIntersect}
-import nl.lumc.sasc.biopet.function.picard.{CollectInsertSizeMetrics, CollectGcBiasMetrics, CalculateHsMetrics, CollectAlignmentSummaryMetrics}
+import nl.lumc.sasc.biopet.function.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
+import nl.lumc.sasc.biopet.function.picard.{ CollectInsertSizeMetrics, CollectGcBiasMetrics, CalculateHsMetrics, CollectAlignmentSummaryMetrics }
 import nl.lumc.sasc.biopet.function.samtools.SamtoolsFlagstat
 
-class BamMetrics(val root:Configurable) extends QScript with BiopetQScript {
+class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
   def this() = this(null)
-  
-  @Input(doc="Bam File", shortName="BAM",required=true)
+
+  @Input(doc = "Bam File", shortName = "BAM", required = true)
   var inputBam: File = _
-    
-  @Input(doc="Bed tracks targets", shortName="target",required=false)
+
+  @Input(doc = "Bed tracks targets", shortName = "target", required = false)
   var bedFiles: List[File] = Nil
-  
-  @Input(doc="Bed tracks bait", shortName="bait",required=false)
+
+  @Input(doc = "Bed tracks bait", shortName = "bait", required = false)
   var baitBedFile: File = _
-  
-  @Argument(doc="",required=false)
+
+  @Argument(doc = "", required = false)
   var wholeGenome = false
-  
+
   def init() {
     for (file <- configfiles) globalConfig.loadConfigFile(file)
     if (outputDir == null) throw new IllegalStateException("Missing Output directory on BamMetrics module")
     else if (!outputDir.endsWith("/")) outputDir += "/"
   }
-  
+
   def biopetScript() {
     add(SamtoolsFlagstat(this, inputBam, outputDir))
     add(BiopetFlagstat(this, inputBam, outputDir))
     add(CollectGcBiasMetrics(this, inputBam, outputDir))
     add(CollectInsertSizeMetrics(this, inputBam, outputDir))
     add(CollectAlignmentSummaryMetrics(this, inputBam, outputDir))
-    
+
     val baitIntervalFile = if (baitBedFile != null) new File(outputDir, baitBedFile.getName.stripSuffix(".bed") + ".interval") else null
     if (baitIntervalFile != null)
       add(BedToInterval(this, baitBedFile, inputBam, outputDir), true)
-    
+
     for (bedFile <- bedFiles) {
       val targetDir = outputDir + bedFile.getName.stripSuffix(".bed") + "/"
       val targetInterval = BedToInterval(this, bedFile, inputBam, targetDir)
       add(targetInterval, true)
       add(CalculateHsMetrics(this, inputBam, if (baitIntervalFile != null) baitIntervalFile
-                             else targetInterval.output, targetInterval.output, targetDir))
-      
+      else targetInterval.output, targetInterval.output, targetDir))
+
       val strictOutputBam = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.bam")
-      add(BedtoolsIntersect(this, inputBam, bedFile, strictOutputBam, minOverlap = config("strictintersectoverlap", default=1.0)), true)
+      add(BedtoolsIntersect(this, inputBam, bedFile, strictOutputBam, minOverlap = config("strictintersectoverlap", default = 1.0)), true)
       add(SamtoolsFlagstat(this, strictOutputBam))
       add(BiopetFlagstat(this, strictOutputBam, targetDir))
-      
+
       val looseOutputBam = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.bam")
-      add(BedtoolsIntersect(this, inputBam, bedFile, looseOutputBam, minOverlap = config("looseintersectoverlap", default=0.01)), true)
+      add(BedtoolsIntersect(this, inputBam, bedFile, looseOutputBam, minOverlap = config("looseintersectoverlap", default = 0.01)), true)
       add(SamtoolsFlagstat(this, looseOutputBam))
       add(BiopetFlagstat(this, looseOutputBam, targetDir))
-      
+
       val coverageFile = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
       add(BedtoolsCoverage(this, inputBam, bedFile, coverageFile, true), true)
       add(CoverageStats(this, coverageFile, targetDir))
@@ -68,12 +68,12 @@ class BamMetrics(val root:Configurable) extends QScript with BiopetQScript {
 
 object BamMetrics extends PipelineCommand {
   override val pipeline = "/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.class"
-  
-  def apply(root:Configurable, bamFile:File, outputDir:String) : BamMetrics = {
+
+  def apply(root: Configurable, bamFile: File, outputDir: String): BamMetrics = {
     val bamMetrics = new BamMetrics(root)
     bamMetrics.inputBam = bamFile
     bamMetrics.outputDir = outputDir
-    
+
     bamMetrics.init
     bamMetrics.biopetScript
     return bamMetrics

bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala

@@ -2,27 +2,27 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics.scripts
 
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 
-class CoverageStats(val root:Configurable) extends PythonCommandLineFunction {
+class CoverageStats(val root: Configurable) extends PythonCommandLineFunction {
   setPythonScript("bedtools_cov_stats.py")
-  
-  @Input(doc="Input file")
+
+  @Input(doc = "Input file")
   var input: File = _
-  
-  @Output(doc="output File")
+
+  @Output(doc = "output File")
   var output: File = _
-  
-  @Output(doc="plot File (png)")
+
+  @Output(doc = "plot File (png)")
   var plot: File = _
-  
+
   def cmdLine = getPythonCommand +
     required(input) + required("--plot", plot) + " > " + required(output)
 }
 
 object CoverageStats {
-  def apply(root:Configurable, input:File, outputDir:String) : CoverageStats = {
+  def apply(root: Configurable, input: File, outputDir: String): CoverageStats = {
     val coverageStats = new CoverageStats(root)
     coverageStats.input = input
     coverageStats.output = new File(outputDir, input.getName + ".stats")

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

 package nl.lumc.sasc.biopet.core
 
-abstract class BiopetCommandLineFunction extends BiopetCommandLineFunctionTrait {  
+abstract class BiopetCommandLineFunction extends BiopetCommandLineFunctionTrait {
   protected def cmdLine: String
   final def commandLine: String = {
     preCmdInternal

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala

@@ -10,45 +10,45 @@ import scala.util.matching.Regex
 
 trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurable {
   analysisName = getClass.getSimpleName
-  
-  @Input(doc="deps", required=false)
+
+  @Input(doc = "deps", required = false)
   var deps: List[File] = Nil
-  
-  @Argument(doc="Threads", required=false)
+
+  @Argument(doc = "Threads", required = false)
   var threads = 0
   val defaultThreads = 1
-  
-  @Argument(doc="Vmem", required=false)
+
+  @Argument(doc = "Vmem", required = false)
   var vmem: String = _
   val defaultVmem: String = ""
-  
-  @Argument(doc="Executable")
+
+  @Argument(doc = "Executable")
   var executable: String = _
-  
+
   protected def beforeCmd {
   }
-  
+
   protected def afterGraph {
   }
-  
+
   override def freezeFieldValues() {
     checkExecutable
     afterGraph
-    jobOutputFile = new File(firstOutput.getParent + "/."  + firstOutput.getName + "." + analysisName + ".out")
-    
+    jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + analysisName + ".out")
+
     if (threads == 0) threads = getThreads(defaultThreads)
     if (threads > 1) nCoresRequest = Option(threads)
-    
+
     if (vmem == null) {
       vmem = config("vmem")
       if (vmem == null && !defaultVmem.isEmpty) vmem = defaultVmem
     }
     if (vmem != null) jobResourceRequests :+= "h_vmem=" + vmem
     jobName = this.analysisName + ":" + firstOutput.getName
-    
+
     super.freezeFieldValues()
   }
-  
+
   protected def checkExecutable {
     try if (executable != null) {
       val buffer = new StringBuffer()
@@ -66,22 +66,22 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
       case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executable skipped: " + ioe)
     }
   }
-  
+
   final protected def preCmdInternal {
     checkExecutable
     //for (input <- this.inputs) if (!input.exists) throw new IllegalStateException("Input: " + input + " for " + analysisName + " is missing")
     //logger.debug("Config for " + analysisName + ": " + localConfig)
-    
+
     beforeCmd
-    
+
     addJobReportBinding("cores", if (nCoresRequest.get.toInt > 0) nCoresRequest.get.toInt else 1)
     addJobReportBinding("version", getVersion)
   }
-  
+
   protected def versionCommand: String = null
   protected val versionRegex: Regex = null
   protected val versionExitcode = List(0) // Can select multiple
-  def getVersion : String = {
+  def getVersion: String = {
     if (versionCommand == null || versionRegex == null) return "N/A"
     val buffer = new StringBuffer()
     val process = Process(versionCommand).run(ProcessLogger(buffer append _))
@@ -91,25 +91,25 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
     }
     val lines = versionCommand lines_! ProcessLogger(buffer append _)
     for (line <- lines) {
-      line match { 
+      line match {
         case versionRegex(m) => return m
-        case _ =>
+        case _               =>
       }
     }
     logger.warn("Version command: '" + versionCommand + "' give a exit code " + process.exitValue + " but no version was found, executable oke?")
     return "N/A"
   }
-  
-  def getThreads(default:Int) : Int = {
-    val maxThreads: Int = config("maxthreads", default=8)
-    val threads: Int = config("threads", default=default)
+
+  def getThreads(default: Int): Int = {
+    val maxThreads: Int = config("maxthreads", default = 8)
+    val threads: Int = config("threads", default = default)
     if (maxThreads > threads) return threads
     else return maxThreads
   }
-  
-  def getThreads(default:Int, module:String) : Int = {
-    val maxThreads: Int = config("maxthreads", default=8, submodule=module)
-    val threads: Int = config("threads", default=default, submodule=module)
+
+  def getThreads(default: Int, module: String): Int = {
+    val maxThreads: Int = config("maxthreads", default = 8, submodule = module)
+    val threads: Int = config("threads", default = default, submodule = module)
     if (maxThreads > threads) return threads
     else return maxThreads
   }

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala

@@ -4,12 +4,12 @@ import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
 
 abstract class BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunctionTrait {
   executable = "java"
-  
+
   override def commandLine: String = {
     preCmdInternal
     val cmd = super.commandLine
     val finalCmd = executable + cmd.substring(cmd.indexOf(" "))
-//    addJobReportBinding("command", cmd)
+    //    addJobReportBinding("command", cmd)
     return cmd
   }
 }

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala

@@ -32,7 +32,7 @@ import org.broadinstitute.gatk.queue.util._
 import org.broadinstitute.gatk.queue.QCommandPlugin
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.queue.QScriptManager
-import org.broadinstitute.gatk.queue.engine.{QStatusMessenger, QGraphSettings, QGraph}
+import org.broadinstitute.gatk.queue.engine.{ QStatusMessenger, QGraphSettings, QGraph }
 import collection.JavaConversions._
 import org.broadinstitute.gatk.utils.classloader.PluginManager
 import org.broadinstitute.gatk.utils.exceptions.UserException
@@ -40,7 +40,7 @@ import org.broadinstitute.gatk.utils.io.IOUtils
 import org.broadinstitute.gatk.utils.help.ApplicationDetails
 import java.io.FileOutputStream
 import java.net.URL
-import java.util.{ResourceBundle, Arrays}
+import java.util.{ ResourceBundle, Arrays }
 import org.broadinstitute.gatk.utils.text.TextFormattingUtils
 import org.apache.commons.io.FilenameUtils
 
@@ -84,11 +84,11 @@ object BiopetQCommandLine extends Logging {
  * Entry point of Queue.  Compiles and runs QScripts passed in to the command line.
  */
 class BiopetQCommandLine extends CommandLineProgram with Logging {
-  @Input(fullName="script", shortName="S", doc="QScript scala file", required=false)
+  @Input(fullName = "script", shortName = "S", doc = "QScript scala file", required = false)
   @ClassType(classOf[File])
   var scripts: Seq[File] = Nil
   var pipelineName: String = _
-  
+
   @ArgumentCollection
   val settings = new QGraphSettings
 
@@ -155,8 +155,7 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
       // TODO: Default command plugin argument?
       val remoteFileConverter = (
         for (commandPlugin <- allCommandPlugins if (commandPlugin.remoteFileConverter != null))
-        yield commandPlugin.remoteFileConverter
-        ).headOption.getOrElse(null)
+          yield commandPlugin.remoteFileConverter).headOption.getOrElse(null)
 
       if (remoteFileConverter != null)
         loadArgumentsIntoObject(remoteFileConverter)
@@ -267,37 +266,35 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
   override def getArgumentTypeDescriptors =
     Arrays.asList(new ScalaCompoundArgumentTypeDescriptor)
 
-  override def getApplicationDetails : ApplicationDetails = {
+  override def getApplicationDetails: ApplicationDetails = {
     new ApplicationDetails(createQueueHeader(),
-                           Seq.empty[String],
-                           ApplicationDetails.createDefaultRunningInstructions(getClass.asInstanceOf[Class[CommandLineProgram]]),
-                           "")
+      Seq.empty[String],
+      ApplicationDetails.createDefaultRunningInstructions(getClass.asInstanceOf[Class[CommandLineProgram]]),
+      "")
   }
 
-  private def createQueueHeader() : Seq[String] = {
+  private def createQueueHeader(): Seq[String] = {
     Seq(String.format("Queue v%s, Compiled %s", getQueueVersion, getBuildTimestamp),
-         "Copyright (c) 2012 The Broad Institute",
-         "For support and documentation go to http://www.broadinstitute.org/gatk")
+      "Copyright (c) 2012 The Broad Institute",
+      "For support and documentation go to http://www.broadinstitute.org/gatk")
   }
 
-  private def getQueueVersion : String = {
-    val stingResources : ResourceBundle = TextFormattingUtils.loadResourceBundle("StingText")
+  private def getQueueVersion: String = {
+    val stingResources: ResourceBundle = TextFormattingUtils.loadResourceBundle("StingText")
 
-    if ( stingResources.containsKey("org.broadinstitute.sting.queue.QueueVersion.version") ) {
+    if (stingResources.containsKey("org.broadinstitute.sting.queue.QueueVersion.version")) {
       stingResources.getString("org.broadinstitute.sting.queue.QueueVersion.version")
-    }
-    else {
+    } else {
       "<unknown>"
     }
   }
 
-  private def getBuildTimestamp : String = {
-    val stingResources : ResourceBundle = TextFormattingUtils.loadResourceBundle("StingText")
+  private def getBuildTimestamp: String = {
+    val stingResources: ResourceBundle = TextFormattingUtils.loadResourceBundle("StingText")
 
-    if ( stingResources.containsKey("build.timestamp") ) {
+    if (stingResources.containsKey("build.timestamp")) {
       stingResources.getString("build.timestamp")
-    }
-    else {
+    } else {
       "<unknown>"
     }
   }

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

@@ -8,19 +8,19 @@ import org.broadinstitute.gatk.queue.QSettings
 import org.broadinstitute.gatk.queue.function.QFunction
 
 trait BiopetQScript extends Configurable {
-  @Argument(doc="Config Json file",shortName="config", required=false)
+  @Argument(doc = "Config Json file", shortName = "config", required = false)
   val configfiles: List[File] = Nil
-  
-  @Argument(doc="Output directory", shortName="outputDir", required=true)
+
+  @Argument(doc = "Output directory", shortName = "outputDir", required = true)
   var outputDir: String = _
-  
-  var outputFiles:Map[String,File] = Map()
-  
+
+  var outputFiles: Map[String, File] = Map()
+
   var qSettings: QSettings
-  
+
   def init
   def biopetScript
-  
+
   final def script() {
     for (file <- configfiles) globalConfig.loadConfigFile(file)
     if (!outputDir.endsWith("/")) outputDir += "/"
@@ -33,12 +33,11 @@ trait BiopetQScript extends Configurable {
     writer.close()
     for (line <- configReport.split("\n")) logger.debug(line)
   }
-  
+
   def add(functions: QFunction*) // Gets implemeted at org.broadinstitute.sting.queue.QScript
-  def add(function: QFunction, isIntermediate:Boolean = false) {
+  def add(function: QFunction, isIntermediate: Boolean = false) {
     function.isIntermediate = isIntermediate
     add(function)
   }
-  
-  
+
 }

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala

@@ -4,33 +4,34 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 trait MultiSampleQScript extends BiopetQScript {
-  var samples:Map[String,Any] = Map()
-  
-  final def runSamplesJobs : Map[String,Map[String,File]] = {
-    var output: Map[String,Map[String,File]] = Map()
+  var samples: Map[String, Any] = Map()
+
+  final def runSamplesJobs: Map[String, Map[String, File]] = {
+    var output: Map[String, Map[String, File]] = Map()
     samples = config("samples")
     if (samples == null) samples = Map()
-    if (globalConfig.contains("samples")) for ((key,value) <- samples) {
+    if (globalConfig.contains("samples")) for ((key, value) <- samples) {
       var sample = Configurable.any2map(value)
       if (!sample.contains("ID")) sample += ("ID" -> key)
       if (sample("ID") == key) {
-        var files:Map[String,List[File]] = runSingleSampleJobs(sample)
+        var files: Map[String, List[File]] = runSingleSampleJobs(sample)
       } else logger.warn("Key is not the same as ID on value for sample")
-    } else logger.warn("No Samples found in config")
+    }
+    else logger.warn("No Samples found in config")
     return output
   }
-  
-  def runSingleSampleJobs(sampleConfig:Map[String,Any]) : Map[String,List[File]]
-  def runSingleSampleJobs(sample:String) : Map[String,List[File]] ={
+
+  def runSingleSampleJobs(sampleConfig: Map[String, Any]): Map[String, List[File]]
+  def runSingleSampleJobs(sample: String): Map[String, List[File]] = {
     return runSingleSampleJobs(Configurable.any2map(samples(sample)))
   }
-  
-  final def runRunsJobs(sampleConfig:Map[String,Any]) : Map[String,Map[String,File]] = {
-    var output: Map[String,Map[String,File]] = Map()
+
+  final def runRunsJobs(sampleConfig: Map[String, Any]): Map[String, Map[String, File]] = {
+    var output: Map[String, Map[String, File]] = Map()
     val sampleID = sampleConfig("ID")
     if (sampleConfig.contains("runs")) {
       val runs = Configurable.any2map(sampleConfig("runs"))
-      for ((key,value) <- runs) {
+      for ((key, value) <- runs) {
         var run = Configurable.any2map(value)
         if (!run.contains("ID")) run += ("ID" -> key)
         if (run("ID") == key) {
@@ -40,5 +41,5 @@ trait MultiSampleQScript extends BiopetQScript {
     } else logger.warn("No runs found in config for sample: " + sampleID)
     return output
   }
-  def runSingleRunJobs(runConfig:Map[String,Any], sampleConfig:Map[String,Any]) : Map[String,File]
+  def runSingleRunJobs(runConfig: Map[String, Any], sampleConfig: Map[String, Any]): Map[String, File]
 }

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala

@@ -11,17 +11,17 @@ import java.io.FileOutputStream
 import org.broadinstitute.gatk.queue.util.Logging
 
 trait PipelineCommand extends Logging {
-//  val src = ""
-//  val extension = ".scala"
+  //  val src = ""
+  //  val extension = ".scala"
   val pipeline = ""
-  
+
   def main(args: Array[String]): Unit = {
-//    val tempFile = java.io.File.createTempFile(src + ".", extension)
-//    val is = getClass.getResourceAsStream(src + extension)
-//    val os = new FileOutputStream(tempFile)
-//    org.apache.commons.io.IOUtils.copy(is, os)
-//    os.close()
-    
+    //    val tempFile = java.io.File.createTempFile(src + ".", extension)
+    //    val is = getClass.getResourceAsStream(src + extension)
+    //    val os = new FileOutputStream(tempFile)
+    //    org.apache.commons.io.IOUtils.copy(is, os)
+    //    os.close()
+
     var argv: Array[String] = Array()
     //argv ++= Array("-S", tempFile.getAbsolutePath)
     argv ++= Array("-S", pipeline)

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/BedToInterval.scala

@@ -5,58 +5,58 @@ import htsjdk.samtools.SAMSequenceRecord
 import java.io.File
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.PrintWriter
 import scala.io.Source
 
-class BedToInterval(val root:Configurable) extends BiopetJavaCommandLineFunction {
+class BedToInterval(val root: Configurable) extends BiopetJavaCommandLineFunction {
   javaMainClass = getClass.getName
-  
-  @Input(doc="Input Bed file", required = true)
+
+  @Input(doc = "Input Bed file", required = true)
   var input: File = _
-  
-  @Input(doc="Bam File", required = true)
-  va