Build with scaliform

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

@@ -66,13 +66,13 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
         logger.error("executable: '" + executable + "' not found, please check config")
         throw new QException("executable: '" + executable + "' not found, please check config")
       }
-    
+
       val is = new FileInputStream(executable)
       val cnt = is.available
       val bytes = Array.ofDim[Byte](cnt)
       is.read(bytes)
       is.close()
-      val md5: String =  MessageDigest.getInstance("MD5").digest(bytes).map("%02X".format(_)).mkString.toLowerCase
+      val md5: String = MessageDigest.getInstance("MD5").digest(bytes).map("%02X".format(_)).mkString.toLowerCase
 
       addJobReportBinding("md5sum_exe", md5)
     } catch {
@@ -107,7 +107,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
     for (line <- stdout.toString.split("\n") ++ stderr.toString.split("\n")) {
       line match {
         case versionRegex(m) => return m
-        case _ =>
+        case _               =>
       }
     }
     logger.warn("getVersion give a exit code " + process.exitValue + " but no version was found, executable correct? \n" + outputLog)

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

@@ -35,7 +35,7 @@ object BiopetExecutable {
       nl.lumc.sasc.biopet.tools.SageCreateLibrary,
       nl.lumc.sasc.biopet.tools.SageCreateTagCounts)
   )
-  
+
   /**
    * @param args the command line arguments
    */
@@ -83,7 +83,7 @@ object BiopetExecutable {
 
     args match {
       case Array("version") => {
-          println("version: " + getVersion)
+        println("version: " + getVersion)
       }
       case Array(module, name, passArgs @ _*) => {
         getCommand(module, name).main(passArgs.toArray)
@@ -98,11 +98,11 @@ object BiopetExecutable {
       }
     }
   }
-  
+
   def getVersion = {
     getClass.getPackage.getImplementationVersion + " (" + getCommitHash + ")"
   }
-  
+
   def getCommitHash = {
     val prop = new Properties()
     prop.load(getClass.getClassLoader.getResourceAsStream("git.properties"))

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

@@ -8,7 +8,7 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
   override def afterGraph {
     memoryLimit = config("memory_limit")
   }
-  
+
   override def commandLine: String = {
     preCmdInternal
     val cmd = super.commandLine

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

@@ -274,16 +274,16 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
   }
 
   private def createQueueHeader(): Seq[String] = {
-    Seq("Biopet version: " + BiopetExecutable.getVersion,"",
-                     "Based on GATK Queue",
-//                     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")
+    Seq("Biopet version: " + BiopetExecutable.getVersion, "",
+      "Based on GATK Queue",
+      //                     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")
   }
 
   private def getQueueVersion: String = {
     val stingResources: ResourceBundle = TextFormattingUtils.loadResourceBundle("StingText")
-    
+
     if (stingResources.containsKey("org.broadinstitute.sting.queue.QueueVersion.version")) {
       stingResources.getString("org.broadinstitute.sting.queue.QueueVersion.version")
     } else {

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

@@ -23,15 +23,15 @@ trait BiopetQScript extends Configurable {
   def biopetScript
 
   var functions: Seq[QFunction]
-  
+
   final def script() {
     for (file <- configfiles) globalConfig.loadConfigFile(file)
     if (!outputDir.endsWith("/")) outputDir += "/"
     init
     biopetScript
     for (function <- functions) function match {
-      case f:BiopetCommandLineFunctionTrait => f.afterGraph
-      case _ =>
+      case f: BiopetCommandLineFunctionTrait => f.afterGraph
+      case _                                 =>
     }
     val configReport = globalConfig.getReport
     val configReportFile = new File(outputDir + qSettings.runName + ".configreport.txt")

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

@@ -5,18 +5,18 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 trait MultiSampleQScript extends BiopetQScript {
   type LibraryOutput <: AbstractLibraryOutput
   type SampleOutput <: AbstractSampleOutput
-  
+
   abstract class AbstractLibraryOutput
   abstract class AbstractSampleOutput {
     var libraries: Map[String, LibraryOutput] = Map()
     def getAllLibraries = libraries
-    def getLibrary(key:String) = libraries(key)
+    def getLibrary(key: String) = libraries(key)
   }
-  
+
   var samplesConfig: Map[String, Any] = Map()
   var samplesOutput: Map[String, SampleOutput] = Map()
   def globalSampleDir: String = outputDir + "samples/"
-  
+
   final def runSamplesJobs() {
     samplesConfig = config("samples")
     if (samplesConfig == null) samplesConfig = Map()
@@ -25,8 +25,7 @@ trait MultiSampleQScript extends BiopetQScript {
       if (!sample.contains("ID")) sample += ("ID" -> key)
       if (sample("ID") == key) {
         samplesOutput += key -> runSingleSampleJobs(sample)
-      }
-      else logger.warn("Key is not the same as ID on value for sample")
+      } else logger.warn("Key is not the same as ID on value for sample")
     }
     else logger.warn("No Samples found in config")
   }
@@ -46,8 +45,7 @@ trait MultiSampleQScript extends BiopetQScript {
         if (!library.contains("ID")) library += ("ID" -> key)
         if (library("ID") == key) {
           output += key -> runSingleLibraryJobs(library, sampleConfig)
-        }
-        else logger.warn("Key is not the same as ID on value for run of sample: " + sampleID)
+        } else logger.warn("Key is not the same as ID on value for run of sample: " + sampleID)
       }
     } else logger.warn("No runs found in config for sample: " + sampleID)
     return output

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

@@ -11,51 +11,55 @@ import java.io.File
 trait ToolCommand extends MainCommand {
   abstract class AbstractArgs {
   }
-  
+
   abstract class AbstractOptParser extends scopt.OptionParser[Args](commandName) {
     opt[Unit]("log_nostderr") foreach { _ =>
-      logger.removeAppender(stderrAppender) } text("No output to stderr")
+      logger.removeAppender(stderrAppender)
+    } text ("No output to stderr")
     opt[File]("log_file") foreach { x =>
-      logger.addAppender(new WriterAppender(logLayout, new java.io.PrintStream(x))) } text("Log file") valueName("<file>")
+      logger.addAppender(new WriterAppender(logLayout, new java.io.PrintStream(x)))
+    } text ("Log file") valueName ("<file>")
     opt[String]('l', "log_level") foreach { x =>
-        x.toLowerCase match {
-          case "debug" => logger.setLevel(org.apache.log4j.Level.DEBUG)
-          case "info" => logger.setLevel(org.apache.log4j.Level.INFO)
-          case "warn" => logger.setLevel(org.apache.log4j.Level.WARN)
-          case "error" => logger.setLevel(org.apache.log4j.Level.ERROR)
-          case _ =>
-        } } text("Log level") validate { x => x match {
-            case "debug" | "info" | "warn" | "error" => success
-            case _ => failure("Log level must be <debug/info/warn/error>")
-          }
-        }
+      x.toLowerCase match {
+        case "debug" => logger.setLevel(org.apache.log4j.Level.DEBUG)
+        case "info"  => logger.setLevel(org.apache.log4j.Level.INFO)
+        case "warn"  => logger.setLevel(org.apache.log4j.Level.WARN)
+        case "error" => logger.setLevel(org.apache.log4j.Level.ERROR)
+        case _       =>
+      }
+    } text ("Log level") validate { x =>
+      x match {
+        case "debug" | "info" | "warn" | "error" => success
+        case _                                   => failure("Log level must be <debug/info/warn/error>")
+      }
+    }
     opt[Unit]('h', "help") foreach { _ =>
       System.err.println(this.usage)
       sys.exit(1)
-    } text("Print usage")
+    } text ("Print usage")
     opt[Unit]('v', "version") foreach { _ =>
       System.err.println("Version: " + BiopetExecutable.getVersion)
       sys.exit(1)
-    } text("Print version")
+    } text ("Print version")
   }
-    
+
   type Args <: AbstractArgs
   type OptParser <: AbstractOptParser
-  
+
   protected val logger = Logger.getLogger(commandName)
-  
+
   private val logLayout = new DateLayout() {
-        val ignoresThrowable = false
-        def format(event:org.apache.log4j.spi.LoggingEvent): String = {
-          val calendar: Calendar = Calendar.getInstance
-          calendar.setTimeInMillis(event.getTimeStamp)
-          val formatter: SimpleDateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
-          val formattedDate: String = formatter.format(calendar.getTime)
-          var logLevel = event.getLevel.toString
-          while (logLevel.size < 6) logLevel += " "
-          logLevel + " [" + formattedDate + "] [" + event.getLoggerName + "] " + event.getMessage + "\n"
-        }
+    val ignoresThrowable = false
+    def format(event: org.apache.log4j.spi.LoggingEvent): String = {
+      val calendar: Calendar = Calendar.getInstance
+      calendar.setTimeInMillis(event.getTimeStamp)
+      val formatter: SimpleDateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
+      val formattedDate: String = formatter.format(calendar.getTime)
+      var logLevel = event.getLevel.toString
+      while (logLevel.size < 6) logLevel += " "
+      logLevel + " [" + formattedDate + "] [" + event.getLoggerName + "] " + event.getMessage + "\n"
     }
+  }
   private val stderrAppender = new WriterAppender(logLayout, sys.process.stderr)
   logger.setLevel(org.apache.log4j.Level.INFO)
   logger.addAppender(stderrAppender)

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

@@ -44,9 +44,9 @@ class Config(var map: Map[String, Any]) extends Logging {
   protected[config] var defaultCache: Map[ConfigValueIndex, ConfigValue] = Map()
 
   def contains(s: String): Boolean = map.contains(s)
-  def contains(requestedIndex: ConfigValueIndex, freeVar:Boolean): Boolean = contains(requestedIndex.module, requestedIndex.path, requestedIndex.key, freeVar)
+  def contains(requestedIndex: ConfigValueIndex, freeVar: Boolean): Boolean = contains(requestedIndex.module, requestedIndex.path, requestedIndex.key, freeVar)
   def contains(requestedIndex: ConfigValueIndex): Boolean = contains(requestedIndex.module, requestedIndex.path, requestedIndex.key, true)
-  def contains(module: String, path: List[String], key: String, freeVar:Boolean = true): Boolean = {
+  def contains(module: String, path: List[String], key: String, freeVar: Boolean = true): Boolean = {
     val requestedIndex = ConfigValueIndex(module, path, key, freeVar)
     if (notFoundCache.contains(requestedIndex)) return false
     else if (foundCache.contains(requestedIndex)) return true
@@ -62,7 +62,7 @@ class Config(var map: Map[String, Any]) extends Logging {
     }
   }
 
-  protected[config] def apply(module: String, path: List[String], key: String, default: Any = null, freeVar:Boolean = true): ConfigValue = {
+  protected[config] def apply(module: String, path: List[String], key: String, default: Any = null, freeVar: Boolean = true): ConfigValue = {
     val requestedIndex = ConfigValueIndex(module, path, key)
     if (contains(requestedIndex, freeVar)) return foundCache(requestedIndex)
     else if (default != null) {
@@ -133,7 +133,7 @@ object Config {
   }
 
   def mergeConfigs(config1: Config, config2: Config): Config = new Config(mergeMaps(config1.map, config2.map))
-  
+
   private def jsonToMap(json: Json): Map[String, Any] = {
     var output: Map[String, Any] = Map()
     if (json.isObject) {
@@ -159,8 +159,8 @@ object Config {
       else return num.toLong
     } else throw new IllegalStateException("Config value type not supported, value: " + json)
   }
-  
-  private def getMapFromPath(map:Map[String,Any], path: List[String]): Map[String, Any] = {
+
+  private def getMapFromPath(map: Map[String, Any], path: List[String]): Map[String, Any] = {
     var returnMap: Map[String, Any] = map
     for (m <- path) {
       if (!returnMap.contains(m)) return Map()
@@ -168,8 +168,8 @@ object Config {
     }
     return returnMap
   }
-  
-  def getValueFromMap(map:Map[String,Any], index:ConfigValueIndex): Option[ConfigValue] = {
+
+  def getValueFromMap(map: Map[String, Any], index: ConfigValueIndex): Option[ConfigValue] = {
     var submodules = index.path.reverse
     while (!submodules.isEmpty) {
       var submodules2 = submodules

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

 package nl.lumc.sasc.biopet.core.config
 
-class ConfigValueIndex(val module: String, val path: List[String], val key: String, val freeVar:Boolean = true) {
+class ConfigValueIndex(val module: String, val path: List[String], val key: String, val freeVar: Boolean = true) {
   override def toString = "Module = " + module + ",  path = " + path + ",  key = " + key + ",  freeVar = " + freeVar
 }
 
 object ConfigValueIndex {
   private var cache: Map[(String, List[String], String), ConfigValueIndex] = Map()
 
-  def apply(module: String, path: List[String], key: String, freeVar:Boolean = true): ConfigValueIndex = {
+  def apply(module: String, path: List[String], key: String, freeVar: Boolean = true): ConfigValueIndex = {
     if (!cache.contains(module, path, key)) cache += ((module, path, key) -> new ConfigValueIndex(module, path, key, freeVar))
     return cache(module, path, key)
   }

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

@@ -9,13 +9,13 @@ trait Configurable extends Logging {
   def configPath: List[String] = if (root != null) root.configFullPath else List()
   protected lazy val configName = getClass.getSimpleName.toLowerCase
   protected lazy val configFullPath = configName :: configPath
-  var defaults: scala.collection.mutable.Map[String,Any] = if (root != null) scala.collection.mutable.Map(root.defaults.toArray:_*)
-                                                          else scala.collection.mutable.Map()
-  
+  var defaults: scala.collection.mutable.Map[String, Any] = if (root != null) scala.collection.mutable.Map(root.defaults.toArray: _*)
+  else scala.collection.mutable.Map()
+
   val config = new ConfigFuntions
-  
+
   protected class ConfigFuntions {
-    def apply(key: String, default: Any = null, submodule: String = null, required: Boolean = false, freeVar:Boolean = true): ConfigValue = {
+    def apply(key: String, default: Any = null, submodule: String = null, required: Boolean = false, freeVar: Boolean = true): ConfigValue = {
       val m = if (submodule != null) submodule else configName
       val p = if (submodule != null) configName :: configPath else configPath
       val d = {
@@ -31,15 +31,15 @@ trait Configurable extends Logging {
       if (d == null) return globalConfig(m, p, key, freeVar)
       else return globalConfig(m, p, key, d, freeVar)
     }
-    
-    def contains(key: String, submodule: String = null, freeVar:Boolean = true) = {
+
+    def contains(key: String, submodule: String = null, freeVar: Boolean = true) = {
       val m = if (submodule != null) submodule else configName
       val p = if (submodule != null) configName :: configPath else configPath
 
       globalConfig.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
     }
   }
-  
+
   implicit def configValue2file(value: ConfigValue): File = if (value != null) new File(Configurable.any2string(value.value)) else null
   implicit def configValue2string(value: ConfigValue): String = if (value != null) Configurable.any2string(value.value) else null
   implicit def configValue2long(value: ConfigValue): Long = if (value != null) Configurable.any2long(value.value) else 0
@@ -104,7 +104,7 @@ object Configurable extends Logging {
       case _ => throw new IllegalStateException("Value '" + any + "' is not an int")
     }
   }
-  
+
   def any2float(any: Any): Float = {
     any match {
       case f: Double => return f.toFloat

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

@@ -16,7 +16,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
  * Written based on cufflinks version v2.2.1.
  */
 class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
-  
+
   /** default executable */
   executable = config("exe", default = "cufflinks")
 
@@ -177,7 +177,7 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
   override def versionCommand = executable
 
   def cmdLine = {
-      required(executable) +
+    required(executable) +
       required("--output-dir", output_dir) +
       optional("--num-threads", num_threads) +
       optional("--seed", seed) +

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

@@ -11,7 +11,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
 
   @Input(doc = "Contaminants", required = false)
   var contaminants: File = _
-  
+
   @Input(doc = "Adapters", required = false)
   var adapters: File = _
 
@@ -39,11 +39,11 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
       val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
       val defaultContams = getVersion match {
         case "v0.11.2" => new File(fastqcDir + "/Configuration/contaminant_list.txt")
-        case _ => new File(fastqcDir + "/Contaminants/contaminant_list.txt")
+        case _         => new File(fastqcDir + "/Contaminants/contaminant_list.txt")
       }
       val defaultAdapters = getVersion match {
         case "v0.11.2" => new File(fastqcDir + "/Configuration/adapter_list.txt")
-        case _ => null
+        case _         => null
       }
       contaminants = config("contaminants", default = defaultContams)
     }

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

@@ -83,12 +83,12 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
   }
 }
 
- object Ln {
-   def apply(root: Configurable, input:File, output:File, relative:Boolean = true): Ln = {
-     val ln = new Ln(root)
-     ln.in = input
-     ln.out = output
-     ln.relative = relative
-     return ln
-   }
- }
+object Ln {
+  def apply(root: Configurable, input: File, output: File, relative: Boolean = true): Ln = {
+    val ln = new Ln(root)
+    ln.in = input
+    ln.out = output
+    ln.relative = relative
+    return ln
+  }
+}

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

@@ -27,7 +27,7 @@ class Seqstat(val root: Configurable) extends BiopetCommandLineFunction {
   executable = config("exe", default = "fastq-seqstat")
 
   def cmdLine = required(executable) + required(input) + " > " + required(output)
-  
+
   def getSummary: Json = {
     val json = Parse.parseOption(Source.fromFile(output).mkString)
     if (json.isEmpty) return jNull
@@ -42,7 +42,7 @@ object Seqstat {
     seqstat.output = output
     return seqstat
   }
-  
+
   def apply(root: Configurable, fastqfile: File, outDir: String): Seqstat = {
     val seqstat = new Seqstat(root)
     val ext = fastqfile.getName.substring(fastqfile.getName.lastIndexOf("."))
@@ -52,7 +52,7 @@ object Seqstat {
   }
 
   def mergeSummaries(jsons: List[Json]): Json = {
-    def addJson(json:Json, total:Map[String, Long]) {
+    def addJson(json: Json, total: Map[String, Long]) {
       for (key <- json.objectFieldsOrEmpty) {
         if (json.field(key).get.isObject) addJson(json.field(key).get, total)
         else if (json.field(key).get.isNumber) {
@@ -63,53 +63,52 @@ object Seqstat {
             } else if (key == "len_max") {
               if (total(key) < number) total(key) = number
             } else total(key) += number
-          }
-          else total += (key -> number)
+          } else total += (key -> number)
         }
       }
     }
-    
+
     var basesTotal: Map[String, Long] = Map()
     var readsTotal: Map[String, Long] = Map()
     var encoding: Set[Json] = Set()
     for (json <- jsons) {
       encoding += json.fieldOrEmptyString("qual_encoding")
-      
+
       val bases = json.fieldOrEmptyObject("bases")
       addJson(bases, basesTotal)
-      
+
       val reads = json.fieldOrEmptyObject("reads")
       addJson(reads, readsTotal)
     }
     return ("bases" := (
-        ("num_n" := basesTotal("num_n")) ->:
-        ("num_total" := basesTotal("num_total")) ->:
-        ("num_qual_gte" := (
-          ("1" := basesTotal("1")) ->: 
-          ("10" := basesTotal("10")) ->: 
-          ("20" := basesTotal("20")) ->: 
-          ("30" := basesTotal("30")) ->: 
-          ("40" := basesTotal("40")) ->: 
-          ("50" := basesTotal("50")) ->: 
-          ("60" := basesTotal("60")) ->: 
-          jEmptyObject
-        ) ) ->: jEmptyObject)) ->:
-      ("reads" := (
-        ("num_with_n" := readsTotal("num_with_n")) ->:
-        ("num_total" := readsTotal("num_total")) ->:
-        ("len_min" := readsTotal("len_min")) ->:
-        ("len_max" := readsTotal("len_max")) ->:
-        ("num_mean_qual_gte" := (
-          ("1" := readsTotal("1")) ->: 
-          ("10" := readsTotal("10")) ->: 
-          ("20" := readsTotal("20")) ->: 
-          ("30" := readsTotal("30")) ->: 
-          ("40" := readsTotal("40")) ->: 
-          ("50" := readsTotal("50")) ->: 
-          ("60" := readsTotal("60")) ->: 
-          jEmptyObject
-        ) ) ->: jEmptyObject)) ->:
-      ("qual_encoding" := encoding.head) ->:
-      jEmptyObject
+      ("num_n" := basesTotal("num_n")) ->:
+      ("num_total" := basesTotal("num_total")) ->:
+      ("num_qual_gte" := (
+        ("1" := basesTotal("1")) ->:
+        ("10" := basesTotal("10")) ->:
+        ("20" := basesTotal("20")) ->:
+        ("30" := basesTotal("30")) ->:
+        ("40" := basesTotal("40")) ->:
+        ("50" := basesTotal("50")) ->:
+        ("60" := basesTotal("60")) ->:
+        jEmptyObject
+      )) ->: jEmptyObject)) ->:
+        ("reads" := (
+          ("num_with_n" := readsTotal("num_with_n")) ->:
+          ("num_total" := readsTotal("num_total")) ->:
+          ("len_min" := readsTotal("len_min")) ->:
+          ("len_max" := readsTotal("len_max")) ->:
+          ("num_mean_qual_gte" := (
+            ("1" := readsTotal("1")) ->:
+            ("10" := readsTotal("10")) ->: