Moved init of vars

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

@@ -20,6 +20,8 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.config.{ ConfigValue, Config, Configurable }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.ConfigUtils._
+import scala.reflect.ClassTag
+import scala.reflect._
 import org.broadinstitute.gatk.utils.commandline.{ Argument }
 
 trait MultiSampleQScript extends BiopetQScript {
@@ -28,12 +30,10 @@ trait MultiSampleQScript extends BiopetQScript {
 
   if (!Config.global.map.contains("samples")) logger.warn("No Samples found in config")
 
-  type Sample <: AbstractSample
-  abstract class AbstractSample {
-    val sampleId: String
+  abstract class AbstractSample(val sampleId: String) {
     val config = new ConfigFunctions(defaultSample = Some(sampleId))
-    abstract class AbstractLibrary {
-      val libraryId: String
+
+    abstract class AbstractLibrary(val libraryId: String) {
       val config = new ConfigFunctions(defaultSample = Some(sampleId), defaultLibrary = Some(libraryId))
       final def run(): Unit = {
         currentSample = Some(sampleId)
@@ -49,8 +49,11 @@ trait MultiSampleQScript extends BiopetQScript {
 
       protected def runJobs()
     }
+
     type Library <: AbstractLibrary
 
+    val libraries: Map[String, Library] = getLibrariesIds.map(id => id -> initClass(id)).toMap
+
     protected def getLibrariesIds: Set[String] = {
       ConfigUtils.getMapFromPath(Config.global.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
     }
@@ -63,8 +66,6 @@ trait MultiSampleQScript extends BiopetQScript {
 
     protected def runJobs()
 
-    val libraries: Map[String, Library]
-
     protected final def runLibraryJobs(): Unit = {
       for ((libraryId, library) <- libraries) {
         library.run()
@@ -76,7 +77,16 @@ trait MultiSampleQScript extends BiopetQScript {
     }
   }
 
-  var samples: Map[String, Sample] = Map()
+  type Sample <: AbstractSample
+
+  final private def initClass[T: ClassTag](arg: String): T = {
+    logger.debug("init of: " + classTag[T])
+    val x = classTag[T].runtimeClass.getConstructor(classOf[String]).newInstance(arg).asInstanceOf[T]
+    logger.debug("init of: " + classTag[T] + "  Done")
+    x
+  }
+
+  val samples: Map[String, Sample] = getSamplesIds.map(id => id -> initClass(id)).toMap
 
   /** Returns a list of all sampleIDs */
   protected def getSamplesIds: Set[String] = if (onlySample != Nil) onlySample.toSet else {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala

@@ -22,11 +22,9 @@ import org.broadinstitute.gatk.queue.QScript
 class MultisamplePipelineTemplate(val root: Configurable) extends QScript with MultiSampleQScript {
   def this() = this(null)
 
-  class Sample(val sampleId: String) extends AbstractSample {
+  class Sample(sampleId: String) extends AbstractSample(sampleId) {
 
-    val libraries: Map[String, Library] = getLibrariesIds.map(id => id -> new Library(id)).toMap
-
-    class Library(val libraryId: String) extends AbstractLibrary {
+    class Library(libraryId: String) extends AbstractLibrary(libraryId) {
       def runJobs(): Unit = {
         // Library jobs
       }
@@ -38,7 +36,6 @@ class MultisamplePipelineTemplate(val root: Configurable) extends QScript with M
   }
 
   def init(): Unit = {
-    samples = getSamplesIds.map(id => id -> new Sample(id)).toMap
   }
 
   def biopetScript() {

public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala

@@ -54,11 +54,9 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
   )
   )
 
-  class Sample(val sampleId: String) extends AbstractSample {
+  class Sample(sampleId: String) extends AbstractSample(sampleId) {
 
-    val libraries: Map[String, Library] = getLibrariesIds.map(id => id -> new Library(id)).toMap
-
-    class Library(val libraryId: String) extends AbstractLibrary {
+    class Library(libraryId: String) extends AbstractLibrary(libraryId) {
       val inputFastq: File = config("R1", required = true)
       val prefixFastq: File = new File(getLibraryDir, sampleId + "-" + libraryId + ".prefix.fastq")
 
@@ -129,7 +127,6 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
   }
 
   def init() {
-    samples = getSamplesIds.map(id => id -> new Sample(id)).toMap
     if (!outputDir.endsWith("/")) outputDir += "/"
     if (transcriptome == null && tagsLibrary == null)
       throw new IllegalStateException("No transcriptome or taglib found")
@@ -198,3 +195,10 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
 }
 
 object Sage extends PipelineCommand
+
+object SageTest {
+  def main(args: Array[String]): Unit = {
+    val sage = new Sage()
+    println("done")
+  }
+}
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