Added empty implementations

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BasesPerExon.scala

+package nl.lumc.sasc.biopet.pipelines.gentrap.measures
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvan_thof on 1/12/16.
+  */
+class BasesPerExon(val root: Configurable) extends QScript with Measurement {
+  /** Init for pipeline */
+  def init(): Unit = ???
+
+  /** Pipeline itself */
+  def biopetScript(): Unit = ???
+
+  /** Must return a map with used settings for this pipeline */
+  def summarySettings: Map[String, Any] = Map()
+
+  /** File to put in the summary for thie pipeline */
+  def summaryFiles: Map[String, File] = Map()
+
+  /** Name of summary output file */
+  def summaryFile: File = new File("BasesPerExon.summary.json")
+}

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BasesPerGene.scala

+package nl.lumc.sasc.biopet.pipelines.gentrap.measures
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvan_thof on 1/12/16.
+  */
+class BasesPerGene(val root: Configurable) extends QScript with Measurement {
+  /** Init for pipeline */
+  def init(): Unit = ???
+
+  /** Pipeline itself */
+  def biopetScript(): Unit = ???
+
+  /** Must return a map with used settings for this pipeline */
+  def summarySettings: Map[String, Any] = Map()
+
+  /** File to put in the summary for thie pipeline */
+  def summaryFiles: Map[String, File] = Map()
+
+  /** Name of summary output file */
+  def summaryFile: File = new File("BasesPerGene.summary.json")
+}

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksBlind.scala

+package nl.lumc.sasc.biopet.pipelines.gentrap.measures
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvan_thof on 1/12/16.
+  */
+class CufflinksBlind(val root: Configurable) extends QScript with Measurement {
+  /** Init for pipeline */
+  def init(): Unit = ???
+
+  /** Pipeline itself */
+  def biopetScript(): Unit = ???
+
+  /** Must return a map with used settings for this pipeline */
+  def summarySettings: Map[String, Any] = Map()
+
+  /** File to put in the summary for thie pipeline */
+  def summaryFiles: Map[String, File] = Map()
+
+  /** Name of summary output file */
+  def summaryFile: File = new File("CufflinksBlind.summary.json")
+}

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksGuided.scala

+package nl.lumc.sasc.biopet.pipelines.gentrap.measures
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvan_thof on 1/12/16.
+  */
+class CufflinksGuided(val root: Configurable) extends QScript with Measurement {
+  /** Init for pipeline */
+  def init(): Unit = ???
+
+  /** Pipeline itself */
+  def biopetScript(): Unit = ???
+
+  /** Must return a map with used settings for this pipeline */
+  def summarySettings: Map[String, Any] = Map()
+
+  /** File to put in the summary for thie pipeline */
+  def summaryFiles: Map[String, File] = Map()
+
+  /** Name of summary output file */
+  def summaryFile: File = new File("CufflinksGuided.summary.json")
+}

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksStrict.scala

+package nl.lumc.sasc.biopet.pipelines.gentrap.measures
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvan_thof on 1/12/16.
+  */
+class CufflinksStrict(val root: Configurable) extends QScript with Measurement {
+  /** Init for pipeline */
+  def init(): Unit = ???
+
+  /** Pipeline itself */
+  def biopetScript(): Unit = ???
+
+  /** Must return a map with used settings for this pipeline */
+  def summarySettings: Map[String, Any] = Map()
+
+  /** File to put in the summary for thie pipeline */
+  def summaryFiles: Map[String, File] = Map()
+
+  /** Name of summary output file */
+  def summaryFile: File = new File("CufflinksStrict.summary.json")
+}

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerExon.scala

+package nl.lumc.sasc.biopet.pipelines.gentrap.measures
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvan_thof on 1/12/16.
+  */
+class FragmentsPerExon(val root: Configurable) extends QScript with Measurement {
+  /** Init for pipeline */
+  def init(): Unit = ???
+
+  /** Pipeline itself */
+  def biopetScript(): Unit = ???
+
+  /** Must return a map with used settings for this pipeline */
+  def summarySettings: Map[String, Any] = Map()
+
+  /** File to put in the summary for thie pipeline */
+  def summaryFiles: Map[String, File] = Map()
+
+  /** Name of summary output file */
+  def summaryFile: File = new File("FragmentsPerExon.summary.json")
+}

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala

+package nl.lumc.sasc.biopet.pipelines.gentrap.measures
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvan_thof on 1/12/16.
+  */
+class FragmentsPerGene(val root: Configurable) extends QScript with Measurement {
+  /** Init for pipeline */
+  def init(): Unit = ???
+
+  /** Pipeline itself */
+  def biopetScript(): Unit = ???
+
+  /** Must return a map with used settings for this pipeline */
+  def summarySettings: Map[String, Any] = Map()
+
+  /** File to put in the summary for thie pipeline */
+  def summaryFiles: Map[String, File] = Map()
+
+  /** Name of summary output file */
+  def summaryFile: File = new File("FragmentsPerGene.summary.json")
+}

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala

+package nl.lumc.sasc.biopet.pipelines.gentrap.measures
+
+import nl.lumc.sasc.biopet.core.Reference
+import nl.lumc.sasc.biopet.core.summary.SummaryQScript
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvan_thof on 1/12/16.
+  */
+trait Measurement extends SummaryQScript with Reference { qscript : QScript =>
+  private var bamFiles: Map[String, File] = Map()
+
+  def addBamfile(id: String, file: File): Unit = {
+    require(!bamFiles.contains(id), s"'$id' already exist")
+    bamFiles += id -> file
+  }
+}