Added heatmap plot

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

 package nl.lumc.sasc.biopet.pipelines.gentrap.measures
 
+import java.io.File
+
 import nl.lumc.sasc.biopet.core.Reference
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.extensions.tools.MergeTables
+import nl.lumc.sasc.biopet.pipelines.gentrap.scripts.PlotHeatmap
 import org.broadinstitute.gatk.queue.QScript
 
 /**
@@ -11,22 +14,32 @@ import org.broadinstitute.gatk.queue.QScript
 trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
   protected var bamFiles: Map[String, File] = Map()
 
+  /**
+    * Method to add a bamFile to the pipeline
+    * @param id Uniqe id used for this bam file, most likly to be a sampleName
+    * @param file Location of the bam file
+    */
   def addBamfile(id: String, file: File): Unit = {
     require(!bamFiles.contains(id), s"'$id' already exist")
     bamFiles += id -> file
   }
 
+  /** Name of job, this is used as prefix for most of the files */
   def name: String = this.getClass.getSimpleName.toLowerCase
 
+  /** Locations of single bam count tables */
   lazy val countFiles: Map[String, File] = bamFiles.map { case (id, bamFile) => bamToCountFile(id, bamFile) }
 
+  /** Location of merge count table */
   def mergedCountFile = new File(outputDir, s"$name.merged.tsv")
 
-  case class MergeArgs(idCols: List[Int],
-                       valCol: Int,
-                       numHeaderLines: Int = 0,
-                       fallback: String = "-")
+  /** Location of heatmap */
+  def heatpMap = new File(outputDir, s"$name.heatmap.png")
+
+  /** Class to store args for MergeTables */
+  case class MergeArgs(idCols: List[Int], valCol: Int, numHeaderLines: Int = 0, fallback: String = "-")
 
+  /** This should contain the args for MergeTables */
   def mergeArgs: MergeArgs
 
   /** Init for pipeline */
@@ -39,9 +52,14 @@ trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
     add(MergeTables(this, countFiles.values.toList, mergedCountFile,
       mergeArgs.idCols, mergeArgs.valCol, mergeArgs.numHeaderLines, mergeArgs.fallback))
 
-    //TODO: Heatmap
+    val job = new PlotHeatmap(qscript)
+    job.input = mergedCountFile
+    job.output = heatpMap
+    job.countType = Some(name)
+    add(job)
   }
 
+  /** This function should add the count table for each bamFile */
   def bamToCountFile(id: String, bamFile: File): (String, File)
 
   /** Must return a map with used settings for this pipeline */