Remove old code

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

@@ -25,6 +25,6 @@ class BaseCounts(val root: Configurable) extends QScript with Measurement with A
     }
 
     //TODO: merges
-    //TODO heatmaps
+    //TODO: heatmaps
   }
 }

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

@@ -9,21 +9,6 @@ import org.broadinstitute.gatk.queue.QScript
  * Created by pjvan_thof on 1/12/16.
  */
 class FragmentsPerGene(val root: Configurable) extends QScript with Measurement with AnnotationGtf {
-  def bamToCountFile(id: String, bamFile: File): (String, File) = {
-    //TODO: ID sorting job
-
-    val job = new HtseqCount(this)
-    job.inputAnnotation = annotationGtf
-    job.inputAlignment = bamFile
-    job.output = new File(outputDir, s"$name.$id.counts")
-    job.format = Option("bam")
-    // We are forcing the sort order to be ID-sorted, since HTSeq-count often chokes when using position-sorting due
-    // to its buffer not being large enough.
-    //TODO: ID sorting job
-    //job.order = Option("name")
-    id -> job.output
-  }
-
   def mergeArgs = MergeArgs(List(1), 2, numHeaderLines = 1, fallback = "0")
 
   /** Pipeline itself */