Added htseqCount job

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

@@ -108,6 +108,11 @@ class Gentrap(val root: Configurable) extends QScript
 
   /** Default pipeline config */
   override def defaults = Map(
+    "htseqcount" -> Map("stranded" -> (strandProtocol match {
+      case NonSpecific => "no"
+      case Dutp        => "reverse"
+      case _           => null
+    }),
     "merge_strategy" -> "preprocessmergesam",
     "gsnap" -> Map(
       "novelsplicing" -> 1,

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.core.annotations.AnnotationGtf
+import nl.lumc.sasc.biopet.extensions.HtseqCount
 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 {
-  def bamToCountFile(id: String, bamFile: File): (String, File) = ???
+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")
 }