Added meta exon counts to pipeline

public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala

@@ -71,6 +71,10 @@ class BaseCounter(val root: Configurable) extends ToolCommandFunction {
   def mergeIntronCounts = new File(outputDir, s"$prefix.base.intron.merge.counts")
   def mergeIntronSenseCounts = new File(outputDir, s"$prefix.base.intron.merge.sense.counts")
   def mergeIntronAntiSenseCounts = new File(outputDir, s"$prefix.base.intron.merge.antisense.counts")
+  def nonStrandedMetaExonCounts = new File(outputDir, s"$prefix.base.metaexons.non_stranded.counts")
+  def strandedMetaExonCounts = new File(outputDir, s"$prefix.base.metaexons.stranded.counts")
+  def strandedSenseMetaExonCounts = new File(outputDir, s"$prefix.base.metaexons.stranded.sense.counts")
+  def strandedAntiSenseMetaExonCounts = new File(outputDir, s"$prefix.base.metaexons.stranded.antisense.counts")
 
   override def beforeGraph(): Unit = {
     super.beforeGraph()
@@ -83,7 +87,9 @@ class BaseCounter(val root: Configurable) extends ToolCommandFunction {
       geneExonicCounts, geneExonicSenseCounts, geneExonicAntiSenseCounts,
       geneIntronicCounts, geneIntronicSenseCounts, geneIntronicAntiSenseCounts,
       mergeExonCounts, mergeExonSenseCounts, mergeExonAntiSenseCounts,
-      mergeIntronCounts, mergeIntronSenseCounts, mergeIntronAntiSenseCounts)
+      mergeIntronCounts, mergeIntronSenseCounts, mergeIntronAntiSenseCounts,
+      nonStrandedMetaExonCounts,
+      strandedMetaExonCounts, strandedSenseMetaExonCounts, strandedAntiSenseMetaExonCounts)
   }
 
   override def cmdLine = super.cmdLine +

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

@@ -63,5 +63,9 @@ class BaseCounts(val root: Configurable) extends QScript with Measurement with A
     addTableAndHeatmap(jobs.values.map(_.mergeIntronCounts).toList, "mergeIntronCounts")
     addTableAndHeatmap(jobs.values.map(_.mergeIntronSenseCounts).toList, "mergeIntronSenseCounts")
     addTableAndHeatmap(jobs.values.map(_.mergeIntronAntiSenseCounts).toList, "mergeIntronAntiSenseCounts")
+    addTableAndHeatmap(jobs.values.map(_.nonStrandedMetaExonCounts).toList, "nonStrandedMetaExonCounts")
+    addTableAndHeatmap(jobs.values.map(_.strandedMetaExonCounts).toList, "strandedMetaExonCounts")
+    addTableAndHeatmap(jobs.values.map(_.strandedSenseMetaExonCounts).toList, "strandedSenseMetaExonCounts")
+    addTableAndHeatmap(jobs.values.map(_.strandedAntiSenseMetaExonCounts).toList, "strandedAntiSenseMetaExonCounts")
   }
 }