Adding a exon flagstat

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala

@@ -33,9 +33,13 @@ class SamtoolsView(val root: Configurable) extends Samtools {
   var f: List[String] = config("f", default = List.empty[String])
   var F: List[String] = config("F", default = List.empty[String])
 
+  @Input(required = false)
+  var L: Option[File] = None
+
   def cmdBase = required(executable) +
     required("view") +
     optional("-q", q) +
+    optional("-L", L) +
     repeat("-f", f) +
     repeat("-F", F) +
     conditional(b, "-b") +

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

@@ -17,7 +17,8 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.measures
 
 import nl.lumc.sasc.biopet.core.annotations.AnnotationBed
 import nl.lumc.sasc.biopet.extensions.bedtools.BedtoolsCoverage
-import nl.lumc.sasc.biopet.pipelines.gentrap.scripts.{ AggrBaseCount, Hist2count }
+import nl.lumc.sasc.biopet.extensions.samtools.{SamtoolsFlagstat, SamtoolsView}
+import nl.lumc.sasc.biopet.pipelines.gentrap.scripts.{AggrBaseCount, Hist2count}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
@@ -76,6 +77,13 @@ class BiosBaseCounts(val root: Configurable) extends QScript with Measurement wi
     exonAggr.inputLabel = sampleName
     add(exonAggr)
 
+    val samtoolsView = new SamtoolsView(this)
+    samtoolsView.input = bamFile
+    samtoolsView.L = Some(annotationBed)
+    val samtoolsFlagstat = new SamtoolsFlagstat(this)
+    samtoolsFlagstat.output = new File(outputDir, s"$sampleName.$name.exon.flagstats")
+    add(samtoolsView | samtoolsFlagstat)
+
     (geneAggr.output, exonAggr.output)
   }
 }