Switch to originals

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala

@@ -89,8 +89,7 @@ object RegionAfCount extends ToolCommand {
             case a: util.ArrayList[_] => a.map(_.toString.toDouble).toArray
             case s                    => Array(s.toString.toDouble)
           }).sum
-          bedRecords
-            .overlapWith(BedRecord(variant.getContig, variant.getStart, variant.getEnd))
+          region.originals
             .map(_.name.getOrElse("error"))
             .distinct
             .foreach(name => afCounts += name -> (afCounts.getOrElse(name, 0.0) + sum))

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala

@@ -4,7 +4,6 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.ToolCommand
 import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
-import nl.lumc.sasc.biopet.utils.intervals.BedRecord
 
 /**
  * Created by pjvanthof on 22/08/15.