Move combine method inside class

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

@@ -68,7 +68,7 @@ object RegionAfCount extends ToolCommand {
 
     logger.info(s"Combine ${bedRecords.allRecords.size} bed records")
 
-    val combinedBedRecords = BedRecordList.combineOverlap(bedRecords)
+    val combinedBedRecords = bedRecords.combineOverlap
 
     logger.info(s"${combinedBedRecords.allRecords.size} left")
 

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

@@ -39,14 +39,14 @@ object SquishBed extends ToolCommand {
 
     val records = BedRecordList.fromFile(cmdArgs.input)
     val length = records.length
-    val refLength = BedRecordList.combineOverlap(records).length
+    val refLength = records.combineOverlap.length
     logger.info(s"Total bases: $length")
     logger.info(s"Total bases on reference: $refLength")
     logger.info("Start squishing")
     val squishBed = records.squishBed(cmdArgs.strandSensitive).sort
     logger.info("Done squishing")
     val squishLength = squishBed.length
-    val squishRefLength = BedRecordList.combineOverlap(squishBed).length
+    val squishRefLength = squishBed.combineOverlap.length
     logger.info(s"Total bases left: $squishLength")
     logger.info(s"Total bases left on reference: $squishRefLength")
     logger.info(s"Total bases removed from ref: ${refLength - squishRefLength}")

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala

@@ -50,6 +50,24 @@ class BedRecordList(val chrRecords: Map[String, List[BedRecord]], header: List[S
     }).flatten
   }
 
+  def combineOverlap: BedRecordList = {
+    new BedRecordList(for ((chr, records) <- sort.chrRecords) yield chr -> {
+      def combineOverlap(records: List[BedRecord],
+                         newRecords: ListBuffer[BedRecord] = ListBuffer()): List[BedRecord] = {
+        if (records.nonEmpty) {
+          val chr = records.head.chr
+          val start = records.head.start
+          val overlapRecords = records.takeWhile(_.start <= records.head.end)
+          val end = overlapRecords.map(_.end).max
+
+          newRecords += BedRecord(chr, start, end, _originals = overlapRecords)
+          combineOverlap(records.drop(overlapRecords.length), newRecords)
+        } else newRecords.toList
+      }
+      combineOverlap(records)
+    })
+  }
+
   def writeToFile(file: File): Unit = {
     val writer = new PrintWriter(file)
     allRecords.foreach(writer.println)
@@ -91,22 +109,4 @@ object BedRecordList {
         throw e
     }
   }
-
-  def combineOverlap(list: BedRecordList): BedRecordList = {
-    new BedRecordList(for ((chr, records) <- list.sort.chrRecords) yield chr -> {
-      def combineOverlap(records: List[BedRecord],
-                         newRecords: ListBuffer[BedRecord] = ListBuffer()): List[BedRecord] = {
-        if (records.nonEmpty) {
-          val chr = records.head.chr
-          val start = records.head.start
-          val overlapRecords = records.takeWhile(_.start <= records.head.end)
-          val end = overlapRecords.map(_.end).max
-
-          newRecords += BedRecord(chr, start, end, _originals = overlapRecords)
-          combineOverlap(records.drop(overlapRecords.length), newRecords)
-        } else newRecords.toList
-      }
-      combineOverlap(records)
-    })
-  }
 }
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