Adding toSamInterval method

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

@@ -85,7 +85,7 @@ object WipeReads extends ToolCommand {
     logger.info("Parsing interval file ...")
 
     /** Function to create iterator from BED file */
-    def makeIntervalFromBed(inFile: File) = BedRecordList.fromFile(inFile).sorted.samIntervals.toIterator
+    def makeIntervalFromBed(inFile: File) = BedRecordList.fromFile(inFile).sorted.toSamIntervals.toIterator
 
     /**
      * Parses a refFlat file to yield Interval objects

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

 package nl.lumc.sasc.biopet.utils.intervals
 
+import htsjdk.samtools.util.Interval
+
 /**
  * Created by pjvanthof on 20/08/15.
  */
@@ -98,6 +100,11 @@ case class BedRecord(chr: String,
     }
     this
   }
+
+  def toSamInterval = (name, strand) match {
+    case (Some(name), Some(strand)) => new Interval(chr, start + 1, end, !strand, name)
+    case _ => new Interval(chr, start + 1, end)
+  }
 }
 
 object BedRecord {

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

@@ -15,12 +15,7 @@ import nl.lumc.sasc.biopet.core.Logging
 class BedRecordList(val chrRecords: Map[String, List[BedRecord]], header: List[String] = Nil) {
   def allRecords = for (chr <- chrRecords; record <- chr._2) yield record
 
-  def samIntervals = allRecords.map({ x =>
-    (x.name, x.strand) match {
-      case (Some(name), Some(strand)) => new Interval(x.chr, x.start + 1, x.end, !strand, name)
-      case _ => new Interval(x.chr, x.start + 1, x.end)
-    }
-  })
+  def toSamIntervals = allRecords.map(_.toSamInterval)
   
   lazy val sorted = {
     val sorted = new BedRecordList(chrRecords.map(x => x._1 -> x._2.sortWith((a, b) => a.start < b.start)))

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordTest.scala

 package nl.lumc.sasc.biopet.utils.intervals
 
+import htsjdk.samtools.util.Interval
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
@@ -43,6 +44,11 @@ class BedRecordTest extends TestNGSuite with Matchers {
     BedRecord("chrQ", 3, 4).length shouldBe 1
   }
 
+  @Test def testToSamInterval: Unit = {
+    BedRecord("chrQ", 0, 4).toSamInterval shouldBe new Interval("chrQ", 1, 4)
+    BedRecord("chrQ", 0, 4, Some("name"), Some(0.0), Some(true)).toSamInterval shouldBe new Interval("chrQ", 1, 4, false, "name")
+  }
+
   @Test def testExons: Unit = {
     BedRecord.fromLine("chrQ\t0\t100\tname\t3\t+\t1\t3\t255,0,0").exons shouldBe None