Add test for overlapping intervals

biopet-framework/src/test/resources/rrna02.bed

+chrQ	300	350	rRNA03	0	+
+chrQ	350	400	rRNA03	0	+
+chrQ	450	480	rRNA02	0	-
+chrQ	470	475	rRNA04	0	-
+chrQ	1	200	rRNA01	0	.
+chrQ	150	250	rRNA01	0	.

biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsUnitTest.scala

@@ -122,6 +122,7 @@ class WipeReadsUnitTest extends TestNGSuite with MockitoSugar with Matchers {
   val pBamFile3 = new File(resourcePath("/paired03.bam"))
 
   val BedFile1 = new File(resourcePath("/rrna01.bed"))
+  val BedFile2 = new File(resourcePath("/rrna02.bed"))
   val RefFlatFile1 = new File(resourcePath("/rrna01.refFlat"))
   val GtfFile1 = new File(resourcePath("/rrna01.gtf"))
 
@@ -168,6 +169,17 @@ class WipeReadsUnitTest extends TestNGSuite with MockitoSugar with Matchers {
     intervals.last.getEnd shouldBe 3063
   }
 
+  @Test def testMakeIntervalFromBedOverlap() = {
+    val intervals: List[Interval] = makeIntervalFromFile(BedFile2)
+    intervals.length shouldBe 4
+    intervals.head.getSequence should ===("chrQ")
+    intervals.head.getStart shouldBe 451
+    intervals.head.getEnd shouldBe 480
+    intervals.last.getSequence should ===("chrQ")
+    intervals.last.getStart shouldBe 2
+    intervals.last.getEnd shouldBe 250
+  }
+
   @Test def testSingleBamDefault() = {
     val intervals: List[Interval] = List(
       new Interval("chrQ", 291, 320), // overlaps r01, second hit,