From 92dd97f7f558100bc6ed0dcc1a9e036fab0a225a Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Fri, 31 Oct 2014 16:34:23 +0100
Subject: [PATCH] Add test for overlapping intervals
---
biopet-framework/src/test/resources/rrna02.bed | 6 ++++++
.../lumc/sasc/biopet/tools/WipeReadsUnitTest.scala | 12 ++++++++++++
2 files changed, 18 insertions(+)
create mode 100644 biopet-framework/src/test/resources/rrna02.bed
diff --git a/biopet-framework/src/test/resources/rrna02.bed b/biopet-framework/src/test/resources/rrna02.bed
new file mode 100644
index 000000000..191138d56
--- /dev/null
+++ b/biopet-framework/src/test/resources/rrna02.bed
@@ -0,0 +1,6 @@
+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 .
diff --git a/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsUnitTest.scala b/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsUnitTest.scala
index 3929f13f8..8c8af38f5 100644
--- a/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsUnitTest.scala
+++ b/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,
--
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