From 23e053739cf5908d21e7084cf8b8e1650b631dd1 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 8 Mar 2016 00:43:56 +0100
Subject: [PATCH] Fixed tests
---
.../sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala | 6 +++---
.../biopet/pipelines/shiva/ShivaVariantcallingTest.scala | 7 ++-----
2 files changed, 5 insertions(+), 8 deletions(-)
diff --git a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
index 52a66932b..4e647e9c2 100644
--- a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
+++ b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
@@ -129,7 +129,7 @@ class ShivaSvCallingTest extends TestNGSuite with Matchers {
)
val pipeline = initPipeline(map)
- pipeline.inputBams = Map("bam" -> ShivaVariantcallingTest.inputTouch("bam" + ".bam"))
+ pipeline.inputBams = Map("bam" -> ShivaSvCallingTest.inputTouch("bam" + ".bam"))
if (!del && !dup && !inv && !tra) intercept[IllegalArgumentException] {
pipeline.init()
@@ -149,7 +149,7 @@ class ShivaSvCallingTest extends TestNGSuite with Matchers {
val map = Map("sv_callers" -> List("this is not a caller"))
val pipeline = initPipeline(map)
- pipeline.inputBams = Map("bam" -> ShivaVariantcallingTest.inputTouch("bam" + ".bam"))
+ pipeline.inputBams = Map("bam" -> ShivaSvCallingTest.inputTouch("bam" + ".bam"))
intercept[IllegalArgumentException] {
pipeline.init()
@@ -181,7 +181,7 @@ object ShivaSvCallingTest {
val outputDir = Files.createTempDir()
outputDir.deleteOnExit()
new File(outputDir, "input").mkdirs()
- def inputTouch(name: String): File = {
+ private def inputTouch(name: String): File = {
val file = new File(outputDir, "input" + File.separator + name).getAbsoluteFile
Files.touch(file)
file
diff --git a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
index 976bf1658..7c40fc993 100644
--- a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+++ b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
@@ -96,16 +96,13 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
pipeline.functions.count(_.isInstanceOf[VcfFilter]) shouldBe (if (raw) bams else 0)
}
}
-
- @AfterClass def removeTempOutputDir() = {
- FileUtils.deleteDirectory(ShivaVariantcallingTest.outputDir)
- }
}
object ShivaVariantcallingTest {
val outputDir = Files.createTempDir()
+ outputDir.deleteOnExit()
new File(outputDir, "input").mkdirs()
- def inputTouch(name: String): File = {
+ private def inputTouch(name: String): File = {
val file = new File(outputDir, "input" + File.separator + name).getAbsoluteFile
Files.touch(file)
file
--
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