From be4fc2248a706647ee426dd39d7b3782f9cf03df Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 14 Jan 2016 19:58:38 +0100
Subject: [PATCH] Fixed reference test
---
.../src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala | 1 +
.../src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala | 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala
index 31b70db9d..79741a2c2 100644
--- a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala
+++ b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala
@@ -19,6 +19,7 @@ class ReferenceTest extends TestNGSuite with Matchers with MockitoSugar {
@Test
def testDefault: Unit = {
+ Logging.errors.clear()
make(config :: testReferenceNoIndex :: Nil).referenceFasta()
Logging.checkErrors(true)
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
index d01755e07..9d4b9dc2b 100644
--- a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
@@ -36,7 +36,7 @@ trait Logging {
object Logging {
val logger = Logger.getRootLogger
- private val errors: ListBuffer[Exception] = ListBuffer()
+ private[biopet] val errors: ListBuffer[Exception] = ListBuffer()
def addError(error: String, debug: String = null): Unit = {
val msg = error + (if (debug != null && logger.isDebugEnabled) "; " + debug else "")
--
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