From 11fe02b4f58db30e4e32085f5eba0472e36fb3a9 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Thu, 29 Oct 2015 14:06:32 +0100
Subject: [PATCH] change pipeline test, not test on sambambaview, but on
samtoolsview
---
.../nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala b/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
index f417bfadd..909163554 100644
--- a/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
+++ b/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
@@ -18,10 +18,10 @@ package nl.lumc.sasc.biopet.pipelines.gears
import java.io.File
import com.google.common.io.Files
-import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
+import nl.lumc.sasc.biopet.extensions.kraken.{Kraken, KrakenReport}
import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
-import nl.lumc.sasc.biopet.extensions.sambamba.SambambaView
-import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, KrakenReportToJson }
+import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
+import nl.lumc.sasc.biopet.extensions.tools.{FastqSync, KrakenReportToJson}
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils
@@ -97,7 +97,8 @@ class GearsPipelineTest(val testset: String) extends TestNGSuite with Matchers {
// SamToFastq should have started if it was started from bam
gears.functions.count(_.isInstanceOf[SamToFastq]) shouldBe (if (fromBam) 1 else 0)
- gears.functions.count(_.isInstanceOf[SambambaView]) shouldBe (if (fromBam) 1 else 0)
+ // gears.functions.count(_.isInstanceOf[SambambaView]) shouldBe (if (fromBam) 1 else 0)
+ gears.functions.count(_.isInstanceOf[SamtoolsView]) shouldBe (if (fromBam) 1 else 0)
gears.functions.count(_.isInstanceOf[FastqSync]) shouldBe (if (fromBam) 1 else 0)
gears.functions.count(_.isInstanceOf[Kraken]) shouldBe 1
--
GitLab