From 16346810a10abc2f200c6d18b57654a741628994 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Fri, 10 Apr 2015 11:16:15 +0200
Subject: [PATCH] VcfWithVcfTest stub
---
.../sasc/biopet/tools/VcfWithVcfTest.scala | 43 +++++++++++++++++++
1 file changed, 43 insertions(+)
create mode 100644 public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
new file mode 100644
index 000000000..395275318
--- /dev/null
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
@@ -0,0 +1,43 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+
+import scala.util.Random
+
+/**
+ * Created by ahbbollen on 10-4-15.
+ */
+class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
+ import VcfWithVcf._
+
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ val vepped_path = resourcePath("/VEP_oneline.vcf")
+ val unvepped_path = resourcePath("/unvepped.vcf")
+ val rand = new Random()
+
+ def testOutputTypeVcf() = {
+ val tmp_path = "/tmp_VcfWithVcf_" + rand.nextString(10) + ".vcf"
+ val arguments = Array("-I", unvepped_path, "-S", vepped_path, "-O", tmp_path, "-f", "CSQ")
+ main(arguments)
+ }
+
+ def testOutputTypeVcfGz() = {
+ val tmp_path = "/tmp_VcfWithVcf_" + rand.nextString(10) + ".vcf.gz"
+ val arguments = Array("-I", unvepped_path, "-S", vepped_path, "-O", tmp_path, "-f", "CSQ")
+ main(arguments)
+ }
+
+ def testOutputTypeBcf() = {
+ val tmp_path = "/tmp_VcfWithVcf_" + rand.nextString(10) + ".bcf"
+ val arguments = Array("-I", unvepped_path, "-S", vepped_path, "-O", tmp_path, "-f", "CSQ")
+ main(arguments)
+ }
+
+}
--
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