From b2226d71ddcc66598bd79246703bce093ec5d51c Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Wed, 26 Aug 2015 18:20:27 +0200
Subject: [PATCH] CheckAllelesVcfInBam testing.
---
.../tools/CheckAllelesVcfInBamTest.scala | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
index 6a99b92d3..ade8c28fa 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
@@ -15,8 +15,11 @@
*/
package nl.lumc.sasc.biopet.tools
+import java.io.File
import java.nio.file.Paths
+import htsjdk.samtools.{SamReaderFactory, SamReader}
+import htsjdk.variant.vcf.VCFFileReader
import org.scalatest.Matchers
import org.scalatest.mock.MockitoSugar
import org.scalatest.testng.TestNGSuite
@@ -38,6 +41,7 @@ class CheckAllelesVcfInBamTest extends TestNGSuite with MockitoSugar with Matche
val vcf = resourcePath("/chrQ.vcf")
val bam = resourcePath("/single01.bam")
+ val vcf2 = new File(resourcePath("/chrQ2.vcf.gz"))
val rand = new Random()
@Test def testOutputTypeVcf() = {
@@ -58,4 +62,19 @@ class CheckAllelesVcfInBamTest extends TestNGSuite with MockitoSugar with Matche
main(arguments)
}
+ @Test
+ def testCheckAllelesNone() = {
+ val variant = new File(vcf)
+ val samRecord = SamReaderFactory.makeDefault().open(new File(bam)).iterator().next()
+ val varRecord = new VCFFileReader(variant, false).iterator().next()
+ checkAlleles(samRecord, varRecord) shouldBe None
+ }
+
+ @Test
+ def testCheckAlleles() = {
+ val samRecord = SamReaderFactory.makeDefault().open(new File(bam)).iterator().next()
+ val varRecord = new VCFFileReader(vcf2).iterator().next()
+ checkAlleles(samRecord, varRecord) shouldBe Some("T")
+ }
+
}
--
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