From d50b72d0d163cc1b8afefdbcdad48498c5bf53e0 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Fri, 14 Aug 2015 11:30:49 +0200
Subject: [PATCH] some more tests for BastyGenerateFasta
---
.../biopet/tools/BastyGenerateFastaTest.scala | 24 +++++++++++++++++++
1 file changed, 24 insertions(+)
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
index 48ff9cfe2..dea9abb7f 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
@@ -22,6 +22,30 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
val vepped_path = resourcePath("/VEP_oneline.vcf")
val vepped = new File(vepped_path)
+ val bam_path = resourcePath("/paired01.bam")
+ val chrQ_path = resourcePath("/chrQ.vcf.gz")
+ val chrQRef_path = resourcePath("/fake_chrQ.fa")
+ val bam = new File(resourcePath("/paired01.bam"))
+ val chrQ = new File(resourcePath("/chrQ.vcf.gz"))
+ val chrQRef = new File(resourcePath("/fake_chrQ.fa"))
+
+ @Test def testMainVcf = {
+ val tmp = File.createTempFile("basty_out", ".fa")
+ val tmppath = tmp.getAbsolutePath
+ tmp.deleteOnExit()
+
+ val arguments = Array("-V", chrQ_path, "--outputVariants", tmppath, "--sampleName", "Child_7006504", "--reference", chrQRef_path, "--outputName", "test")
+ main(arguments)
+ }
+
+ @Test def testMainVcfAndBam = {
+ val tmp = File.createTempFile("basty_out", ".fa")
+ val tmppath = tmp.getAbsolutePath
+ tmp.deleteOnExit()
+
+ val arguments = Array("-V", chrQ_path, "--outputVariants", tmppath, "--bamFile", bam_path, "--sampleName", "Child_7006504", "--reference", chrQRef_path, "--outputName", "test")
+ main(arguments)
+ }
@Test def testGetMaxAllele = {
val reader = new VCFFileReader(vepped, false)
--
GitLab