From 86ad25938ac9b954a4996e59a27b15d2fb73068b Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Tue, 19 Jan 2016 12:01:41 +0100
Subject: [PATCH] add varscan test to shiva variantcalling test
---
.../shiva/ShivaVariantcallingTest.scala | 17 ++++++++++-------
1 file changed, 10 insertions(+), 7 deletions(-)
diff --git a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
index 94edda97a..23480d4dc 100644
--- a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+++ b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
@@ -53,28 +53,31 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
bams <- 0 to 3;
raw <- bool;
bcftools <- bool;
- bcftools_singlesample <- bool;
- freebayes <- bool
- ) yield Array(bams, raw, bcftools, bcftools_singlesample, freebayes)).toArray
+ bcftoolsSinglesample <- bool;
+ freebayes <- bool;
+ varscanCnsSinglesample <- bool
+ ) yield Array(bams, raw, bcftools, bcftoolsSinglesample, freebayes, varscanCnsSinglesample)).toArray
}
@Test(dataProvider = "shivaVariantcallingOptions")
def testShivaVariantcalling(bams: Int,
raw: Boolean,
bcftools: Boolean,
- bcftools_singlesample: Boolean,
- freebayes: Boolean) = {
+ bcftoolsSinglesample: Boolean,
+ freebayes: Boolean,
+ varscanCnsSinglesample: Boolean) = {
val callers: ListBuffer[String] = ListBuffer()
if (raw) callers.append("raw")
if (bcftools) callers.append("bcftools")
- if (bcftools_singlesample) callers.append("bcftools_singlesample")
+ if (bcftoolsSinglesample) callers.append("bcftools_singlesample")
if (freebayes) callers.append("freebayes")
+ if (varscanCnsSinglesample) callers.append("varscan_cns_singlesample")
val map = Map("variantcallers" -> callers.toList)
val pipeline = initPipeline(map)
pipeline.inputBams = (for (n <- 1 to bams) yield n.toString -> ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toMap
- val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools && !bcftools_singlesample && !freebayes)
+ val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools && !bcftoolsSinglesample && !freebayes)
if (illegalArgumentException) intercept[IllegalArgumentException] {
pipeline.script()
--
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