Commit 86ad2593 authored by Sander van der Zeeuw's avatar Sander van der Zeeuw

add varscan test to shiva variantcalling test

parent ca40d875
......@@ -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()
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment