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

add varscan test to shiva variantcalling test

parent ca40d875
...@@ -53,28 +53,31 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers { ...@@ -53,28 +53,31 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
bams <- 0 to 3; bams <- 0 to 3;
raw <- bool; raw <- bool;
bcftools <- bool; bcftools <- bool;
bcftools_singlesample <- bool; bcftoolsSinglesample <- bool;
freebayes <- bool freebayes <- bool;
) yield Array(bams, raw, bcftools, bcftools_singlesample, freebayes)).toArray varscanCnsSinglesample <- bool
) yield Array(bams, raw, bcftools, bcftoolsSinglesample, freebayes, varscanCnsSinglesample)).toArray
} }
@Test(dataProvider = "shivaVariantcallingOptions") @Test(dataProvider = "shivaVariantcallingOptions")
def testShivaVariantcalling(bams: Int, def testShivaVariantcalling(bams: Int,
raw: Boolean, raw: Boolean,
bcftools: Boolean, bcftools: Boolean,
bcftools_singlesample: Boolean, bcftoolsSinglesample: Boolean,
freebayes: Boolean) = { freebayes: Boolean,
varscanCnsSinglesample: Boolean) = {
val callers: ListBuffer[String] = ListBuffer() val callers: ListBuffer[String] = ListBuffer()
if (raw) callers.append("raw") if (raw) callers.append("raw")
if (bcftools) callers.append("bcftools") if (bcftools) callers.append("bcftools")
if (bcftools_singlesample) callers.append("bcftools_singlesample") if (bcftoolsSinglesample) callers.append("bcftools_singlesample")
if (freebayes) callers.append("freebayes") if (freebayes) callers.append("freebayes")
if (varscanCnsSinglesample) callers.append("varscan_cns_singlesample")
val map = Map("variantcallers" -> callers.toList) val map = Map("variantcallers" -> callers.toList)
val pipeline = initPipeline(map) val pipeline = initPipeline(map)
pipeline.inputBams = (for (n <- 1 to bams) yield n.toString -> ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toMap 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] { if (illegalArgumentException) intercept[IllegalArgumentException] {
pipeline.script() pipeline.script()
......
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