Commit 4194de0a authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added testing for delly options

parent 08bedeee
......@@ -54,6 +54,8 @@ class Delly(val root: Configurable) extends SvCaller {
add(delly)
}
require(catVariants.inputFiles.nonEmpty, "Must atleast 1 SV-type be selected for Delly")
add(catVariants)
}
}
......
......@@ -61,10 +61,10 @@ class ShivaSvCallingTest extends TestNGSuite with Matchers {
}
@Test(dataProvider = "shivaSvCallingOptions")
def testShivaSvCcalling(bams: Int,
delly: Boolean,
clever: Boolean,
breakdancer: Boolean) = {
def testShivaSvCalling(bams: Int,
delly: Boolean,
clever: Boolean,
breakdancer: Boolean) = {
val callers: ListBuffer[String] = ListBuffer()
if (delly) callers.append("delly")
if (clever) callers.append("clever")
......@@ -94,6 +94,40 @@ class ShivaSvCallingTest extends TestNGSuite with Matchers {
}
}
@DataProvider(name = "dellyOptions")
def dellyOptions = {
val bool = Array(true, false)
(for (
del <- bool;
dup <- bool;
inv <- bool;
tra <- bool
) yield Array(1, del, dup, inv, tra)).toArray
}
@Test(dataProvider = "dellyOptions")
def testShivaDelly(bams: Int, del: Boolean, dup: Boolean, inv: Boolean, tra: Boolean): Unit = {
val map = Map("variantcallers" -> List("delly"), "delly" ->
Map("DEL" -> del, "DUP" -> dup, "INV" -> inv, "TRA" -> tra)
)
val pipeline = initPipeline(map)
pipeline.inputBams = Map("bam" -> ShivaVariantcallingTest.inputTouch("bam" + ".bam"))
if (!del && !dup && !inv && !tra) intercept[IllegalArgumentException] {
pipeline.init()
pipeline.script()
}
else {
pipeline.init()
pipeline.script()
pipeline.functions.count(_.isInstanceOf[DellyCaller]) shouldBe
((if (del) 1 else 0) + (if (dup) 1 else 0) + (if (inv) 1 else 0) + (if (tra) 1 else 0))
}
}
@AfterClass def removeTempOutputDir() = {
FileUtils.deleteDirectory(ShivaSvCallingTest.outputDir)
}
......
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