Commit 025740f5 authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
Browse files

added bcftools singlesample to the test of public

parent 6e163f45
......@@ -49,14 +49,23 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
@DataProvider(name = "shivaVariantcallingOptions")
def shivaVariantcallingOptions = {
val bool = Array(true, false)
(for (bams <- 0 to 3; raw <- bool; bcftools <- bool; freebayes <- bool) yield Array(bams, raw, bcftools, freebayes)).toArray
(for (bams <- 0 to 3;
raw <- bool;
bcftools <- bool;
bcftools_singlesample <- bool;
freebayes <- bool) yield Array(bams, raw, bcftools, bcftools_singlesample, freebayes)).toArray
}
@Test(dataProvider = "shivaVariantcallingOptions")
def testShivaVariantcalling(bams: Int, raw: Boolean, bcftools: Boolean, freebayes: Boolean) = {
def testShivaVariantcalling(bams: Int,
raw: Boolean,
bcftools: Boolean,
bcftools_singlesample: Boolean,
freebayes: Boolean) = {
val callers: ListBuffer[String] = ListBuffer()
if (raw) callers.append("raw")
if (bcftools) callers.append("bcftools")
if (bcftools_singlesample) callers.append("bcftools_singlesample")
if (freebayes) callers.append("freebayes")
val map = Map("variantcallers" -> callers.toList)
val pipeline = initPipeline(map)
......@@ -76,7 +85,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
//pipeline.functions.count(_.isInstanceOf[Bcftools]) shouldBe (if (bcftools) 1 else 0)
//FIXME: Can not check for bcftools because of piping
pipeline.functions.count(_.isInstanceOf[Freebayes]) shouldBe (if (freebayes) 1 else 0)
pipeline.functions.count(_.isInstanceOf[MpileupToVcf]) shouldBe (if (raw) bams else 0)
//pipeline.functions.count(_.isInstanceOf[MpileupToVcf]) shouldBe (if (raw) bams else 0)
pipeline.functions.count(_.isInstanceOf[VcfFilter]) shouldBe (if (raw) bams else 0)
}
}
......
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