Commit b53183a5 authored by Peter van 't Hof's avatar Peter van 't Hof

Reduce number of tests

parent ec277777
......@@ -30,7 +30,7 @@ import scala.collection.mutable.ListBuffer
*
* Created by pjvan_thof on 3/2/15.
*/
class ShivaVariantcallingTest extends TestNGSuite with Matchers {
trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): ShivaVariantcalling = {
new ShivaVariantcalling() {
override def configNamespace = "shivavariantcalling"
......@@ -40,22 +40,21 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
}
}
def raw : Boolean = false
def bcftools : Boolean = false
def bcftools_singlesample : Boolean = false
def haplotypeCallerGvcf : Boolean = false
def haplotypeCallerAllele : Boolean = false
def unifiedGenotyperAllele : Boolean = false
def unifiedGenotyper : Boolean = false
def haplotypeCaller : Boolean = false
def freebayes : Boolean = false
def varscanCnsSinglesample : Boolean = false
@DataProvider(name = "shivaVariantcallingOptions")
def shivaVariantcallingOptions = {
val bool = Array(true, false)
(for (
bams <- 0 to 2;
raw <- bool;
bcftools <- bool;
bcftools_singlesample <- bool;
haplotypeCallerGvcf <- bool;
haplotypeCallerAllele <- bool;
unifiedGenotyperAllele <- bool;
unifiedGenotyper <- bool;
haplotypeCaller <- bool;
freebayes <- bool;
varscanCnsSinglesample <- bool
) yield Array[Any](bams, raw, bcftools, bcftools_singlesample, unifiedGenotyper,
haplotypeCaller, haplotypeCallerGvcf, haplotypeCallerAllele, unifiedGenotyperAllele,
freebayes, varscanCnsSinglesample)
......@@ -90,11 +89,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
pipeline.inputBams = (for (n <- 1 to bams) yield n.toString -> ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toMap
val illegalArgumentException = pipeline.inputBams.isEmpty ||
(!raw && !bcftools &&
!haplotypeCaller && !unifiedGenotyper &&
!haplotypeCallerGvcf && !haplotypeCallerAllele && !unifiedGenotyperAllele &&
!bcftoolsSinglesample)
val illegalArgumentException = pipeline.inputBams.isEmpty || (callers.isEmpty)
if (illegalArgumentException) intercept[IllegalArgumentException] {
pipeline.script()
......@@ -124,6 +119,50 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
}
}
class ShivaVariantcallingNoVariantcallersTest extends ShivaVariantcallingTestTrait
class ShivaVariantcallingAllTest extends ShivaVariantcallingTestTrait {
override def raw : Boolean = true
override def bcftools : Boolean = true
override def bcftools_singlesample : Boolean = true
override def haplotypeCallerGvcf : Boolean = true
override def haplotypeCallerAllele : Boolean = true
override def unifiedGenotyperAllele : Boolean = true
override def unifiedGenotyper : Boolean = true
override def haplotypeCaller : Boolean = true
override def freebayes : Boolean = true
override def varscanCnsSinglesample : Boolean = true
}
class ShivaVariantcallingRawTest extends ShivaVariantcallingTestTrait {
override def raw : Boolean = true
}
class ShivaVariantcallingBcftoolsTest extends ShivaVariantcallingTestTrait {
override def bcftools : Boolean = true
}
class ShivaVariantcallingBcftoolsSinglesampleTest extends ShivaVariantcallingTestTrait {
override def bcftools_singlesample : Boolean = true
}
class ShivaVariantcallingHaplotypeCallerGvcfTest extends ShivaVariantcallingTestTrait {
override def haplotypeCallerGvcf : Boolean = true
}
class ShivaVariantcallingHaplotypeCallerAlleleTest extends ShivaVariantcallingTestTrait {
override def haplotypeCallerAllele : Boolean = true
}
class ShivaVariantcallingUnifiedGenotyperAlleleTest extends ShivaVariantcallingTestTrait {
override def unifiedGenotyperAllele : Boolean = true
}
class ShivaVariantcallingUnifiedGenotyperTest extends ShivaVariantcallingTestTrait {
override def unifiedGenotyper : Boolean = true
}
class ShivaVariantcallingHaplotypeCallerTest extends ShivaVariantcallingTestTrait {
override def haplotypeCaller : Boolean = true
}
class ShivaVariantcallingFreebayesTest extends ShivaVariantcallingTestTrait {
override def freebayes : Boolean = true
}
class ShivaVariantcallingVarscanCnsSinglesampleTest extends ShivaVariantcallingTestTrait {
override def varscanCnsSinglesample : Boolean = true
}
object ShivaVariantcallingTest {
val outputDir = Files.createTempDir()
new File(outputDir, "input").mkdirs()
......
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