Skip to content
Snippets Groups Projects
Commit c7cca543 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Style fixes

parent fbc7a317
No related branches found
No related tags found
No related merge requests found
......@@ -15,20 +15,20 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.{File, FileOutputStream}
import java.io.{ File, FileOutputStream }
import java.nio.file.Paths
import com.google.common.io.Files
import nl.lumc.sasc.biopet.extensions.breakdancer.{BreakdancerCaller, BreakdancerConfig, BreakdancerVCF}
import nl.lumc.sasc.biopet.extensions.breakdancer.{ BreakdancerCaller, BreakdancerConfig, BreakdancerVCF }
import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
import nl.lumc.sasc.biopet.extensions.pindel.{PindelCaller, PindelConfig, PindelVCF}
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import nl.lumc.sasc.biopet.extensions.pindel.{ PindelCaller, PindelConfig, PindelVCF }
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Config
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{DataProvider, Test}
import org.testng.annotations.{ DataProvider, Test }
import scala.collection.mutable.ListBuffer
......
......@@ -39,16 +39,16 @@ trait ShivaVariantcallingTestTrait 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
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 = {
......@@ -114,46 +114,46 @@ trait ShivaVariantcallingTestTrait 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
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
override def raw: Boolean = true
}
class ShivaVariantcallingBcftoolsTest extends ShivaVariantcallingTestTrait {
override def bcftools : Boolean = true
override def bcftools: Boolean = true
}
class ShivaVariantcallingBcftoolsSinglesampleTest extends ShivaVariantcallingTestTrait {
override def bcftools_singlesample : Boolean = true
override def bcftools_singlesample: Boolean = true
}
class ShivaVariantcallingHaplotypeCallerGvcfTest extends ShivaVariantcallingTestTrait {
override def haplotypeCallerGvcf : Boolean = true
override def haplotypeCallerGvcf: Boolean = true
}
class ShivaVariantcallingHaplotypeCallerAlleleTest extends ShivaVariantcallingTestTrait {
override def haplotypeCallerAllele : Boolean = true
override def haplotypeCallerAllele: Boolean = true
}
class ShivaVariantcallingUnifiedGenotyperAlleleTest extends ShivaVariantcallingTestTrait {
override def unifiedGenotyperAllele : Boolean = true
override def unifiedGenotyperAllele: Boolean = true
}
class ShivaVariantcallingUnifiedGenotyperTest extends ShivaVariantcallingTestTrait {
override def unifiedGenotyper : Boolean = true
override def unifiedGenotyper: Boolean = true
}
class ShivaVariantcallingHaplotypeCallerTest extends ShivaVariantcallingTestTrait {
override def haplotypeCaller : Boolean = true
override def haplotypeCaller: Boolean = true
}
class ShivaVariantcallingFreebayesTest extends ShivaVariantcallingTestTrait {
override def freebayes : Boolean = true
override def freebayes: Boolean = true
}
class ShivaVariantcallingVarscanCnsSinglesampleTest extends ShivaVariantcallingTestTrait {
override def varscanCnsSinglesample : Boolean = true
override def varscanCnsSinglesample: Boolean = true
}
object ShivaVariantcallingTest {
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment