Commit c7cca543 authored by Peter van 't Hof's avatar Peter van 't Hof

Style fixes

parent fbc7a317
......@@ -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 {
......
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