Commit 9812237c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Optimize imports

parent 7f2580f2
......@@ -6,6 +6,7 @@
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
class AnalyzeCovariates(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.AnalyzeCovariates with GatkGeneral {
......
......@@ -6,6 +6,7 @@
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.ApplyRecalibration with GatkGeneral {
......
......@@ -6,6 +6,7 @@
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
class BaseRecalibrator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.BaseRecalibrator with GatkGeneral {
......
......@@ -6,6 +6,7 @@
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
class CombineGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.CombineGVCFs with GatkGeneral {
......
......@@ -6,6 +6,7 @@
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
class CombineVariants(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.CombineVariants with GatkGeneral {
......
......@@ -5,7 +5,7 @@
*/
package nl.lumc.sasc.biopet.extensions.gatk.broad
import nl.lumc.sasc.biopet.core.{ Reference, BiopetJavaCommandLineFunction }
import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Reference }
import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction with Reference {
......
......@@ -6,6 +6,7 @@
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
class GenotypeGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.GenotypeGVCFs with GatkGeneral {
......
......@@ -6,6 +6,7 @@
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
class IndelRealigner(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.IndelRealigner with GatkGeneral {
......
......@@ -6,6 +6,7 @@
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
class PrintReads(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.PrintReads with GatkGeneral {
......
......@@ -6,6 +6,7 @@
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
class RealignerTargetCreator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.RealignerTargetCreator with GatkGeneral {
......
......@@ -6,6 +6,7 @@
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
class SelectVariants(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.SelectVariants with GatkGeneral {
......
......@@ -6,6 +6,7 @@
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
class VariantAnnotator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantAnnotator with GatkGeneral {
......
......@@ -6,6 +6,7 @@
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {
......
......@@ -6,6 +6,7 @@
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
......
......@@ -5,10 +5,10 @@
*/
package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
import scala.util.Random
class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with BiopetQScript {
......
......@@ -5,11 +5,10 @@
*/
package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.gatk.broad.{ SelectVariants, GenotypeGVCFs }
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.gatk.broad.{ GenotypeGVCFs, SelectVariants }
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript {
def this() = this(null)
......
......@@ -5,20 +5,18 @@
*/
package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.MultiSampleQScript
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import htsjdk.samtools.SamReaderFactory
import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.gatk.broad.{ CombineVariants, CombineGVCFs }
import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import scala.collection.JavaConversions._
import nl.lumc.sasc.biopet.extensions.picard.AddOrReplaceReadGroups
import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import nl.lumc.sasc.biopet.extensions.gatk.broad.{ CombineGVCFs, CombineVariants }
import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, SamToFastq }
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.utils.commandline.{ Argument }
import scala.collection.JavaConversions._
class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScript with SummaryQScript {
qscript =>
......
......@@ -5,8 +5,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.BiopetQScript
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.gatk.broad.{ ApplyRecalibration, VariantAnnotator, VariantRecalibrator }
import org.broadinstitute.gatk.queue.QScript
......
......@@ -5,17 +5,18 @@
*/
package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.gatk.broad._
import nl.lumc.sasc.biopet.tools.{ VcfStats, MpileupToVcf, VcfFilter, MergeAlleles }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import nl.lumc.sasc.biopet.tools.{ MergeAlleles, MpileupToVcf, VcfFilter, VcfStats }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
import scala.collection.SortedMap
import scala.language.reflectiveCalls
......
......@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.gatk.broad._
import nl.lumc.sasc.biopet.pipelines.shiva.{ ShivaVariantcallingTrait, ShivaTrait }
import nl.lumc.sasc.biopet.pipelines.shiva.{ ShivaTrait, ShivaVariantcallingTrait }
import org.broadinstitute.gatk.queue.QScript
/**
......
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