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

Optimize imports

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