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

Optimize imports

parent 7f2580f2
......@@ -19,7 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Created by pjvan_thof on 1/29/15.
......
......@@ -15,10 +15,11 @@
*/
package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
/** Extension for zcat */
class Zcat(val root: Configurable) extends BiopetCommandLineFunction {
......
......@@ -15,10 +15,11 @@
*/
package nl.lumc.sasc.biopet.extensions.bedtools
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for bedtools coverage */
class BedtoolsCoverage(val root: Configurable) extends Bedtools {
......
......@@ -15,10 +15,11 @@
*/
package nl.lumc.sasc.biopet.extensions.bedtools
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Wrapper for the bedtools groupby tool
* Written based on bedtools v2.21.0 (md5: b5a9a64bad721d96f6cbf2b3805b0fbe)
......
......@@ -15,10 +15,11 @@
*/
package nl.lumc.sasc.biopet.extensions.bedtools
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for bedtools intersect */
class BedtoolsIntersect(val root: Configurable) extends Bedtools {
......
......@@ -19,7 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Extension for bwa aln
......
......@@ -17,9 +17,8 @@ package nl.lumc.sasc.biopet.extensions.bwa
import java.io.File
import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
......
......@@ -19,7 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* BWA sampe wrapper
......
......@@ -19,7 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* BWA samse wrapper
......
......@@ -15,7 +15,6 @@
*/
package nl.lumc.sasc.biopet.extensions.conifer
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
abstract class Conifer extends PythonCommandLineFunction {
......
......@@ -18,7 +18,6 @@ package nl.lumc.sasc.biopet.extensions.conifer
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.Ln
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class ConiferAnalyze(val root: Configurable) extends Conifer {
......
......@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.conifer
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class ConiferCall(val root: Configurable) extends Conifer {
......
......@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.conifer
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class ConiferRPKM(val root: Configurable) extends Conifer {
......
......@@ -2,14 +2,11 @@ package nl.lumc.sasc.biopet.extensions.delly
import java.io.File
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.extensions.gatk.CatVariants
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
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.Ln
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.extensions.gatk.CatVariants
class Delly(val root: Configurable) extends QScript with BiopetQScript {
def this() = this(null)
......
......@@ -2,10 +2,9 @@ package nl.lumc.sasc.biopet.extensions.delly
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class DellyCaller(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "delly")
......
......@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Created by pjvan_thof on 2/26/15.
......
......@@ -17,8 +17,7 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.{ Reference, BiopetJavaCommandLineFunction }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Reference }
import org.broadinstitute.gatk.utils.commandline.Input
/**
......
......@@ -16,9 +16,10 @@
package nl.lumc.sasc.biopet.extensions.igvtools
import java.io.{ File, FileNotFoundException }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import java.io.{ FileNotFoundException, File }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* IGVTools `count` wrapper
......
......@@ -22,8 +22,6 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.util.matching.Regex
/** Extension for Kraken */
class Kraken(val root: Configurable) extends BiopetCommandLineFunction {
......
......@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.macs2
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for macs2*/
class Macs2CallPeak(val root: Configurable) extends Macs2 {
......
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