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

Optimize imports

parent 7f2580f2
......@@ -45,24 +45,21 @@
package nl.lumc.sasc.biopet.core.workaround
import collection.JavaConversions._
import java.io.{ File, FileOutputStream }
import java.net.URL
import java.util.{ ResourceBundle, Arrays }
import java.util.{ Arrays, ResourceBundle }
import org.apache.commons.io.FilenameUtils
import org.broadinstitute.gatk.utils.commandline._
import org.broadinstitute.gatk.queue.util._
import nl.lumc.sasc.biopet.FullVersion
import nl.lumc.sasc.biopet.core.Logging
import org.broadinstitute.gatk.queue.engine.{ QGraph, QGraphSettings }
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging, ScalaCompoundArgumentTypeDescriptor, ClassFieldCache }
import org.broadinstitute.gatk.queue.{ QCommandPlugin, QScript, QScriptManager }
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
import org.broadinstitute.gatk.queue.engine.{ QStatusMessenger, QGraphSettings, QGraph }
import org.broadinstitute.gatk.utils.classloader.PluginManager
import org.broadinstitute.gatk.utils.exceptions.UserException
import org.broadinstitute.gatk.utils.io.IOUtils
import org.broadinstitute.gatk.utils.commandline._
import org.broadinstitute.gatk.utils.help.ApplicationDetails
import org.broadinstitute.gatk.utils.io.IOUtils
import org.broadinstitute.gatk.utils.text.TextFormattingUtils
import nl.lumc.sasc.biopet.FullVersion
import scala.collection.JavaConversions._
/**
* Entry point of Queue. Compiles and runs QScripts passed in to the command line.
......
......@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
......
......@@ -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 GNU cat
......
......@@ -16,9 +16,10 @@
package nl.lumc.sasc.biopet.extensions
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Wrapper for the cufflinks command line tool.
......
......@@ -15,11 +15,12 @@
*/
package nl.lumc.sasc.biopet.extensions
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.mutable
import scala.io.Source
......
......@@ -17,10 +17,9 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Extension for fastqc
......
......@@ -17,9 +17,9 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Created by pjvan_thof on 3/3/15.
......
......@@ -17,10 +17,9 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Wrapper for the gsnap command line tool
......
......@@ -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
class Gzip(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Input file", required = true)
......
......@@ -16,9 +16,10 @@
package nl.lumc.sasc.biopet.extensions
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Wrapper for the htseq-count command line tool
......
......@@ -16,10 +16,12 @@
package nl.lumc.sasc.biopet.extensions
import java.io.File
import scala.sys.process.{ Process, ProcessLogger }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.queue.function.InProcessFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.config.Configurable
import scala.sys.process.{ Process, ProcessLogger }
/**
* This class can execute ln as InProcessFunction or used to only generate the ln command
......
......@@ -15,13 +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
import argonaut._, Argonaut._
import scalaz._, Scalaz._
import scala.io.Source
/** Extension for md5sum */
class Md5sum(val root: Configurable) extends BiopetCommandLineFunction {
......
......@@ -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 pbzip2 */
class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
......
......@@ -15,11 +15,10 @@
*/
package nl.lumc.sasc.biopet.extensions
import java.io.FileOutputStream
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input }
import java.io.{ File, FileOutputStream }
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import scala.collection.JavaConversions._
import org.broadinstitute.gatk.utils.commandline.Input
trait PythonCommandLineFunction extends BiopetCommandLineFunction {
@Input(doc = "Python script", required = false)
......
......@@ -15,10 +15,12 @@
*/
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, Argument }
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
import scalaz.std.boolean.option
/**
......
......@@ -15,9 +15,10 @@
*/
package nl.lumc.sasc.biopet.extensions
import java.io.{ FileOutputStream, File }
import java.io.{ File, FileOutputStream }
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import scala.sys.process._
/**
......
......@@ -15,13 +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
import argonaut._, Argonaut._
import scalaz._, Scalaz._
import scala.io.Source
/** Extension for sha1sum */
class Sha1sum(val root: Configurable) extends BiopetCommandLineFunction {
......
......@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for stampy */
......
......@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
......
......@@ -17,9 +17,9 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Extension for VariantEffectPredictor
......
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