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

Optimize imports

parent 7f2580f2
......@@ -16,8 +16,9 @@
package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for picard AddOrReplaceReadGroups */
class AddOrReplaceReadGroups(val root: Configurable) extends Picard {
......
......@@ -4,7 +4,7 @@ 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 }
/**
* Created by pjvan_thof on 4/15/15.
......
......@@ -16,10 +16,11 @@
package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
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, Argument }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for picard CalculateHsMetrics */
class CalculateHsMetrics(val root: Configurable) extends Picard with Summarizable with Reference {
......
......@@ -16,9 +16,10 @@
package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for picard CollectAlignmentSummaryMetrics */
class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with Summarizable {
......
......@@ -16,10 +16,11 @@
package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
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, Argument }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for picard CollectGcBiasMetrics */
class CollectGcBiasMetrics(val root: Configurable) extends Picard with Summarizable with Reference {
......
......@@ -16,9 +16,10 @@
package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
import scala.collection.immutable.Nil
......
......@@ -5,7 +5,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.BiopetQScript
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
import org.broadinstitute.gatk.utils.commandline.{ Output, Argument, Input }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Created by pjvan_thof on 4/16/15.
......
......@@ -16,9 +16,10 @@
package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
import picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
/**
......
......@@ -5,7 +5,7 @@ import java.io.File
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.{ Argument, Output, Input }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Created by pjvan_thof on 4/16/15.
......
......@@ -5,7 +5,7 @@ import java.io.File
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.{ Argument, Output, Input }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Created by pjvan_thof on 4/16/15.
......
......@@ -17,9 +17,8 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class GatherBamFiles(val root: Configurable) extends Picard {
......
......@@ -16,9 +16,10 @@
package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for picard MarkDuplicates */
class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
......
......@@ -16,8 +16,9 @@
package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for picard MergeSamFiles */
class MergeSamFiles(val root: Configurable) extends Picard {
......
......@@ -15,13 +15,13 @@
*/
package nl.lumc.sasc.biopet.extensions.picard
import java.io.{ FileReader, File }
import scala.io.Source
import java.io.File
import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Logging }
import nl.lumc.sasc.biopet.utils.tryToParseNumber
import org.broadinstitute.gatk.utils.commandline.Argument
import nl.lumc.sasc.biopet.core.{ Logging, BiopetJavaCommandLineFunction }
import nl.lumc.sasc.biopet.utils.tryToParseNumber
import scala.io.Source
/**
* General picard extension
......
......@@ -18,9 +18,8 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.Reference
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class ReorderSam(val root: Configurable) extends Picard with Reference {
......
......@@ -16,8 +16,9 @@
package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for picard SamToFastq */
class SamToFastq(val root: Configurable) extends Picard {
......
......@@ -16,8 +16,9 @@
package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for picard SortSam */
class SortSam(val root: Configurable) extends Picard {
......
......@@ -15,15 +15,12 @@
*/
package nl.lumc.sasc.biopet.extensions.pindel
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import org.broadinstitute.gatk.queue.QScript
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.core.BiopetQScript
import nl.lumc.sasc.biopet.core.PipelineCommand
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.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/// Pindel is actually a mini pipeline executing binaries from the pindel package
class Pindel(val root: Configurable) extends QScript with BiopetQScript {
def this() = this(null)
......
......@@ -15,10 +15,11 @@
*/
package nl.lumc.sasc.biopet.extensions.pindel
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 }
class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "pindel", freeVar = false)
......
......@@ -15,13 +15,12 @@
*/
package nl.lumc.sasc.biopet.extensions.pindel
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.ToolCommand
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.{ BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class PindelConfig(val root: Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = getClass.getName
@Input(doc = "Bam File")
......
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