Removed unused imports

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

@@ -2,8 +2,8 @@ package nl.lumc.sasc.biopet.core
 
 import java.io.File
 import java.io.PrintWriter
-import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.gatk.utils.commandline._
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.Argument
 import org.broadinstitute.gatk.queue.QSettings
 import org.broadinstitute.gatk.queue.function.QFunction
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala

-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-
 package nl.lumc.sasc.biopet.core
 
-import java.io.FileOutputStream
-//import org.broadinstitute.sting.queue.QCommandLine
 import org.broadinstitute.gatk.queue.util.Logging
 
 trait PipelineCommand extends Logging {
-  //  val src = ""
-  //  val extension = ".scala"
   val pipeline = ""
 
   def main(args: Array[String]): Unit = {
-    //    val tempFile = java.io.File.createTempFile(src + ".", extension)
-    //    val is = getClass.getResourceAsStream(src + extension)
-    //    val os = new FileOutputStream(tempFile)
-    //    org.apache.commons.io.IOUtils.copy(is, os)
-    //    os.close()
-
     var argv: Array[String] = Array()
     //argv ++= Array("-S", tempFile.getAbsolutePath)
     argv ++= Array("-S", pipeline)

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/BiopetFlagstat.scala

@@ -2,9 +2,8 @@ package nl.lumc.sasc.biopet.core.apps
 
 import htsjdk.samtools.SAMFileReader
 import htsjdk.samtools.SAMRecord
-import java.io.{ BufferedInputStream, File, FileInputStream, PrintWriter }
+import java.io.File
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import scala.io.Source
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import org.broadinstitute.gatk.queue.util.Logging

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala

 package nl.lumc.sasc.biopet.core.config
 
-import nl.lumc.sasc.biopet.core._
 import java.io.File
 import org.broadinstitute.gatk.queue.util.Logging
 import argonaut._, Argonaut._
@@ -131,15 +130,6 @@ class Config(var map: Map[String, Any]) extends Logging {
     }
   }
 
-//  def apply(module: String, path: List[String], key: String, freeVar:Boolean = true): ConfigValue = {
-//    val requestedIndex = ConfigValueIndex(module, path, key)
-//    if (contains(requestedIndex, freeVar)) return foundCache(requestedIndex)
-//    else {
-//      logger.error("Value in config could not be found but it seems required, index: " + requestedIndex)
-//      throw new IllegalStateException("Value in config could not be found but it seems required, index: " + requestedIndex)
-//    }
-//  }
-
   private def getMapFromPath(path: List[String]): Map[String, Any] = {
     var returnMap: Map[String, Any] = map
     for (m <- path) {

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.extensions
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline._
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 
 class Cat(val root: Configurable) extends BiopetCommandLineFunction {

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala

@@ -4,8 +4,8 @@ import java.io.File
 
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
 
 class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.extensions
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline._
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 
 class Gzip(val root: Configurable) extends BiopetCommandLineFunction {

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala

@@ -2,7 +2,6 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 import scala.sys.process.Process
-import org.apache.commons.io.FilenameUtils;
 import org.broadinstitute.gatk.queue.function.InProcessFunction
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import nl.lumc.sasc.biopet.core.config.Configurable

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.extensions
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline._
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 import argonaut._, Argonaut._
 import scalaz._, Scalaz._

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.extensions
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline._
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 import argonaut._, Argonaut._
 import scalaz._, Scalaz._

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -5,7 +5,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
 
 import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.{ Gzip, Ln, Pbzip2, Md5sum, Zcat }
+import nl.lumc.sasc.biopet.extensions.{ Gzip, Pbzip2, Md5sum, Zcat }
 import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts._
 
 class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {

gatk/gatk-variantcalling/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

 package nl.lumc.sasc.biopet.pipelines.gatk
 
-import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions._
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.queue.extensions.gatk.{ BaseRecalibrator, CommandLineGATK, HaplotypeCaller, IndelRealigner, PrintReads, RealignerTargetCreator, GenotypeGVCFs, AnalyzeCovariates }

mapping/src/main/scala/nl/lumc/sasc/biopet/extensions/aligners/Bwa.scala

 package nl.lumc.sasc.biopet.extensions.aligners
 
-import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
+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 scala.sys.process._
 
 class Bwa(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Fastq file R1", shortName = "R1")

mapping/src/main/scala/nl/lumc/sasc/biopet/extensions/aligners/Star.scala

 package nl.lumc.sasc.biopet.extensions.aligners
 
-import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
+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 scala.sys.process._
 
 class Star(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "The reference file for the bam files.", required = false)

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -10,7 +10,7 @@ import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
 import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument, ClassType }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Argument, ClassType }
 import org.broadinstitute.gatk.queue.extensions.picard.{ MergeSamFiles, SortSam, AddOrReplaceReadGroups }
 import scala.math._
 

pipeline-template/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/PipelineTemplate.scala

 package nl.lumc.sasc.biopet.pipelines.pipelinetemplate
 
-import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
-import nl.lumc.sasc.biopet.extensions._
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.queue.function._
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
 class PipelineTemplate(val root: Configurable) extends QScript with BiopetQScript {
   def this() = this(null)