Moved config to utils

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

@@ -18,7 +18,7 @@ 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 nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**

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

@@ -18,7 +18,7 @@ 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 nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /** Extension for zcat */

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.bcftools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /** This extension is based on bcftools 1.1-134 */

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.bedtools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 /** Extension for bedtools coverage */

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.bedtools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 /**

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.bedtools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 /** Extension for bedtools intersect */

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.breakdancer
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.{ Reference, BiopetQScript, PipelineCommand }
 import org.broadinstitute.gatk.queue.QScript
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.breakdancer
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunction {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.breakdancer
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class BreakdancerConfig(val root: Configurable) extends BiopetCommandLineFunction {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.breakdancer
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.bwa
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.Reference
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.bwa
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.Reference
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.bwa
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.Reference
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.bwa
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.Reference
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.clever
 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.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction with Reference {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.conifer
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 class ConiferAnalyze(val root: Configurable) extends Conifer {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.conifer
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class ConiferCall(val root: Configurable) extends Conifer {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.conifer
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class ConiferExport(val root: Configurable) extends Conifer {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.conifer
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class ConiferRPKM(val root: Configurable) extends Conifer {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.delly
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.{ Reference, BiopetQScript, PipelineCommand }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.extensions.Ln
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.queue.extensions.gatk.CatVariants