Moving utils

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

@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.core
 import java.io.{ PrintWriter, StringWriter }
 
 import nl.lumc.sasc.biopet.core.BiopetExecutable._
+import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.{ FullVersion, LastCommitHash }
 import org.apache.log4j.Logger
 

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

@@ -19,6 +19,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
+import nl.lumc.sasc.biopet.utils.Logging
 import org.broadinstitute.gatk.queue.QSettings
 import org.broadinstitute.gatk.queue.function.QFunction
 import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction

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

@@ -19,6 +19,7 @@ import java.io.{ File, PrintWriter }
 
 import nl.lumc.sasc.biopet.core.config.Config
 import nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
+import nl.lumc.sasc.biopet.utils.Logging
 import org.apache.log4j.{ PatternLayout, WriterAppender }
 import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
 

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

@@ -16,6 +16,7 @@
 package nl.lumc.sasc.biopet.core
 
 import nl.lumc.sasc.biopet.FullVersion
+import nl.lumc.sasc.biopet.utils.Logging
 
 /**
  * Trait for biopet tools, sets some default args

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

@@ -16,9 +16,7 @@
 package nl.lumc.sasc.biopet.core.config
 
 import java.io.{ File, PrintWriter }
-
-import nl.lumc.sasc.biopet.core.Logging
-import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.{Logging, ConfigUtils}
 import nl.lumc.sasc.biopet.utils.ConfigUtils._
 
 /**

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -18,8 +18,8 @@ package nl.lumc.sasc.biopet.core.report
 import java.io._
 
 import nl.lumc.sasc.biopet.core.summary.Summary
-import nl.lumc.sasc.biopet.core.{ Logging, ToolCommand, ToolCommandFuntion }
-import nl.lumc.sasc.biopet.utils.IoUtils
+import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
+import nl.lumc.sasc.biopet.utils.{Logging, IoUtils}
 import org.broadinstitute.gatk.utils.commandline.Input
 import org.fusesource.scalate.{ TemplateEngine, TemplateSource }
 import scala.collection.mutable

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala

@@ -50,7 +50,7 @@ import java.util
 import java.util.ResourceBundle
 
 import nl.lumc.sasc.biopet.FullVersion
-import nl.lumc.sasc.biopet.core.Logging
+import nl.lumc.sasc.biopet.utils.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 }

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

@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.picard
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Logging }
-import nl.lumc.sasc.biopet.utils.tryToParseNumber
+import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
+import nl.lumc.sasc.biopet.utils.{Logging, tryToParseNumber}
 import org.broadinstitute.gatk.utils.commandline.Argument
 
 import scala.io.Source

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala → public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala

@@ -19,7 +19,8 @@ import java.io.File
 
 import argonaut.Argonaut._
 import argonaut._
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, Logging }
+import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.core.{ BiopetQScript }
 import nl.lumc.sasc.biopet.core.config.ConfigValue
 import org.yaml.snakeyaml.Yaml
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala → public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala

@@ -13,7 +13,7 @@
  * license; For commercial users or users who do not want to follow the AGPL
  * license, please contact us to obtain a separate license.
  */
-package nl.lumc.sasc.biopet.core
+package nl.lumc.sasc.biopet.utils
 
 import org.apache.log4j.Logger
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala → public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala

@@ -9,7 +9,7 @@ import scala.collection.JavaConversions._
 import scala.collection.mutable
 import scala.collection.mutable.ListBuffer
 import scala.io.Source
-import nl.lumc.sasc.biopet.core.Logging
+import nl.lumc.sasc.biopet.utils.Logging
 
 /**
  * Created by pjvan_thof on 8/20/15.