Commit 5a381b3d authored by Peter van 't Hof's avatar Peter van 't Hof

Moving utils

parent 1028f4da
......@@ -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
......
......@@ -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
......
......@@ -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 }
......
......@@ -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
......
......@@ -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._
/**
......
......@@ -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
......
......@@ -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 }
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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.
......
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