From 5a381b3dae97231bffb599b0494573ffdc4b6623 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 10 Sep 2015 20:28:19 +0200
Subject: [PATCH] Moving utils
---
.../scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala | 1 +
.../main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala | 1 +
.../main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala | 1 +
.../src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala | 1 +
.../main/scala/nl/lumc/sasc/biopet/core/config/Config.scala | 4 +---
.../scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala | 4 ++--
.../lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala | 4 ++--
.../main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala | 3 ++-
.../src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala | 0
.../src/main/scala/nl/lumc/sasc/biopet/utils}/Logging.scala | 2 +-
.../src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala | 0
.../scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala | 0
.../nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala | 2 +-
.../src/main/scala/nl/lumc/sasc/biopet/utils/package.scala | 0
15 files changed, 14 insertions(+), 11 deletions(-)
rename public/{biopet-framework => biopet-utils}/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala (99%)
rename public/{biopet-framework => biopet-utils}/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala (100%)
rename public/{biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core => biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils}/Logging.scala (96%)
rename public/{biopet-framework => biopet-utils}/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala (100%)
rename public/{biopet-framework => biopet-utils}/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala (100%)
rename public/{biopet-framework => biopet-utils}/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala (99%)
rename public/{biopet-framework => biopet-utils}/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala (100%)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
index 749ac33a2..0e8e31ba4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
+++ b/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
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 8bcb35458..24bed211d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/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
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
index 612a3753d..90857d202 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
+++ b/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 }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
index 68451bc26..091da17d6 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
+++ b/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
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
index 10099c579..e7c86664b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
+++ b/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._
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
index e52bb1f5a..21970b6ea 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
+++ b/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
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
index 2092ea732..a2c4b8c25 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
+++ b/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 }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
index d5f3b2078..dbfedea6a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
+++ b/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
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
similarity index 99%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
index 6c1795f48..bb324e572 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
+++ b/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
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
index 4566cd4f1..318948613 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
+++ b/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
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
similarity index 99%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
index c03c4bccc..56b2f303b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
+++ b/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.
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala
--
GitLab