From f4a4073739940f494774fc1708920f6d000a20e1 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 5 Nov 2014 15:00:25 +0100
Subject: [PATCH] Moved package because of implicit log appender
---
.../scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala | 1 +
.../sasc/biopet/core/{ => broad}/BiopetQCommandLine.scala | 6 ++++--
2 files changed, 5 insertions(+), 2 deletions(-)
rename biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/{ => broad}/BiopetQCommandLine.scala (98%)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
index 6a245cdfd..0d984f1a3 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
@@ -1,6 +1,7 @@
package nl.lumc.sasc.biopet.core
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
+import nl.lumc.sasc.biopet.core.broad.BiopetQCommandLine
trait PipelineCommand extends MainCommand with GatkLogging {
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/broad/BiopetQCommandLine.scala
similarity index 98%
rename from biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala
rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/broad/BiopetQCommandLine.scala
index 02c17e2f8..fef362a56 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/broad/BiopetQCommandLine.scala
@@ -24,7 +24,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
-package nl.lumc.sasc.biopet.core
+package nl.lumc.sasc.biopet.core.broad
import java.io.File
import org.broadinstitute.gatk.utils.commandline._
@@ -32,6 +32,7 @@ import org.broadinstitute.gatk.queue.util._
import org.broadinstitute.gatk.queue.QCommandPlugin
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.QScriptManager
+import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
import org.broadinstitute.gatk.queue.engine.{ QStatusMessenger, QGraphSettings, QGraph }
import collection.JavaConversions._
import org.broadinstitute.gatk.utils.classloader.PluginManager
@@ -43,11 +44,12 @@ import java.net.URL
import java.util.{ ResourceBundle, Arrays }
import org.broadinstitute.gatk.utils.text.TextFormattingUtils
import org.apache.commons.io.FilenameUtils
+import nl.lumc.sasc.biopet.core.BiopetExecutable
/**
* Entry point of Queue. Compiles and runs QScripts passed in to the command line.
*/
-object BiopetQCommandLine extends Logging {
+object BiopetQCommandLine extends GatkLogging {
/**
* Main.
* @param argv Arguments.
--
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