From dd9b9bb99ecec221d8a18de0600accb540866911 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Thu, 5 Mar 2015 09:53:44 +0100
Subject: [PATCH] Move custom RScript wrapper to Gentrap directory
---
.../gentrap}/extensions/RscriptCommandLineFunction.scala | 9 ++++-----
.../biopet/pipelines/gentrap/scripts/AggrBaseCount.scala | 2 +-
.../biopet/pipelines/gentrap/scripts/PlotHeatmap.scala | 2 +-
.../sasc/biopet/pipelines/gentrap/scripts/PlotPca.scala | 2 +-
4 files changed, 7 insertions(+), 8 deletions(-)
rename public/{biopet-framework/src/main/scala/nl/lumc/sasc/biopet => gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap}/extensions/RscriptCommandLineFunction.scala (84%)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RscriptCommandLineFunction.scala
similarity index 84%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
rename to public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RscriptCommandLineFunction.scala
index d666fa377..391514a39 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RscriptCommandLineFunction.scala
@@ -4,13 +4,12 @@
* @author Wibowo Arindrarto
*/
-package nl.lumc.sasc.biopet.extensions
+package nl.lumc.sasc.biopet.pipelines.gentrap.extensions
+
+import java.io.{File, FileOutputStream}
-import java.io.FileOutputStream
-import java.io.File
-import org.broadinstitute.gatk.utils.commandline.{ Input }
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import scala.collection.JavaConversions._
+import org.broadinstitute.gatk.utils.commandline.Input
/**
* Trait for RScript wrappers
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala
index 7c6ab60c5..21b745a7a 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala
@@ -9,7 +9,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.RScriptCommandLineFunction
+import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.RScriptCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
index 6398ceefc..fefd3b9a0 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
@@ -9,7 +9,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.RScriptCommandLineFunction
+import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.RScriptCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotPca.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotPca.scala
index f9acc7673..b82cca7a8 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotPca.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotPca.scala
@@ -9,7 +9,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.RScriptCommandLineFunction
+import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.RScriptCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
--
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