From c4c8292b867c5a0e98091079ebc4a11e5166ec9f Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 13 Sep 2015 12:00:00 +0200
Subject: [PATCH] Move abstract commandlines function for Rscript and Python
---
.../{ => core}/extensions/PythonCommandLineFunction.scala | 4 ++--
.../{ => core}/extensions/RscriptCommandLineFunction.scala | 4 ++--
.../sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala | 2 +-
.../lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala | 2 +-
8 files changed, 10 insertions(+), 10 deletions(-)
rename public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/{ => core}/extensions/PythonCommandLineFunction.scala (96%)
rename public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/{ => core}/extensions/RscriptCommandLineFunction.scala (96%)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
similarity index 96%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
index 59e4ed04c..000c77a9a 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
@@ -13,9 +13,9 @@
* 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.extensions
+package nl.lumc.sasc.biopet.core.extensions
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.Input
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala
similarity index 96%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala
index cd45ff92b..cce714ef1 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala
@@ -13,9 +13,9 @@
* 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.extensions
+package nl.lumc.sasc.biopet.core.extensions
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
index 01b78279c..5174f66af 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.breakdancer
import java.io.File
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BreakdancerVCF(val root: Configurable) extends PythonCommandLineFunction {
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
index 7d061ed81..1488cabc4 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.extensions.conifer
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
abstract class Conifer extends PythonCommandLineFunction {
override def subPath = "conifer" :: super.subPath
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala
index 373bf282a..4ff413b1f 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.rscript
import java.io.File
+import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
index 58c3e7c53..ad3533ced 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.rscript
import java.io.File
+import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
index 7a1d4a36b..2bf533f81 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.rscript
import java.io.File
+import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
index 5aedfa001..79ab04b94 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
@@ -17,9 +17,9 @@ package nl.lumc.sasc.biopet.scripts
import java.io.File
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
--
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