From f4b5230cd4a7be4fe3d23d296f35980cd3286fe7 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 10 Sep 2015 21:34:13 +0200
Subject: [PATCH] Moved core sources
---
public/biopet-core/pom.xml | 7 +++++++
.../lumc/sasc/biopet/core/BiopetCommandLineFunction.scala | 0
.../sasc/biopet/core/BiopetCommandLineFunctionTrait.scala | 0
.../scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala | 0
.../sasc/biopet/core/BiopetJavaCommandLineFunction.scala | 0
.../scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala | 4 ++--
.../main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala | 0
.../nl/lumc/sasc/biopet/core/MultiSampleQScript.scala | 0
.../scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala | 0
.../main/scala/nl/lumc/sasc/biopet/core/Reference.scala | 0
.../scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala | 0
.../main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala | 0
.../sasc/biopet/core/report/MultisampleReportBuilder.scala | 0
.../nl/lumc/sasc/biopet/core/report/ReportBuilder.scala | 0
.../scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala | 0
.../nl/lumc/sasc/biopet/core/report/ReportSection.scala | 0
.../nl/lumc/sasc/biopet/core/summary/Summarizable.scala | 0
.../scala/nl/lumc/sasc/biopet/core/summary/Summary.scala | 0
.../nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala | 0
.../nl/lumc/sasc/biopet/core/summary/SummaryValue.scala | 0
.../nl/lumc/sasc/biopet/core/summary/WriteSummary.scala | 0
.../sasc/biopet/core/workaround/BiopetQCommandLine.scala | 0
.../nl/lumc/sasc/biopet/extensions/picard/Picard.scala | 2 +-
public/biopet-utils/pom.xml | 3 ++-
.../src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala | 2 +-
25 files changed, 13 insertions(+), 5 deletions(-)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala (95%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryValue.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala (100%)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala (100%)
diff --git a/public/biopet-core/pom.xml b/public/biopet-core/pom.xml
index 09a46daf4..0075eb771 100644
--- a/public/biopet-core/pom.xml
+++ b/public/biopet-core/pom.xml
@@ -6,12 +6,19 @@
<artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId>
<version>0.5.0-SNAPSHOT</version>
+ <relativePath>../</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>BiopetCore</artifactId>
+ <packaging>jar</packaging>
<dependencies>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetUtils</artifactId>
+ <version>0.5.0-SNAPSHOT</version>
+ </dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
similarity index 95%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index d8b1f81af..f35c07a0a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -84,11 +84,11 @@ trait BiopetQScript extends Configurable with GatkLogging {
if (outputDir.getParentFile.canWrite || (outputDir.exists && outputDir.canWrite))
globalConfig.writeReport(qSettings.runName, new File(outputDir, ".log/" + qSettings.runName))
- else BiopetQScript.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, outputdir can not be created")
+ else Logging.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, outputdir can not be created")
reportClass.foreach(add(_))
- BiopetQScript.checkErrors()
+ Logging.checkErrors()
}
/** Get implemented from org.broadinstitute.gatk.queue.QScript */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryValue.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryValue.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryValue.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryValue.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
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 dbfedea6a..9d00e0608 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
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.utils.{Logging, tryToParseNumber}
+import nl.lumc.sasc.biopet.utils.{ Logging, tryToParseNumber }
import org.broadinstitute.gatk.utils.commandline.Argument
import scala.io.Source
diff --git a/public/biopet-utils/pom.xml b/public/biopet-utils/pom.xml
index 30bae7c8d..34a98474b 100644
--- a/public/biopet-utils/pom.xml
+++ b/public/biopet-utils/pom.xml
@@ -6,11 +6,12 @@
<artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId>
<version>0.5.0-SNAPSHOT</version>
+ <relativePath>../</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>BiopetUtils</artifactId>
-
+ <packaging>jar</packaging>
<dependencies>
<dependency>
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
index 419fd24fe..93a43e273 100644
--- a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
@@ -43,7 +43,7 @@ object Logging {
errors.append(new Exception(msg))
}
- protected def checkErrors(): Unit = {
+ def checkErrors(): Unit = {
if (errors.nonEmpty) {
logger.error("*************************")
logger.error("Biopet found some errors:")
--
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