Commit f4b5230c authored by Peter van 't Hof's avatar Peter van 't Hof

Moved core sources

parent 7854fb6e
......@@ -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>
......
......@@ -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 */
......
......@@ -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
......
......@@ -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>
......
......@@ -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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