Moved core sources

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>

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala → 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 */