Moved core sources

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

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>

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:")