Merge branch 'refactor_core-funcs' into 'master'

Refactor core funcs

mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala → mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala

-package nl.lumc.sasc.biopet.wrappers.aligners
+package nl.lumc.sasc.biopet.function.aligners
 
 import nl.lumc.sasc.biopet.core._
 import org.broadinstitute.sting.queue.function.CommandLineFunction

mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala → mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

 package nl.lumc.sasc.biopet.pipelines.mapping
 
-import nl.lumc.sasc.biopet.wrappers._
-import nl.lumc.sasc.biopet.wrappers.aligners._
+import nl.lumc.sasc.biopet.function._
+import nl.lumc.sasc.biopet.function.aligners._
 import java.util.Date
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.pipelines.flexiprep._