Moved Sage tools to nl.lumc.biopet.tools

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala

@@ -30,9 +30,9 @@ object BiopetExecutable {
       nl.lumc.sasc.biopet.tools.MpileupToVcf,
       nl.lumc.sasc.biopet.tools.FastqSplitter,
       nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts,
-      nl.lumc.sasc.biopet.pipelines.sage.SageCountFastq,
-      nl.lumc.sasc.biopet.pipelines.sage.SageCreateLibrary,
-      nl.lumc.sasc.biopet.pipelines.sage.SageCreateTagCounts)
+      nl.lumc.sasc.biopet.tools.SageCountFastq,
+      nl.lumc.sasc.biopet.tools.SageCreateLibrary,
+      nl.lumc.sasc.biopet.tools.SageCreateTagCounts)
   )
   
   /**

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala

@@ -10,6 +10,9 @@ import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
 import nl.lumc.sasc.biopet.scripts.PrefixFastq
 import nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts
 import nl.lumc.sasc.biopet.scripts.SquishBed
+import nl.lumc.sasc.biopet.tools.SageCountFastq
+import nl.lumc.sasc.biopet.tools.SageCreateLibrary
+import nl.lumc.sasc.biopet.tools.SageCreateTagCounts
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.queue.function._
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/SageCountFastq.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala

-package nl.lumc.sasc.biopet.pipelines.sage
+package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 import java.io.PrintWriter

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/SageCreateLibrary.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala

-package nl.lumc.sasc.biopet.pipelines.sage
+package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 import java.io.PrintWriter

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/SageCreateTagCounts.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala

-package nl.lumc.sasc.biopet.pipelines.sage
+package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 import java.io.PrintWriter