Merge branch 'refactor_core-funcs' into 'master'

Refactor core funcs

biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala

-  /*
+/*
 * Copyright (c) 2012 The Broad Institute
+* Modifications (c) 2014 Leiden University Medical Center
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation

biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala

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

biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Python.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Python.scala

-package nl.lumc.sasc.biopet.wrappers
+package nl.lumc.sasc.biopet.function
 
 import java.io.FileOutputStream
 import nl.lumc.sasc.biopet.core._

biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sha1sum.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala

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

biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala

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

flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Cutadapt.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala

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

flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Fastqc.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala

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

flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala

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

flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

 package nl.lumc.sasc.biopet.pipelines.flexiprep
 
 import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.wrappers._
-import nl.lumc.sasc.biopet.wrappers.fastq._
+import nl.lumc.sasc.biopet.function._
+import nl.lumc.sasc.biopet.function.fastq._
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.extensions.gatk._
 import org.broadinstitute.sting.queue.extensions.picard._

flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 
 //import java.io.FileOutputStream
 import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.wrappers._
+import nl.lumc.sasc.biopet.function._
 import org.broadinstitute.sting.queue.function.CommandLineFunction
 import org.broadinstitute.sting.commandline._
 import java.io.File

flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 
 import nl.lumc.sasc.biopet.core._
 import org.broadinstitute.sting.queue.function.CommandLineFunction
-import nl.lumc.sasc.biopet.wrappers.Python
+import nl.lumc.sasc.biopet.function.Python
 import org.broadinstitute.sting.commandline._
 import java.io.File
 

flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 
 import nl.lumc.sasc.biopet.core._
 import org.broadinstitute.sting.queue.function.CommandLineFunction
-import nl.lumc.sasc.biopet.wrappers.Python
+import nl.lumc.sasc.biopet.function.Python
 import org.broadinstitute.sting.commandline._
 import java.io.File
 

flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 
 import nl.lumc.sasc.biopet.core._
 import org.broadinstitute.sting.queue.function.CommandLineFunction
-import nl.lumc.sasc.biopet.wrappers.Python
+import nl.lumc.sasc.biopet.function.Python
 import org.broadinstitute.sting.commandline._
 import java.io.File
 

flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala → flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 
 import nl.lumc.sasc.biopet.core._
 import org.broadinstitute.sting.queue.function.CommandLineFunction
-import nl.lumc.sasc.biopet.wrappers.Python
+import nl.lumc.sasc.biopet.function.Python
 import org.broadinstitute.sting.commandline._
 import java.io.File
 

gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala → gatk/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala

 package nl.lumc.sasc.biopet.pipelines.gatk
 
-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 nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.pipelines.mapping._
 import nl.lumc.sasc.biopet.pipelines.flexiprep._

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