changed function to extensions

bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -6,9 +6,9 @@ import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import java.io.File
 import nl.lumc.sasc.biopet.core.apps.{ BedToInterval, BiopetFlagstat }
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.function.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
-import nl.lumc.sasc.biopet.function.picard.{ CollectInsertSizeMetrics, CollectGcBiasMetrics, CalculateHsMetrics, CollectAlignmentSummaryMetrics }
-import nl.lumc.sasc.biopet.function.samtools.SamtoolsFlagstat
+import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
+import nl.lumc.sasc.biopet.extensions.picard.{ CollectInsertSizeMetrics, CollectGcBiasMetrics, CalculateHsMetrics, CollectAlignmentSummaryMetrics }
+import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
 
 class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
   def this() = this(null)

bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala

 package nl.lumc.sasc.biopet.pipelines.bammetrics.scripts
 
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Cat.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala

-package nl.lumc.sasc.biopet.function
+package nl.lumc.sasc.biopet.extensions
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable

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

-package nl.lumc.sasc.biopet.function
+package nl.lumc.sasc.biopet.extensions
 
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.queue.function.InProcessFunction

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala

-package nl.lumc.sasc.biopet.function
+package nl.lumc.sasc.biopet.extensions
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/PythonCommandLineFunction.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala

-package nl.lumc.sasc.biopet.function
+package nl.lumc.sasc.biopet.extensions
 
 import java.io.FileOutputStream
 import java.io.File

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Seqtk.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqtk.scala

@@ -4,7 +4,7 @@
  * @author  Wibowo Arindrarto
  */
 
-package nl.lumc.sasc.biopet.function
+package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }

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

-package nl.lumc.sasc.biopet.function
+package nl.lumc.sasc.biopet.extensions
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable

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

-package nl.lumc.sasc.biopet.function
+package nl.lumc.sasc.biopet.extensions
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/Bedtools.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala

-package nl.lumc.sasc.biopet.function.bedtools
+package nl.lumc.sasc.biopet.extensions.bedtools
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsCoverage.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala

-package nl.lumc.sasc.biopet.function.bedtools
+package nl.lumc.sasc.biopet.extensions.bedtools
 
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsIntersect.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala

-package nl.lumc.sasc.biopet.function.bedtools
+package nl.lumc.sasc.biopet.extensions.bedtools
 
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CalculateHsMetrics.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala

-package nl.lumc.sasc.biopet.function.picard
+package nl.lumc.sasc.biopet.extensions.picard
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectAlignmentSummaryMetrics.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala

-package nl.lumc.sasc.biopet.function.picard
+package nl.lumc.sasc.biopet.extensions.picard
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectGcBiasMetrics.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala

-package nl.lumc.sasc.biopet.function.picard
+package nl.lumc.sasc.biopet.extensions.picard
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectInsertSizeMetrics.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala

-package nl.lumc.sasc.biopet.function.picard
+package nl.lumc.sasc.biopet.extensions.picard
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/MarkDuplicates.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala

-package nl.lumc.sasc.biopet.function.picard
+package nl.lumc.sasc.biopet.extensions.picard
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/Picard.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala

-package nl.lumc.sasc.biopet.function.picard
+package nl.lumc.sasc.biopet.extensions.picard
 
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument }

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/Samtools.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala

-package nl.lumc.sasc.biopet.function.samtools
+package nl.lumc.sasc.biopet.extensions.samtools
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/SamtoolsFlagstat.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala

-package nl.lumc.sasc.biopet.function.samtools
+package nl.lumc.sasc.biopet.extensions.samtools
 
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }