Commit dd4f0175 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

changed function to extensions

parent 8e67bf4f
......@@ -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)
......
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
......
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
......
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
......
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
......
......@@ -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 }
......
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
......
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
......
package nl.lumc.sasc.biopet.function.bedtools
package nl.lumc.sasc.biopet.extensions.bedtools
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
......
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 }
......
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 }
......
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
......
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
......
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
......
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
......
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
......
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 }
......
package nl.lumc.sasc.biopet.function.samtools
package nl.lumc.sasc.biopet.extensions.samtools
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
......
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 }
......
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