Commit 76383bf1 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Move Bowtie2 to package bowtie

parent 394f32a2
package nl.lumc.sasc.biopet.extensions
package nl.lumc.sasc.biopet.extensions.bowtie
import java.io.File
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version }
import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Reference, Version}
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
/**
* Extension for bowtie 2
......
......@@ -20,7 +20,7 @@ import java.util.Date
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.bowtie.Bowtie
import nl.lumc.sasc.biopet.extensions.bowtie.{Bowtie2, Bowtie}
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam }
......
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