Commit 6f595a73 authored by akaljuvee's avatar akaljuvee
Browse files


parent c8821092
......@@ -15,12 +15,12 @@
package nl.lumc.sasc.biopet.pipelines.shiva
import htsjdk.variant.vcf.VCFFileReader
import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
import nl.lumc.sasc.biopet.core.{ Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.core.summary.{Summarizable, SummaryQScript}
import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference, SampleLibraryTag}
import nl.lumc.sasc.biopet.extensions.Pysvtools
import nl.lumc.sasc.biopet.pipelines.shiva.svcallers._
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
import nl.lumc.sasc.biopet.utils.{BamUtils, Logging}
import org.broadinstitute.gatk.queue.QScript
......@@ -152,4 +152,6 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
Map("DEL" -> delCounts, "INS" -> insCounts, "DUP" -> dupCounts, "INV" -> invCounts, "TRA" -> traCount)
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object ShivaSvCalling extends PipelineCommand
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