Commit c3e801d4 authored by Peter van 't Hof's avatar Peter van 't Hof

Workaround for index creation

parent cb4cfc7e
......@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.extensions.Tabix
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
......@@ -28,7 +29,16 @@ class GatherVcfs(val parent: Configurable) extends Picard {
@Output(doc = "The output file to bam file to", required = true)
var output: File = _
val tabix: Option[Tabix] = if (createIndex) Some(Tabix(this, output)) else None
//FIXME: This is a workaround for this issue: https://github.com/broadinstitute/picard/issues/789
def tabix: Option[Tabix] = if (createIndex) Some(Tabix(this, output)) else None
@Output(required = false)
private var index: File = _
override def beforeGraph(): Unit = {
super.beforeGraph()
if (createIndex) index = VcfUtils.getVcfIndexFile(output)
}
override def cmdLine: String =
super.cmdLine +
......
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