Commit d03ff5ff authored by Sander Bollen's avatar Sander Bollen
Browse files

attempt to fix cyclic errors

parent 8bb2e6d9
......@@ -106,16 +106,12 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
@Gather(enabled = false)
private var outputIndex: File = _
@Output
@Gather(enabled = false)
private var dbsnpIndex: File = _
override def beforeGraph() {
super.beforeGraph()
deps ++= variant.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => VcfUtils.getVcfIndexFile(orig))
if (out != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(out))
outputIndex = VcfUtils.getVcfIndexFile(out)
dbsnp.foreach(x => dbsnpIndex = VcfUtils.getVcfIndexFile(x))
dbsnp.foreach(x => deps :+= VcfUtils.getVcfIndexFile(x))
}
override def cmdLine = super.cmdLine +
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment