Commit 5370d60d authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix graph error

parent 613c89ec
......@@ -111,8 +111,7 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
super.freezeFieldValues()
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))
if (!org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor.isCompressed(out.getPath))
outputFiles :+= VcfUtils.getVcfIndexFile(out)
outputFiles :+= VcfUtils.getVcfIndexFile(out)
dbsnp.foreach(VcfUtils.getVcfIndexFile(_))
}
......
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