Commit 7594b89f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed compile error

parent 6cbf2b4a
......@@ -402,7 +402,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
if (out != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(out))
outputFiles :+= VcfUtils.getVcfIndexFile(out)
dbsnp.foreach(deps :+= VcfUtils.getVcfIndexFile(_))
deps ++= comp.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => orig + ".idx")
deps ++= comp.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => new File(orig + ".idx"))
if (bamOutput != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(bamOutput))
if (!disable_bam_indexing)
outputFiles :+= new File(bamOutput.getPath.stripSuffix(".bam") + ".bai")
......
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