Commit 1afacc17 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix output file of index

parent 7b7ef123
......@@ -400,10 +400,9 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
override def beforeGraph() {
super.beforeGraph()
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(deps :+= VcfUtils.getVcfIndexFile(_))
deps ++= comp.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => VcfUtils.getVcfIndexFile(orig))
deps ++= comp.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => 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")
......
......@@ -258,8 +258,7 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
dbsnp.foreach(deps :+= VcfUtils.getVcfIndexFile(_))
deps ++= comp.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)
}
override def cmdLine = super.cmdLine +
......
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