Commit d8056e3d authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added targetBed option

parent d94892dd
......@@ -19,7 +19,7 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
var reference: File = _
@Argument(doc = "Target bed", shortName = "targetBed", required = false)
var targetBed: File = _
var targetBed: List[File] = Nil
@Argument(doc = "Samples", shortName = "sample", required = false)
var samples: List[String] = Nil
......@@ -35,7 +35,9 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
def init() {
if (reference == null) reference = config("reference")
if (targetBed == null) targetBed = config("targetBed")
if (configContains("targetBed"))
for (bed <- config("targetBed").getList)
targetBed :+= bed.toString
if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
else if (!outputDir.endsWith("/")) outputDir += "/"
}
......
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