Commit a39f363c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding dbsnp automatic again

parent 9e5c572d
......@@ -157,8 +157,10 @@ class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with S
@Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
var filter_bases_not_stored: Boolean = _
override def freezeFieldValues() {
super.freezeFieldValues()
if (config.contains("dbsnp")) knownSites :+= new File(config("dbsnp").asString)
override def beforeGraph() {
super.beforeGraph()
knownSitesIndexes ++= knownSites.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => new File(orig.getPath + ".idx"))
}
......
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