Commit 405ecae2 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added warning on use of old argument

parent 2b62b86b
......@@ -31,6 +31,20 @@ trait PipelineCommand extends MainCommand with GatkLogging {
if (t >= argsSize) throw new IllegalStateException("-config needs a value")
Config.global.loadConfigFile(new File(args(t + 1)))
}
if (args(t) == "--logging_level" || args(t) == "-l") {
args(t + 1).toLowerCase match {
case "debug" => Logging.logger.setLevel(org.apache.log4j.Level.DEBUG)
case "info" => Logging.logger.setLevel(org.apache.log4j.Level.INFO)
case "warn" => Logging.logger.setLevel(org.apache.log4j.Level.WARN)
case "error" => Logging.logger.setLevel(org.apache.log4j.Level.ERROR)
case _ =>
}
}
}
for (t <- 0 until argsSize) {
if (args(t) == "--outputDir" || args(t) == "-outDir") {
throw new IllegalArgumentException("Commandline argument is deprecated, should use config for this now")
}
}
var argv: Array[String] = Array()
......
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