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Commit 982c9348 authored by Peter van 't Hof's avatar Peter van 't Hof
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Format fixes

parent 68c080d8
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
View file @ 982c9348
......@@ -19,7 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Wrapper for the bgzip command */
class Bgzip(val root: Configurable) extends BiopetCommandLineFunction {
......@@ -35,8 +35,8 @@ class Bgzip(val root: Configurable) extends BiopetCommandLineFunction {
override def beforeGraph(): Unit = {
super.beforeGraph()
if (input.isEmpty && ! inputAsStdin) Logging.addError("Input is missing in Bgzip")
if (output == null && ! outputAsStsout) Logging.addError("Output is missing in Bgzip")
if (input.isEmpty && !inputAsStdin) Logging.addError("Input is missing in Bgzip")
if (output == null && !outputAsStsout) Logging.addError("Output is missing in Bgzip")
}
def cmdLine = required(executable) +
......
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