Commit a4fd6fcd authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added a deprecated message

parent d49e8e65
......@@ -24,6 +24,9 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.PrintWriter
import scala.io.Source
/**
* @deprecated Use picard.util.BedToIntervalList instead
*/
class BedToInterval(val root: Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = getClass.getName
......@@ -41,6 +44,9 @@ class BedToInterval(val root: Configurable) extends BiopetJavaCommandLineFunctio
override def commandLine = super.commandLine + required("-I", input) + required("-b", bamFile) + required("-o", output)
}
/**
* @deprecated Use picard.util.BedToIntervalList instead
*/
object BedToInterval extends ToolCommand {
def apply(root: Configurable, inputBed: File, inputBam: File, output: File): BedToInterval = {
val bedToInterval = new BedToInterval(root)
......
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