From a4fd6fcdb5b98863629eb5cc8e7e09581343d43d Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 16 Apr 2015 09:52:41 +0200
Subject: [PATCH] Added a deprecated message
---
.../scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
index 58b9500ad..ddfb57439 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
@@ -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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