From 862aefe339d4383376163f2774fdf9b52cc97cef Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 16 Feb 2015 19:34:07 +0100
Subject: [PATCH] Remove obselete apply methods
---
.../scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala | 6 ------
1 file changed, 6 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
index 3aa5a2282..e99398ff4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
@@ -46,12 +46,6 @@ object BiopetFlagstat extends ToolCommand {
flagstat.output = output
return flagstat
}
- def apply(root: Configurable, input: File, outputDir: String): BiopetFlagstat = {
- val flagstat = new BiopetFlagstat(root)
- flagstat.input = input
- flagstat.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".biopetflagstat")
- return flagstat
- }
case class Args(inputFile: File = null, region: Option[String] = None) extends AbstractArgs
--
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