From 1c1ac1f020fbf4c28c975a99119e8e47178a8646 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 16 Feb 2015 19:37:09 +0100
Subject: [PATCH] Remove unused apply methods
---
.../extensions/samtools/SamtoolsFlagstat.scala | 12 ------------
1 file changed, 12 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
index b57e67732..0551f1c6b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
@@ -36,16 +36,4 @@ object SamtoolsFlagstat {
flagstat.output = output
return flagstat
}
-
- def apply(root: Configurable, input: File, outputDir: String): SamtoolsFlagstat = {
- val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
- val outputFile = new File(dir + swapExtension(input.getName))
- return apply(root, input, outputFile)
- }
-
- def apply(root: Configurable, input: File): SamtoolsFlagstat = {
- return apply(root, input, new File(swapExtension(input.getAbsolutePath)))
- }
-
- private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".flagstat"
}
\ No newline at end of file
--
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