From 0e3c76ab848e1adc43b59c314c2364ddadccbb98 Mon Sep 17 00:00:00 2001 From: kshakir Date: Thu, 27 May 2010 21:23:02 +0000 Subject: [PATCH] GSA-333 Meant to use getAbsolutePath and not deref symlinks. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3449 348d0f76-0448-11de-a6fe-93d51630548a --- scala/src/org/broadinstitute/sting/queue/engine/QFile.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scala/src/org/broadinstitute/sting/queue/engine/QFile.scala b/scala/src/org/broadinstitute/sting/queue/engine/QFile.scala index 435cb0938..7f443ceb9 100755 --- a/scala/src/org/broadinstitute/sting/queue/engine/QFile.scala +++ b/scala/src/org/broadinstitute/sting/queue/engine/QFile.scala @@ -18,7 +18,7 @@ class QFile(val fileType: String, val parts: String*) { def matchesFile(path: String): Boolean = matchesFile(new File(path)) def matchesFile(file: File): Boolean = file.getCanonicalPath.endsWith(extension) def baseName(path: String): String = baseName(new File(path)) - def baseName(file: File): String = StringUtils.removeEnd(file.getCanonicalPath, extension) + def baseName(file: File): String = StringUtils.removeEnd(file.getAbsolutePath, extension) def fullName(baseName: String) = baseName + extension }