From e96bcf212890bf32bf8a5ffa53f5d8a393d84c3c Mon Sep 17 00:00:00 2001 From: kshakir Date: Fri, 28 May 2010 22:27:05 +0000 Subject: [PATCH] GSA-333 Replaced all accidental usages of getCanonicalPath (which should never be used) with getAbsolutePath. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3463 348d0f76-0448-11de-a6fe-93d51630548a --- scala/src/org/broadinstitute/sting/queue/engine/QFile.scala | 2 +- .../sting/queue/engine/graphing/TreeJobGrapher.scala | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/scala/src/org/broadinstitute/sting/queue/engine/QFile.scala b/scala/src/org/broadinstitute/sting/queue/engine/QFile.scala index 7f443ceb9..27c11b545 100755 --- a/scala/src/org/broadinstitute/sting/queue/engine/QFile.scala +++ b/scala/src/org/broadinstitute/sting/queue/engine/QFile.scala @@ -16,7 +16,7 @@ class QFile(val fileType: String, val parts: String*) { override def hashCode = HashCodeBuilder.reflectionHashCode(this) def matchesFile(path: String): Boolean = matchesFile(new File(path)) - def matchesFile(file: File): Boolean = file.getCanonicalPath.endsWith(extension) + def matchesFile(file: File): Boolean = file.getAbsolutePath.endsWith(extension) def baseName(path: String): String = baseName(new File(path)) def baseName(file: File): String = StringUtils.removeEnd(file.getAbsolutePath, extension) def fullName(baseName: String) = baseName + extension diff --git a/scala/src/org/broadinstitute/sting/queue/engine/graphing/TreeJobGrapher.scala b/scala/src/org/broadinstitute/sting/queue/engine/graphing/TreeJobGrapher.scala index ed8e2d05c..149cef2ed 100644 --- a/scala/src/org/broadinstitute/sting/queue/engine/graphing/TreeJobGrapher.scala +++ b/scala/src/org/broadinstitute/sting/queue/engine/graphing/TreeJobGrapher.scala @@ -56,7 +56,7 @@ class TreeJobGrapher extends JobGrapher { } private def addPaths(shortestPath: java.util.List[QCommand], qArgs: QArguments) { - for (inputFile <- qArgs.inputPaths.map(_.getCanonicalPath)) + for (inputFile <- qArgs.inputPaths.map(_.getAbsolutePath)) if (modelGraph.getEdgeSource(shortestPath.head).matchesFile(inputFile)) addPath(shortestPath, inputFile) }