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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
This commit is contained in:
kshakir 2010-05-28 22:27:05 +00:00
parent eb25e41111
commit e96bcf2128
2 changed files with 2 additions and 2 deletions
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2
scala/src/org/broadinstitute/sting/queue/engine/QFile.scala
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@ -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

2
scala/src/org/broadinstitute/sting/queue/engine/graphing/TreeJobGrapher.scala
View File

@ -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)
}