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Fixed SortSam bug, for .done file 

The *.bai.done file for the .bai file was written in the run directory instead of in the specified output directory.
Changing getName() to getAbsolutePath() fixes this.

Signed-off-by: Joel Thibault <thibault@broadinstitute.org>
This commit is contained in:
Johan Dahlberg 2012-10-03 11:35:43 +02:00 committed by Joel Thibault
parent b543bddbb7
commit e9b9e2318c
1 changed files with 1 additions and 1 deletions
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2
public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala
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@ -50,7 +50,7 @@ class SortSam extends org.broadinstitute.sting.queue.function.JavaCommandLineFun
override def freezeFieldValues() {
super.freezeFieldValues()
if (outputIndex == null && output != null)
outputIndex = new File(output.getName.stripSuffix(".bam") + ".bai")
outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
}