From 03a018556652b9ef4760bfed39997df5de399c7c Mon Sep 17 00:00:00 2001 From: fromer Date: Fri, 17 Jun 2011 15:53:25 +0000 Subject: [PATCH] Control unscattered output file location git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6011 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/oneoffs/fromer/CNV/ReadDepthCNVanalysis.scala | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/scala/qscript/oneoffs/fromer/CNV/ReadDepthCNVanalysis.scala b/scala/qscript/oneoffs/fromer/CNV/ReadDepthCNVanalysis.scala index c5e28668e..779b05135 100644 --- a/scala/qscript/oneoffs/fromer/CNV/ReadDepthCNVanalysis.scala +++ b/scala/qscript/oneoffs/fromer/CNV/ReadDepthCNVanalysis.scala @@ -111,12 +111,16 @@ class ReadDepthCNVanalysis extends QScript { @Gather(classOf[org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction]) var intervalSampleOut: File = new File(t.DoC_output.getPath() + DOC_OUTPUT_SUFFIX) + val outFile = new File(intervalSampleOut.getParentFile(), t.DoC_output.getName()) + override def commandLine = super.commandLine + " --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality " + minMappingQuality + " --start " + START_BIN + " --stop " + MAX_DEPTH + " --nBins " + NUM_BINS + - " -o " + new File(intervalSampleOut.getParentFile(), t.DoC_output.getName()) + " -o " + outFile override def dotString = "DOC: " + t.DoC_output + + this.jobOutputFile = outFile + ".out" } class combineDoC(DoCsToCombine: List[File]) extends CommandLineFunction {