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Control unscattered output file location 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6011 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2011-06-17 15:53:25 +00:00
parent 285da580f3
commit 03a0185566
1 changed files with 5 additions and 1 deletions
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6
scala/qscript/oneoffs/fromer/CNV/ReadDepthCNVanalysis.scala
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@ -111,12 +111,16 @@ class ReadDepthCNVanalysis extends QScript {
@Gather(classOf[org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction]) @Gather(classOf[org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction])
var intervalSampleOut: File = new File(t.DoC_output.getPath() + DOC_OUTPUT_SUFFIX) 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 + override def commandLine = super.commandLine +
" --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality " + minMappingQuality + " --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality " + minMappingQuality +
" --start " + START_BIN + " --stop " + MAX_DEPTH + " --nBins " + NUM_BINS + " --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 override def dotString = "DOC: " + t.DoC_output
this.jobOutputFile = outFile + ".out"
} }
class combineDoC(DoCsToCombine: List[File]) extends CommandLineFunction { class combineDoC(DoCsToCombine: List[File]) extends CommandLineFunction {