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biopet.biopet
Commit 5da52a7b authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub
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Merge pull request #33 from biopet/fix-biopet-592 

Remove hard-coded settings in XhmmMatrix.
parents e863bf38 1f852510
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kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
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......@@ -64,13 +64,6 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
val firstMatrix = new XhmmMatrix(this)
firstMatrix.inputMatrix = merged.output
firstMatrix.outputMatrix = swapExt(xhmmDir, merged.output, ".depths.data", ".filtered_centered.data")
firstMatrix.minTargetSize = 10
firstMatrix.maxTargetSize = 10000
firstMatrix.minMeanTargetRD = 10
firstMatrix.maxMeanTargetRD = 500
firstMatrix.minMeanSampleRD = 25
firstMatrix.maxMeanSampleRD = 200
firstMatrix.maxSdSampleRD = 150
firstMatrix.outputExcludedSamples = Some(swapExt(xhmmDir, merged.output, ".depths.data", ".filtered.samples.txt"))
firstMatrix.outputExcludedTargets = Some(swapExt(xhmmDir, merged.output, ".depths.data", ".filtered.targets.txt"))
add(firstMatrix)
......
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