Commit c55f3de2 authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub

Merge branch 'develop' into Fix_BIOPET_557

parents bf363cf7 5da52a7b
......@@ -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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