Commit 85c9703c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge remote-tracking branch 'remotes/origin/develop' into fix-biopet-498

parents 21da59ab 2fbebdfb
...@@ -31,7 +31,7 @@ CNRoutput <- opt$cnr ...@@ -31,7 +31,7 @@ CNRoutput <- opt$cnr
windowLength <- opt$wl windowLength <- opt$wl
bamFile <- args bamFile <- args
BAMFiles <- strsplit(c(bamFile), " ")[[1]] BAMFiles <- bamFile
bamDataRanges <- tryCatch( bamDataRanges <- tryCatch(
{ {
getReadCountsFromBAM(BAMFiles, mode="paired", refSeqName=chromosome, WL=windowLength, parallel=opt$threads) getReadCountsFromBAM(BAMFiles, mode="paired", refSeqName=chromosome, WL=windowLength, parallel=opt$threads)
......
...@@ -21,6 +21,8 @@ class XcnvToBed(val root: Configurable) extends ToolCommandFunction { ...@@ -21,6 +21,8 @@ class XcnvToBed(val root: Configurable) extends ToolCommandFunction {
@Argument @Argument
var sample: String = _ var sample: String = _
override def defaultCoreMemory = 4
override def cmdLine = { override def cmdLine = {
super.cmdLine + required("-I", inputXcnv) + required("-O", outpuBed) + required("-S", sample) super.cmdLine + required("-I", inputXcnv) + required("-O", outpuBed) + required("-S", sample)
} }
......
...@@ -49,7 +49,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference { ...@@ -49,7 +49,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
// the filtered and centered matrix // the filtered and centered matrix
val firstMatrix = new XhmmMatrix(this) val firstMatrix = new XhmmMatrix(this)
firstMatrix.inputMatrix = merged.output firstMatrix.inputMatrix = merged.output
firstMatrix.outputMatrix = swapExt(merged.output, ".depths.data", ".filtered_centered.data") firstMatrix.outputMatrix = swapExt(xhmmDir, merged.output, ".depths.data", ".filtered_centered.data")
firstMatrix.minTargetSize = 10 firstMatrix.minTargetSize = 10
firstMatrix.maxTargetSize = 10000 firstMatrix.maxTargetSize = 10000
firstMatrix.minMeanTargetRD = 10 firstMatrix.minMeanTargetRD = 10
...@@ -57,21 +57,21 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference { ...@@ -57,21 +57,21 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
firstMatrix.minMeanSampleRD = 25 firstMatrix.minMeanSampleRD = 25
firstMatrix.maxMeanSampleRD = 200 firstMatrix.maxMeanSampleRD = 200
firstMatrix.maxSdSampleRD = 150 firstMatrix.maxSdSampleRD = 150
firstMatrix.outputExcludedSamples = Some(swapExt(merged.output, ".depths.data", ".filtered.samples.txt")) firstMatrix.outputExcludedSamples = Some(swapExt(xhmmDir, merged.output, ".depths.data", ".filtered.samples.txt"))
firstMatrix.outputExcludedTargets = Some(swapExt(merged.output, ".depths.data", ".filtered.targets.txt")) firstMatrix.outputExcludedTargets = Some(swapExt(xhmmDir, merged.output, ".depths.data", ".filtered.targets.txt"))
add(firstMatrix) add(firstMatrix)
// pca generation // pca generation
val pca = new XhmmPca(this) val pca = new XhmmPca(this)
pca.inputMatrix = firstMatrix.outputMatrix pca.inputMatrix = firstMatrix.outputMatrix
pca.pcaFile = swapExt(firstMatrix.outputMatrix, ".filtered_centered.data", ".rd_pca.data") pca.pcaFile = swapExt(xhmmDir, firstMatrix.outputMatrix, ".filtered_centered.data", ".rd_pca.data")
add(pca) add(pca)
// normalization // normalization
val normalize = new XhmmNormalize(this) val normalize = new XhmmNormalize(this)
normalize.inputMatrix = firstMatrix.outputMatrix normalize.inputMatrix = firstMatrix.outputMatrix
normalize.pcaFile = pca.pcaFile normalize.pcaFile = pca.pcaFile
normalize.normalizeOutput = swapExt(firstMatrix.outputMatrix, ".filtered_centered.data", ".normalized.data") normalize.normalizeOutput = swapExt(xhmmDir, firstMatrix.outputMatrix, ".filtered_centered.data", ".normalized.data")
add(normalize) add(normalize)
// normalized & filtered matrix // normalized & filtered matrix
...@@ -81,9 +81,9 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference { ...@@ -81,9 +81,9 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
secondMatrix.centerType = "sample" secondMatrix.centerType = "sample"
secondMatrix.zScoreData = true secondMatrix.zScoreData = true
secondMatrix.maxsdTargetRD = 30 secondMatrix.maxsdTargetRD = 30
secondMatrix.outputExcludedTargets = Some(swapExt(normalize.normalizeOutput, ".data", ".filtered.targets.txt")) secondMatrix.outputExcludedTargets = Some(swapExt(xhmmDir, normalize.normalizeOutput, ".data", ".filtered.targets.txt"))
secondMatrix.outputExcludedSamples = Some(swapExt(normalize.normalizeOutput, ".data", ".filtered.samples.txt")) secondMatrix.outputExcludedSamples = Some(swapExt(xhmmDir, normalize.normalizeOutput, ".data", ".filtered.samples.txt"))
secondMatrix.outputMatrix = swapExt(normalize.normalizeOutput, ".data", "filtered.data") secondMatrix.outputMatrix = swapExt(xhmmDir, normalize.normalizeOutput, ".data", "filtered.data")
add(secondMatrix) add(secondMatrix)
// re-synced matrix // re-synced matrix
...@@ -91,7 +91,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference { ...@@ -91,7 +91,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
thirdMatrix.inputMatrix = merged.output thirdMatrix.inputMatrix = merged.output
thirdMatrix.inputExcludeSamples = List(firstMatrix.outputExcludedSamples, secondMatrix.outputExcludedSamples).flatten thirdMatrix.inputExcludeSamples = List(firstMatrix.outputExcludedSamples, secondMatrix.outputExcludedSamples).flatten
thirdMatrix.inputExcludeTargets = List(firstMatrix.outputExcludedTargets, secondMatrix.outputExcludedTargets).flatten thirdMatrix.inputExcludeTargets = List(firstMatrix.outputExcludedTargets, secondMatrix.outputExcludedTargets).flatten
thirdMatrix.outputMatrix = swapExt(merged.output, ".depths.data", ".same_filtered.data") thirdMatrix.outputMatrix = swapExt(xhmmDir, merged.output, ".depths.data", ".same_filtered.data")
add(thirdMatrix) add(thirdMatrix)
// discovering cnvs // discovering cnvs
......
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