Commit 71705119 authored by Sander Bollen's avatar Sander Bollen
Browse files

add all ze options

parent 833cf3c1
......@@ -69,5 +69,19 @@ class VcfFilter(val root: Configurable) extends ToolCommandFunction {
optional("--minAlternateDepth", minAlternateDepth) +
optional("--minSamplesPass", minSamplesPass) +
optional("--minGenomeQuality", minGenomeQuality) +
conditional(filterRefCalls, "--filterRefCalls")
conditional(filterRefCalls, "--filterRefCalls") +
optional("--invertedOutputVcf", invertedOutputVcf) +
optional("--resToDom", resToDom) +
optional("--trioCompound", trioCompound) +
optional("--deNovoInSample", deNovoInSample) +
optional("--deNovoTrio", deNovoTrio) +
optional("--trioLossOfHet", trioLossOfHet) +
repeat("--mustHaveVariant", mustHaveVariant) +
repeat("--calledIn", calledIn) +
repeat("--mustHaveGenotype", mustHaveGenotype) +
repeat("--diffGenotype", diffGenotype) +
repeat("--filterHetVarToHomVar", filterHetVarToHomVar) +
optional("--minQualScore", minQualScore) +
repeat("--id", id) +
optional("--idFile", idFile)
}
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