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### =========================================================================
### VRangesList: Where there is an IntegerRanges, there must be a List
### -------------------------------------------------------------------------
###
VRangesList <- function(...) {
new("SimpleVRangesList", GRangesList(..., compress=FALSE),
elementType="VRanges")
}
setMethod("stackSamples", "VRangesList", function(x) {
stacked <- unlist(x, use.names=FALSE)
if (!is.null(names(x)))
sampleNames(stacked) <- Rle(names(x), elementNROWS(x))
stacked
})
setMethod("ref", "VRangesList", function(x) List(lapply(x, ref)))
setMethod("alt", "VRangesList", function(x) List(lapply(x, alt)))
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