R/methods-VRangesList-class.R

In VariantAnnotation: Annotation of Genetic Variants

### =========================================================================
### 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)))