Add a converter from _CNEr_'s Axt and GPairs format to GBreaks

[charles-plessy]

Something like:

GPairs2GBreaks <- function(GPairs, tGenome = NULL, qGenome = NULL, fix = TRUE) {
  if(isTRUE(fix))
    GPairs <- fixCoordinates(GPairs)
  target <- granges(first(GPairs))
  if(! is.null(tGenome))
    target <- GRanges(target, seqinfo = seqinfo(tGenome))
  query <- granges(second(GPairs))
  if(! is.null(qGenome))
    query <- GRanges(query, seqinfo = seqinfo(qGenome))
  gb <- GBreaks(target = target, query = query)
  ### Remove this once Issue 9 is resolved
  strand(gb) <- strand(gb$query)
  strand(gb$query) <- "*"
  ###
  mcols(gb) <- cbind(mcols(gb), mcols(GPairs))
  sort(gb, ignore.strand = TRUE)
}