An all R GenomicRanges::order implementation

GenomicRanges-comparison.R

setMethod("order", "GenomicRanges",
    function(..., ignore.strand=FALSE, na.last=TRUE, decreasing=FALSE) {
        if (!isTRUEorFALSE(decreasing)) {
            stop("'decreasing' must be TRUE or FALSE")
        }
        args <- list(...)
        if (length(args) != 1L) {
            stop("ordering more than one GRanges is undefined")
        }
        x <- args[[1L]]
        seqnames.order <- seqlevels(x)
        
        ordered <- integer(length(x))
        iranges <- ranges(x)
        sofar <- 0L
        
        ## Logical operations over the vectors are noticably faster than the
        ## same over Rle's returned from seqnames() and strand()
        all.seqnames <- as.vector(seqnames(x))
        is.seqname <- lapply(seqnames.order, function(seqname) {
            all.seqnames == seqname
        })
        
        if (ignore.strand) {
          for (which.seq in is.seqname) {
              take <- which(which.seq)
              n <- length(take)
              if (n > 0L) {
                  o <- order(iranges[take], decreasing=decreasing)
                  ordered[seq_along(o) + sofar] <- take[o]
                  sofar <- sofar + n
              }
          }
        } else {
            all.strands <- as.vector(strand(x))
            is.strand <- lapply(levels(strand()), function(.strand) {
                all.strands == .strand
            })
            
            for (which.seq in is.seqname) {
                for (which.strand in is.strand) {
                    take <- which(which.seq & which.strand)
                    n <- length(take)
                    if (n > 0L) {
                        o <- order(iranges[take], decreasing=decreasing)
                        ordered[seq_along(o) + sofar] <- take[o]
                        sofar <- sofar + n
                    }
                }
            }
        }
        
        ordered
    })

setMethod("sort", "GenomicRanges",
    function(x, decreasing=FALSE, ...) {
        x[order(x, decreasing=decreasing)]
    })