GENOME <- "monDom5"
ORGANISM <- "Monodelphis domestica"
ASSEMBLED_MOLECULES <- paste0("chr", c(1:8, "X", "M"))
CIRC_SEQS <- "chrM"

library(GenomeInfoDb)  # for fetch_chrom_sizes_from_UCSC()

.order_seqlevels <- function(seqlevels)
{
    ordered_seqlevels <- c(ASSEMBLED_MOLECULES, "chrUn")
    stopifnot(length(seqlevels) == length(ordered_seqlevels))
    idx <- match(ordered_seqlevels, seqlevels)
    stopifnot(!anyNA(idx))
    idx
}

GET_CHROM_SIZES <- function(goldenPath.url=getOption("UCSC.goldenPath.url"))
{
    chrom_sizes <- GenomeInfoDb:::fetch_chrom_sizes_from_UCSC(GENOME,
                                              goldenPath.url=goldenPath.url)
    oo <- .order_seqlevels(chrom_sizes[ , "chrom"])
    S4Vectors:::extract_data_frame_rows(chrom_sizes, oo)
}

NCBI_LINKER <- list(
    assembly_accession="GCF_000002295.2",
    special_mappings=c(chrM="MT"),
    unmapped_seqs=list(`pseudo-scaffold`="chrUn")
)

ENSEMBL_LINKER <- "chromAlias"

