inst/registered/UCSC_genomes/hg16.R

In Bioconductor/GenomeInfoDb: Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

GENOME <- "hg16"
ORGANISM <- "Homo sapiens"
ASSEMBLED_MOLECULES <- paste0("chr", c(1:22, "X", "Y", "M"))
CIRC_SEQS <- "chrM"

.random_sequences <- paste0("chr", c(1:10, 13, 15, 17:19, "X", "Un"),
                            "_random")

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

FETCH_ORDERED_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)
}

#.special_mappings <- c(chr5_random="Hs5_79578",
#                       chr13_random="Hs13_78161",
#                       chr18_random="Hs18_79637",
#                       chr19_random="Hs19_78172")

NCBI_LINKER <- list(
    assembly_accession="GCF_000001405.10",
    #special_mappings=.special_mappings,
    unmapped_seqs=list(
        `assembled-molecule`="chrM",
        #`pseudo-scaffold`=setdiff(.random_sequences, names(.special_mappings)))
        `pseudo-scaffold`=.random_sequences)
)