admixtools_present <- function() {
as.vector(Sys.which("qpDstat") != "")
}
read_pops <- function(filename, columns) {
df <- setNames(read.table(filename, stringsAsFactors = FALSE), columns)
lapply(df, function(col) unique(col))
}
read_snp_file <- function(path) {
readr::read_table2(
path,
col_types = "ccdicc",
col_names = c("id", "chrom", "gen", "pos", "ref", "alt")
)
}
snp_to_bed <- function(snp, bed) {
read_snp_file(snp) %>%
dplyr::mutate(start = pos - 1, end = pos) %>%
dplyr::select(chrom, start, end) %>%
readr::write_tsv(bed, col_names = FALSE)
}
# Find the path to the root of the ADMIXTOOLS directory
admixtools_path <- function() {
path <- Sys.which("qpDstat")
is_symlink <- base::isTRUE(base::nzchar(base::Sys.readlink(path), keepNA = TRUE))
if (is_symlink) path <- Sys.readlink(path)
stringr::str_replace(path, "/bin.*", "")
}
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