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Added read.genepop() to greedyMix() (closes #19)

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This commit is contained in:
Waldir Leoncio 2022-01-27 11:16:32 +01:00
parent c5cf0edd1d
commit 95ff85f021
2 changed files with 117 additions and 2 deletions
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11
R/greedyMix.R
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@ -5,6 +5,7 @@
#' @importFrom utils read.delim
#' @importFrom vcfR read.vcfR
#' @importFrom Rsamtools scanBam
#' @importFrom adegenet read.genepop .readExt
#' @references Samtools: a suite of programs for interacting
#' with high-throughput sequencing data. <http://www.htslib.org/>
#' @export
@ -33,8 +34,14 @@ greedyMix <- function(data, format, verbose = TRUE) {
} else if (format == "bam") {
out <- Rsamtools::scanBam(data)
} else if (format == "genepop") {
# TODO #19: implement load_genepop()
stop("GenePop files not yet supported.")
if (toupper(adegenet::.readExt(data)) == "TXT") {
message("Creating a copy of the file with the .gen extension")
dataGen <- gsub("txt", "gen", data)
file.copy(data, dataGen)
out <- adegenet::read.genepop(dataGen)
} else {
out <- adegenet::read.genepop(data)
}
} else {
stop("Format not supported.")
}