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Dropped support for GenePop on importFile()

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File should be handled by `process_GenePop_data()`, as per original BAPS.
This commit is contained in:
Waldir Leoncio 2024-09-13 13:52:39 +02:00
parent 00605016d6
commit 31575a5b9e
1 changed files with 1 additions and 11 deletions
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12
R/importFile.R
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@ -1,6 +1,5 @@
#' @title Import data file
#' @description Imports data from several formats (FASTA, VCF, SAM, BAM,
#' Genepop).
#' @description Imports data from several formats (FASTA, VCF, SAM, BAM).
#' @param data raw dataset
#' @param format data format (guesses from extension if not provided)
#' @param verbose if \code{TRUE}, prints extra output information
@ -33,15 +32,6 @@ importFile <- function(data, format, verbose) {
)
} else if (format == "bam") {
out <- Rsamtools::scanBam(data)
} else if (format == "genepop") {
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.")
}