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#' Read a VCF file.
#'
#' @param vcf vcf filename
#'
#' @family read functions
#' @return `data_frame`
#'
#' @note return value has `chrom`, `start` and `end` columns.
#' Interval lengths are the size of the 'REF' field.
#'
#' @examples
#' vcf_file <- valr_example("test.vcf.gz")
#' read_vcf(vcf_file)
#'
#' @export
read_vcf <- function(vcf) {
check_required(vcf)
res <- suppressMessages(readr::read_tsv(vcf, comment = "##"))
colnames(res) <- stringr::str_replace(colnames(res), "^#", "")
res <- mutate(
res,
chrom = stringr::str_c("chr", CHROM),
start = POS,
end = POS + stringr::str_length(REF)
)
res
}
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