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minor fix bug in loading LD sketch #500

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Merged
danielnachun merged 1 commit into from
May 27, 2026
Merged

minor fix bug in loading LD sketch #500

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11 changes: 7 additions & 4 deletions R/genotype_io.R
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Original file line number Diff line number Diff line change
Expand Up @@ -460,7 +460,7 @@ computeBlockLdCor <- function(handle, snp_idx, backend = "internal",

ext <- tolower(file_ext(path))
if (nzchar(ext)) {
return(switch(ext,
detected <- switch(ext,
"vcf" = "vcf",
"bcf" = "vcf",
"bed" = "plink1",
Expand All @@ -475,16 +475,19 @@ computeBlockLdCor <- function(handle, snp_idx, backend = "internal",
"annot" = "ldsc_annot",
"bw" = "bigwig",
"bigwig" = "bigwig",
stop("Cannot detect format from extension: ", ext)
))
NULL
)
if (!is.null(detected)) return(detected)
}
# No extension — check for plink stem files
# Check for file stems, including dotted prefixes such as sample.EUR.chr21.
if (file.exists(paste0(path, ".pgen")) || file.exists(paste0(path, ".pvar")))
return("plink2")
if (file.exists(paste0(path, ".bed")) || file.exists(paste0(path, ".bim")))
return("plink1")
if (file.exists(paste0(path, ".gds")))
return("gds")
if (nzchar(ext))
stop("Cannot detect format from extension: ", ext)
stop("Cannot detect genotype format for path: ", path)
}

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9 changes: 9 additions & 0 deletions tests/testthat/test_load_genotype.R
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Expand Up @@ -13,6 +13,15 @@ region_sub <- "chr21:17513228-17550000"
n_samples <- 100L
n_variants <- 349L

test_that("format detection supports dotted PLINK2 prefixes", {
tmp <- tempfile("plink2_dotted_prefix_")
prefix <- file.path(dirname(tmp), "ADSP.R4.EUR.chr21")
file.create(paste0(prefix, ".pgen"), paste0(prefix, ".pvar"), paste0(prefix, ".psam"))
on.exit(unlink(paste0(prefix, c(".pgen", ".pvar", ".psam"))), add = TRUE)

expect_equal(pecotmr:::.h2_detect_format(prefix), "plink2")
})

# Shared helper: validate the output structure from load_genotype_region
# (with return_variant_info=TRUE)
check_genotype_result <- function(result, expected_nrow = n_samples, expected_ncol = n_variants,
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