Nothing
test_that("reading VCF's works", {
vcf_file <- system.file("tests/testthat/sim.vcf.gz", package = "GenoPop")
index_file <- system.file("tests/testthat/sim.vcf.gz.tbi", package = "GenoPop")
# Check that both files exist
expect_true(file.exists(vcf_file))
expect_true(file.exists(index_file))
x <- process_vcf_in_batches(vcf_file, batch_size = 100, custom_function = function(index, fix, sep_gt, chrom, start_pos, end_pos, pop1_individuals = NULL, pop2_individuals = NULL) {
return(sep_gt)
})
expect_true(class(x) == "list")
expect_true(class(x[[1]])[1] == "matrix")
y <- process_vcf_in_windows(vcf_file, window_size = 50000, skip_size = 10000, custom_function = function(index, fix, sep_gt, chrom, start_pos, end_pos, pop1_individuals = NULL, pop2_individuals = NULL) {
return(sep_gt)
})
expect_true(class(y) == "list")
expect_true(class(y[[1]])[1] == "matrix")
})
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