Nothing
context("dEploid")
vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
package = "DEploid")
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
package = "DEploid")
panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
package = "DEploid")
test_that("printing help & verison information works", {
for (version in list(dEploid("-v"), dEploid("-version"))) {
expect_that(version, is_a("list"))
expect_that(version$version, is_a("character"))
}
expect_error(dEploid("-h"))
expect_error(dEploid("--help"))
})
test_that("parsing arguments works", {
expect_error(dEploid("--version"))
expect_error(dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName)))
expect_error(dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
"-panel", panelFileName, "-noPanel")))
})
test_that("runs a reproducible", {
set.seed(119)
res1 <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
"-noPanel"))
set.seed(119)
res2 <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
"-noPanel"))
expect_equal(res1, res2)
set.seed(119)
res3 <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName, "-panel",
panelFileName))
set.seed(119)
res4 <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName, "-panel",
panelFileName))
expect_equal(res3, res4)
})
test_that("warning is given when using -seed", {
expect_warning(dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
"-noPanel -seed 1")))
})
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