Nothing
test_that("filemismatch12", {
gen3afile <- system.file("extdata", "set3a.imp", package = "BinaryDosage")
gen3asample <- system.file("extdata", "set3a.sample", package = "BinaryDosage")
bdfile3a <- tempfile()
bdfam3a <- tempfile()
bdmap3a <- tempfile()
gentobd(genfiles = c(gen3afile, gen3asample),
snpcolumns = c(0L, 2L:5L),
bdfiles = c(bdfile3a, bdfam3a, bdmap3a),
format = 3)
vcf1basnpfile <- system.file("extdata", "set1b_asnp.vcf", package = "BinaryDosage")
bdfile1basnp <- tempfile()
bdfam1basnp <- tempfile()
bdmap1basnp <- tempfile()
vcftobd(vcffiles = vcf1basnpfile,
bdfiles = c(bdfile1basnp, bdfam1basnp, bdmap1basnp),
format = 3)
expect_error(getbdinfo(bdfiles = c(bdfile1basnp, bdfam3a, bdmap3a)),
"Subject file does not line up with binary dosage file")
vcf2bfile <- system.file("extdata", "set2b.vcf", package = "BinaryDosage")
bdfile2b <- tempfile()
bdfam2b <- tempfile()
bdmap2b <- tempfile()
vcftobd(vcffiles = vcf2bfile,
bdfiles = c(bdfile2b, bdfam2b, bdmap2b),
format = 3)
expect_error(getbdinfo(bdfiles = c(bdfile2b, bdfam3a, bdmap3a)),
"Subject file does not line up with binary dosage file")
})
test_that("filemismatch34", {
gen3afile <- system.file("extdata", "set3a.imp", package = "BinaryDosage")
gen3asample <- system.file("extdata", "set3a.sample", package = "BinaryDosage")
bdfile3a <- tempfile()
bdfam3a <- tempfile()
bdmap3a <- tempfile()
gentobd(genfiles = c(gen3afile, gen3asample),
snpcolumns = c(0L, 2L:5L),
bdfiles = c(bdfile3a, bdfam3a, bdmap3a),
format = 3)
vcf1basnpfile <- system.file("extdata", "set1b_asnp.vcf", package = "BinaryDosage")
bdfile1basnp <- tempfile()
bdfam1basnp <- tempfile()
bdmap1basnp <- tempfile()
vcftobd(vcffiles = vcf1basnpfile,
bdfiles = c(bdfile1basnp, bdfam1basnp, bdmap1basnp),
format = 3,
subformat = 4)
expect_error(getbdinfo(bdfiles = c(bdfile1basnp, bdfam3a, bdmap3a)),
"Subject file does not line up with binary dosage file")
expect_error(getbdinfo(bdfiles = c(bdfile1basnp, bdfam1basnp, bdmap3a)),
"Map file does not line up with binary dosage file")
vcf2bfile <- system.file("extdata", "set2b.vcf", package = "BinaryDosage")
bdfile2b <- tempfile()
bdfam2b <- tempfile()
bdmap2b <- tempfile()
vcftobd(vcffiles = vcf2bfile,
bdfiles = c(bdfile2b, bdfam2b, bdmap2b),
format = 3,
subformat = 3)
expect_error(getbdinfo(bdfiles = c(bdfile2b, bdfam3a, bdmap3a)),
"Subject file does not line up with binary dosage file")
expect_error(getbdinfo(bdfiles = c(bdfile2b, bdfam2b, bdmap3a)),
"Map file does not line up with binary dosage file")
})
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