Nothing
test_that("VCFArraySeed arguments check works", {
## singleString input
fl <- system.file("extdata", "chr22.vcf.gz",
package="VariantAnnotation")
vcf <- VcfFile(fl)
seed <- VCFArraySeed(fl, name = "GT")
expect_s4_class(seed, "VCFArraySeed")
## "index": input is indexed "VcfFile", and the "index" argument
## is not NULL.
expect_error(VCFArraySeed(vcf, index=index(vcf), name="DS"))
index(vcf) <- NA
seed <- VCFArraySeed(vcf, name="DS")
expect_true(validObject(seed))
index(vcf) <- NA
index <- paste(path(vcf), "tbi", sep=".")
seed <- VCFArraySeed(vcf, vindex = index, name="DS")
expect_true(validObject(seed))
expect_equal(index(vcffile(seed)), index)
## "name"
expect_error(VCFArraySeed(fl, name = "inValidName"))
expect_error(VCFArraySeed(fl))
})
test_that("VCFArraySeed and VCFArray constructor works", {
fl <- system.file("extdata", "chr22.vcf.gz",
package="VariantAnnotation")
## geno()
seed <- VCFArraySeed(fl, name = "GT")
expect_true(validObject(seed))
expect_identical(dim(seed), c(10376L, 5L))
## info()
seed <- VCFArraySeed(fl, name = "LDAF")
expect_equal(dim(seed), 10376L)
va <- VCFArray(seed)
expect_true(validObject(va))
expect_identical(dim(seed), dim(va))
fl1 <- SeqArray::seqExampleFileName("vcf")
expect_error(VCFArraySeed(fl1, name = "DP")) ## multiple "DP" record
va <- VCFArray(fl1, name="DP", pfix="info")
expect_identical(dim(va), 1348L)
## fixed()
seed <- VCFArraySeed(fl, name = "REF")
expect_equal(dim(seed), 10376L)
va <- VCFArray(seed)
va1 <- VCFArray(fl, name = "REF")
expect_equal(va, va1)
## XStringSetList, IntegerList...
va <- VCFArray(fl, name = "CIEND")
expect_true(validObject(va))
## DelayedArray::type(va), "IntegerList"
##----------------
## RangedVcfStack
##----------------
extdata <- system.file(package = "GenomicFiles", "extdata")
files <- dir(extdata, pattern="^CEUtrio.*bgz$", full=TRUE)[1:2]
names(files) <- sub(".*_([0-9XY]+).*", "\\1", basename(files))
seqinfo <- as(readRDS(file.path(extdata, "seqinfo.rds")), "Seqinfo")
stack <- GenomicFiles::VcfStack(files, seqinfo)
gr <- as(GenomicFiles::seqinfo(stack)[rownames(stack)], "GRanges")
rgstack <- GenomicFiles::RangedVcfStack(stack, rowRanges = gr)
## geno()
seed <- VCFArraySeed(rgstack, name = "GT")
expect_identical(dim(seed), c(318L, 3L))
## fixed()
seed <- VCFArraySeed(rgstack, name = "FILTER")
expect_identical(dim(seed), 318L)
va <- VCFArray(seed)
expect_s4_class(va, "VCFArray")
## info()
seed <- VCFArraySeed(rgstack, name = "set")
expect_identical(dim(seed), 318L)
## 3-dim array
seed <- VCFArraySeed(rgstack, name = "SB")
va <- VCFArray(seed)
expect_identical(dim(va), c(318L, 3L, 4L))
expect_s4_class(va, "VCFArray")
va1 <- VCFArray(rgstack, name = "SB")
expect_identical(va, va1)
})
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