Nothing
context("getVariant")
test_that("getVariant works", {
skip_on_bioc()
host <- "http://1kgenomes.ga4gh.org/"
datasetId <- searchDatasets(host, nrows = 1)$id
variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id
variantId <- searchVariants(host, variantSetId, referenceName = "1",
start = 15000, end = 16000, nrows = 1, asVCF = FALSE)$id
variant <- getVariant(host, variantId)
expect_s4_class(variant, "VCF")
})
test_that("getVariant asVCF=FALSE works", {
skip_on_bioc()
host <- "http://1kgenomes.ga4gh.org/"
datasetId <- searchDatasets(host, nrows = 1)$id
variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id
variantId <- searchVariants(host, variantSetId, referenceName = "1",
start = 15000, end = 16000, nrows = 1, asVCF = FALSE)$id
variant <- getVariant(host, variantId, asVCF = FALSE)
expect_s4_class(variant, "DataFrame")
expect_equal(ncol(variant), 24)
})
test_that("getVariant multiple alt bases works", {
skip_on_bioc()
library(VariantAnnotation)
host <- "http://1kgenomes.ga4gh.org/"
datasetId <- searchDatasets(host, nrows = 1)$id
variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id
variantId <- searchVariants(host, variantSetId, referenceName = "1",
start = 15274, end = 15274, nrows = 1, asVCF = FALSE)$id
variant.vcf <- getVariant(host, variantId)
expect_equal(alt(variant.vcf), CharacterList("G", "T"))
variant.df <- getVariant(host, variantId, asVCF = FALSE)
expect_equal(dim(variant.df), c(2, 24))
})
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