context("Masking non-standard DNA bases")
test_that("stddna returns GRanges-class for Views", {
expect_is(stddna_from_views(views), "GRanges")
})
test_that("stddna validates bsgenome", {
expect_error(stddna_from_genome(NULL), "BSgenomeViews")
expect_error(stddna_from_genome(GRanges()), "BSgenomeViews")
expect_error(stddna_from_genome("sacCer2"), "BSgenomeViews")
expect_error(stddna_from_genome("BSgenome.Scerevisiae.UCSC.sacCer2"),
"BSgenomeViews")
})
test_that("stddna returns empty XRanges for empty Views", {
gr_ <- GRanges(seqinfo = seqinfo(bsgenome))
views_ <- Views(bsgenome, gr_)
expect_is(stddna_from_views(views_), "GRanges")
expect_equal(stddna_from_views(views_), gr_)
})
test_that("stddna returns correct GRanges value for Views", {
result <- stddna_from_views(views)
expect_equal(sort(result),
reduce(gr))
expect_true(GenomicRanges::isDisjoint(stddna_from_views(views)))
})
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