Nothing
genome_path <- system.file("extdata", "hg19.chrom.sizes.gz", package = "valr")
genome <- read_genome(genome_path)
test_that("genomes are correctly read", {
expect_equal(nrow(genome), 25)
expect_equal(colnames(genome), c("chrom", "size"))
expect_true("data.frame" %in% class(genome))
})
test_that("unbounded intervals are removed", {
x <- tibble::tribble(
~chrom, ~start, ~end,
"chr1", -100, 500,
"chr1", 100, 1e9,
"chr1", 500, 1000
)
expect_equal(nrow(bound_intervals(x, genome)), 1)
})
test_that("trim param removes dangling intervals", {
x <- tibble::tribble(
~chrom, ~start, ~end,
"chr1", 1, 249250721
)
res <- bound_intervals(x, genome, trim = TRUE)
expect_equal(res$end, 249250621)
})
test_that("duplicate chroms throw an error.", {
genome <- tibble::tribble(
~chrom, ~size,
"chr1", 1000,
"chr1", 1000
)
x <- tibble::tribble(
~chrom, ~start, ~end,
"chr1", 1, 10000
)
expect_error(bed_complement(x, genome))
})
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