context("long reads")
flog.threshold(WARN)
test_that("configuration is good", {
config <- config_align()
expect_type(config, "list")
expect_s3_class(config, "config")
expect_true(length(config) > 3)
config <- config_preprocess(threads = 2)
expect_equal(config$threads, 2)
})
path <- system.file("extdata/nanopore", package = "mbtools")
ref <- system.file("extdata/genomes/zymo_mock.fna.gz",
package = "mbtools")
files <- find_read_files(path)[1:2]
test_that("alignments work", {
alns <- align_long_reads(files,
alignment_dir = file.path(tempdir(), "aln"),
reference = ref)
expect_named(alns, c("alignments", "logs", "disk_size", "steps"))
expect_s3_class(alns$alignments, "data.table")
expect_true(alns$alignments[, all(success)])
expect_true(alns$alignments[, all(file.exists(alignment))])
})
flog.threshold(INFO)
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