Nothing
test_that("set_tools", {
config.file <- system.file("extdata", "demo/tools_config.json", package = "ngstk")
config.list <- list(gatk = "/path/gatk")
config.vec <- c("/path/samtools")
names(config.vec) <- "samtools"
tools <- set_tools(config.file, config.list, config.vec, eval.params = list(config = "tools"))
expect_that(is.list(tools), equals(TRUE))
expect_that(length(tools), equals(3))
expect_that(names(tools)[1], equals("gmap"))
})
test_that("set_colors", {
red_blue <- set_colors("red_blue")
expect_that(length(red_blue) > 0, equals(TRUE))
default <- set_colors("default")
expect_that(length(default) > 0, equals(TRUE))
colors <- set_colors(show_all_themes = TRUE)
expect_that(is.list(colors), equals(TRUE))
})
test_that("batch_file", {
dat <- data.frame(a = 1:100, b = 1:100)
filename <- tempfile()
write.table(dat, filename, sep = "\t", row.names = F, quote = F)
handler_fun <- function(x, i = 1, ...) {
return(x[i])
}
x <- batch_file(filename = filename, batch_lines = 10, handler = handler_fun)
expect_that(x[[1]], equals("a\tb"))
x <- batch_file(filename = filename, batch_lines = 10, handler = handler_fun,
extra_fread_params = list(sep = "\t", header = FALSE, return_1L = FALSE))
x <- rbindlist(x)
expect_that(nrow(x), equals(10))
})
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