context("readLogRatioFile")
data(purecn.example.output)
test_that("Example data matches", {
logratio.file <- system.file("extdata", "example_gatk4_denoised_cr.tsv.gz",
package = "PureCN")
logratio <- readLogRatioFile(logratio.file)
expect_equal(21, length(logratio))
expect_equal(0.109473, logratio$log.ratio[1], tolerance = .00001)
expect_equal(-0.185664, logratio$log.ratio[21], tolerance = .00001)
expect_equivalent(seqlengths(logratio), c(248956422, 242193529, 156040895))
logratio.file2 <- system.file("extdata", "example_logratio.txt.gz",
package = "PureCN")
logratio2 <- readLogRatioFile(logratio.file2)
expect_equal(as.character(logratio), as.character(logratio2))
expect_equal(logratio$log.ratio, logratio2$log.ratio)
})
test_that("parsing -> writing -> parsing works", {
x <- purecn.example.output$input
y <- x
y$log.ratio$log.ratio <- NULL
output.file <- tempfile(fileext = ".tsv")
expect_error(
PureCN:::.writeLogRatioFileGATK4(y, 1, output.file),
"log.ratio NULL"
)
PureCN:::.writeLogRatioFileGATK4(x, 1, output.file)
z <- readLogRatioFile(output.file)
expect_equivalent(x$log.ratio$log.ratio, z$log.ratio)
file.remove(output.file)
})
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