tests/testthat/test-roxytest-testexamples-utils.R

In umccr/gpgr: Genomics Platform Group Reporting

# Generated by roxytest: do not edit by hand!

# File R/utils.R: @testexamples

test_that("Function is_vcf() @ L21", {
  
  x <- system.file("extdata/umccrise/snv/somatic-ensemble-PASS.vcf.gz", package = "gpgr")
  (y <- is_vcf(x))
  tmp_file <- tempfile(pattern = "fakeFile", fileext = "vcf")
  writeLines(c("col1\tcol2\tcol3", "1\t2\t3"), con = tmp_file)
  (z <- is_vcf(tmp_file))
  expect_true(y)
  expect_false(z)
})


test_that("Function vcf_is_empty() @ L97", {
  
  x <- system.file("extdata/umccrise/snv/somatic-ensemble-PASS.vcf.gz", package = "gpgr")
  (y <- vcf_is_empty(x))
  
  tmp1 <- tempfile(pattern = "fakeFile", fileext = "vcf")
  writeLines(c("col1\tcol2\tcol3", "1\t2\t3"), con = tmp1)
  
  
  vcf_cols <- c(
    "#CHROM", "POS", "ID", "REF", "ALT", "QUAL",
    "FILTER", "INFO", "FORMAT"
  )
  tmp2 <- tempfile(pattern = "fakeFile", fileext = "vcf")
  writeLines(paste(vcf_cols, collapse = "\t"), con = tmp2)
  (z <- vcf_is_empty(tmp2))
  
  tmp3 <- tempfile(pattern = "fakeFile", fileext = "FOO")
  writeLines(paste(vcf_cols, collapse = "\t"), con = tmp3)
  
  
  expect_false(y)
  expect_error(vcf_is_empty(tmp1))
  expect_error(vcf_is_empty(tmp3))
})


test_that("Function tsv_is_empty() @ L133", {
  
  
  tmp1 <- tempfile()
  writeLines(c("col1\tcol2\tcol3", "1\t2\t3"), con = tmp1)
  (a <- tsv_is_empty(tmp1))
  
  tmp2 <- tempfile()
  writeLines(c("col1\tcol2\tcol3"), con = tmp2)
  (b <- tsv_is_empty(tmp2))
  
  tmp3 <- tempfile()
  writeLines(c("##meta1", "##meta2", "col1\tcol2\tcol3"), con = tmp3)
  (c <- tsv_is_empty(tmp3))
  expect_false(a)
  expect_true(b)
  expect_true(c)
})