tests/testthat/test-get_vcf_sample_dt.R

In immune-health/antigen.garnish: Tumor neoantigen prediction

testthat::test_that("get_vcf_sample_dt", {
  d <- test_data_dir()

  # load test data

  dt <- file.path(d, "antigen.garnish_test.vcf") %>%
    vcfR::read.vcfR(verbose = TRUE) %>%
    antigen.garnish:::get_vcf_sample_dt()

  # run test

  testthat::expect_equal(
    dt %>% names(),
    c(
      "FORMAT",
      "normal_sample",
      "tumor_sample",
      "normal_sample_GT",
      "normal_sample_BQ",
      "normal_sample_DP",
      "normal_sample_FA",
      "normal_sample_SS",
      "tumor_sample_GT",
      "tumor_sample_BQ",
      "tumor_sample_DP",
      "tumor_sample_FA",
      "tumor_sample_SS",
      "normal_sample_AD_ref",
      "normal_sample_AD_alt",
      "tumor_sample_AD_ref",
      "tumor_sample_AD_alt"
    )
  )

  testthat::expect_equal(dt %>% nrow(), 61)
  testthat::expect_equal(dt %>% length(), 17)
})