tests/testthat/test-get_vcf_info_dt.R

In andrewrech/antigen.garnish: Tumor neoantigen prediction

testthat::test_that("get_vcf_info_dt", {

  # load test data

  d <- test_data_dir()

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

  testthat::expect_true((dt %>% names()) %chin%
    c(
      "CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO",
      "AC", "AF", "AN", "DB", "SOMATIC", "VT", "set", "OnTarget", "SM0",
      "SM1", "SM2", "SM3", "SM4", "SM5", "SM6", "SM7", "GM0", "GM1", "GM2",
      "GM3", "GM4", "GM5", "GM6", "GM7", "GCONTHIGH", "GCONTLOW",
      "GHOMOZYGOUS", "ML.SOMATIC", "ML.M", "ML.C", "ML.M.SEGMENT", "ML.AR",
      "CF", "PS", "LR", "ANN", "Cosmic.CNT", "LOF", "ML.LOH", "V1"
    ) %>% all())

  testthat::expect_equal(dt %>% nrow(), 61)
  testthat::expect_equal(dt %>% length(), 47)
})