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)
})
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