test_that("format_pangolin works on pangolin example file", {
pangolin_file <- system.file("extdata", "spliceai_output.pangolin.vcf", package = "splice2neo")
pangolin_df <- parse_pangolin(pangolin_file)
df <- format_pangolin(pangolin_df)
expect_true(nrow(df) >= 10)
expect_true(!"gene_id" %in% names(df))
expect_true(all(df$score > 0))
})
test_that("format_pangolin works on pangolin example file with keep_gene_id = TRUE", {
pangolin_file <- system.file("extdata", "spliceai_output.pangolin.vcf", package = "splice2neo")
pangolin_df <- parse_pangolin(pangolin_file)
df <- format_pangolin(pangolin_df, keep_gene_id = TRUE)
expect_true(nrow(df) >= 10)
expect_true(all(df$score > 0))
expect_true("gene_id" %in% names(df))
expect_true(all(!is.na(df$gene_id)))
})
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