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context("test-mutations_from_vcf")
# Read vcfs
vcfs <- readRDS(system.file("states/read_vcfs_as_granges_output.rds",
package = "MutationalPatterns"
))
vcf <- vcfs[[1]]
# Run function
output <- mutations_from_vcf(vcf)
# Check it works on empty input
output_empty <- mutations_from_vcf(vcf[0])
# Check it works on lowercase input
vcf_lowercase <- vcf
colnames(mcols(vcf_lowercase)) <- c("paramRangeID", "ref", "alt", "QUAL", "FILTER")
output_lowercase <- mutations_from_vcf(vcf_lowercase)
# Check it gives a warning on data with no ref or alt
vcf_noref <- vcf
colnames(mcols(vcf_noref)) <- c("paramRangeID", "a", "ALT", "QUAL", "FILTER")
vcf_noalt <- vcf
colnames(mcols(vcf_noalt)) <- c("paramRangeID", "REF", "a", "QUAL", "FILTER")
# Unit tests
test_that("Output has correct class", {
expect_true(inherits(output, c("character")))
expect_true(inherits(output_empty, c("character")))
})
test_that("The 12 substitution types are returned", {
types <- sort(unique(output))
expect_equal(types, c(
"A>C", "A>G", "A>T", "C>A", "C>G", "C>T",
"G>A", "G>C", "G>T", "T>A", "T>C", "T>G"
))
})
test_that("GRanges with 0 muts as input gives empty output", {
expect_equal(length(output_empty), 0)
})
test_that("Input with lowercase doesn't change result", {
expect_equal(output, output_lowercase)
})
test_that("GR with no REF or ALT gives an error.", {
expect_error(
{
output_noref <- mutations_from_vcf(vcf_noref)
},
"missing a REF column"
)
expect_error(
{
output_noalt <- mutations_from_vcf(vcf_noalt)
},
"missing a ALT column"
)
})
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