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context("test-get_indel_context")
## Get a GRangesList object with only indels.
indel_grl <- readRDS(system.file("states/blood_grl_indel.rds",
package = "MutationalPatterns"
))
## Load the corresponding reference genome.
ref_genome <- "BSgenome.Hsapiens.UCSC.hg19"
library(ref_genome, character.only = TRUE)
## Get the indel contexts
output <- get_indel_context(indel_grl, ref_genome)
expected <- readRDS(system.file("states/blood_grl_indel_context.rds",
package = "MutationalPatterns"
))
test_that("Output has correct class", {
expect_true(inherits(output, c("GRanges", "CompressedGRangesList")))
})
test_that("Output is equal to expected", {
expect_equal(output, expected)
})
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