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Adjusted unit tests for #25

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This commit is contained in:
Waldir Leoncio 2023-09-11 13:14:23 +02:00
parent 2b756576ac
commit ce954bf801
1 changed files with 16 additions and 6 deletions
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22
tests/testthat/test-greedyMix.R
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@ -33,24 +33,25 @@ test_that("handleData works as expected", {
context("Processing files through greedyMix") context("Processing files through greedyMix")
df_fasta <- greedyMix( raw_fasta <- importFile(
data = file.path(path_inst, "FASTA_clustering_haploid.fasta"), data = file.path(path_inst, "FASTA_clustering_haploid.fasta"),
format = "FASTA" format = "FASTA"
) )
df_vcf <- greedyMix( raw_vcf <- importFile(
data = file.path(path_inst, "vcf_example.vcf"), data = file.path(path_inst, "vcf_example.vcf"),
format = "VCF", format = "VCF",
verbose = FALSE verbose = FALSE
) )
df_bam <- greedyMix( df_bam <- importFile(
data = file.path(path_inst, "bam_example.bam"), data = file.path(path_inst, "bam_example.bam"),
format = "BAM", format = "BAM",
) )
test_that("Files are imported correctly", { test_that("Files are imported correctly", {
expect_equal(dim(df_fasta), c(5, 99)) expect_equal(dim(raw_fasta), c(5, 99))
expect_equal(dim(df_vcf), c(variants = 2, fix_cols = 8, gt_cols = 3)) expect_equal(dim(raw_vcf), c(variants = 2, fix_cols = 8, gt_cols = 3))
expect_error( expect_error(
greedyMix( importFile(
data = paste(path_inst, "sam_example.sam", sep = "/"), data = paste(path_inst, "sam_example.sam", sep = "/"),
format = "SAM", format = "SAM",
) )
@ -58,6 +59,15 @@ test_that("Files are imported correctly", {
expect_equal(length(df_bam[[1]]), 13) expect_equal(length(df_bam[[1]]), 13)
}) })
df_fasta <- greedyMix(
data = file.path(path_inst, "FASTA_clustering_haploid.fasta"),
format = "FASTA"
)
test_that("greedyMix() works", {
expect_error(greedyMix(file.path(path_inst, "vcf_example.vcf")))
expect_error(greedyMix(file.path(path_inst, "bam_example.bam")))
})
context("Linkage") context("Linkage")
test_that("Linkages are properly calculated", { test_that("Linkages are properly calculated", {