improve vcf tests

EvolEcolGroup · May 13, 2024 · 9eb84cd · 9eb84cd
1 parent a7e28ec
commit 9eb84cd
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Showing 2 changed files with 7 additions and 1 deletion.
diff --git a/R/utils.R b/R/utils.R
@@ -21,6 +21,7 @@ tidy_dist_matrix<- function(mat){
   xy %>% tibble::as_tibble() %>%
     dplyr::mutate(value=mat[xy])
 }
+
 # stop if not diploid
 stopifnot_diploid <- function(x){
   if (attr(x,"ploidy")!=2){

diff --git a/tests/testthat/test_gen_tibble.R b/tests/testthat/test_gen_tibble.R
@@ -91,6 +91,11 @@ test_that("gen_tibble from files",{
   # now read in vcf
   vcf_path <- system.file("extdata/pop_a.vcf", package = "tidypopgen")
   pop_a_vcf_gt <- gen_tibble(vcf_path, quiet=TRUE,backingfile = tempfile())
-  all.equal(show_genotypes(pop_a_gt),show_genotypes(pop_a_vcf_gt))
+  expect_true(all.equal(show_genotypes(pop_a_gt),show_genotypes(pop_a_vcf_gt)))
+  # reload it in chunks
+  pop_a_vcf_gt2 <- gen_tibble(vcf_path, quiet=TRUE,backingfile = tempfile(), loci_per_chunk=2)
+  expect_true(all.equal(show_genotypes(pop_a_vcf_gt2),show_genotypes(pop_a_vcf_gt)))
+  expect_true(all.equal(show_loci(pop_a_vcf_gt2),show_loci(pop_a_vcf_gt)))
+  # we should add similar tests for pop b, which has missing data
 
 })