plot_base_quality returns ggplot with overlap box

plot_base_quality downsamples if more than 10 000 reads

"Invalid value for 'strand'. Choose from 'plus' or 'both'.")
test_that("error when lca_cutoff value is out of range", {
"Invalid value for 'lca_cutoff'. Must be between 0.5 and 1.0.")
test_that("error when wrong columns in fastx_input fastq", {
fastx_input <- readRDS(test_path("testdata", "R1_fastq_df.rds")) |>
db <- readRDS(test_path("testdata", "output", "merged_fq_files_fq_tibble.rds"))
test_that("error when wrong columns in db fastq", {
db <- readRDS(test_path("testdata", "output", "merged_fq_files_fq_tibble.rds"))|>
test_that("error when wrong columns in fastx_input fasta", {
db <- readRDS(test_path("testdata", "output", "merged_fq_files_fq_tibble.rds")) |>
"FASTA object must contain columns: Header and Sequence")
test_that("error when wrong columns in db fasta", {
test_that("error when fastx_input does not exist", {
paste0("Cannot find input file: ", fastx_input))
test_that("error when db does not exist", {
test_that("allignment with default values with fasta files as input", {
return_value <- vs_alignment_classification(fastx_input = fastx_input,
expected <- read.delim(test_path("testdata", "output", "alignment_classification_default.tsv"),
test_that("allignment with default values with fasta tables as input, and table as output", {
expected <- readRDS(test_path("testdata", "output", "alignment_classification_default.rds"))
test_that("alignment returns tibble with top_hits_only = TRUE", {
test_that("alignment runs with strand = 'both'", {
test_that("character FASTQ input path is handled and joined back to sequences", {
fq_file <- withr::local_tempfile(fileext = ".fq")
fastx_input = fq_file,   # karaktersti -> dekker readFastq + header-rydding
test_that("non-NULL tmpdir is accepted and used", {
test_that("alignment accepts FASTQ tibble as database (covers writeFastq branch)", {
db_fastq_tbl <- readRDS(test_path("testdata", "output", "merged_fq_files_fq_tibble.rds"))

"Invalid value for 'strand'. Choose from 'plus' or 'both'."
"error when lca_cutoff value is out of range"
"Invalid value for 'lca_cutoff'. Must be between 0.5 and 1.0."
"error when wrong columns in fastx_input fastq"
"error when wrong columns in fastx_input fasta"
"FASTA object must contain columns: Header and Sequence"
"allignment with default values with fasta files as input"
"allignment with default values with fasta tables as input, and table as output"
"alignment returns tibble with top_hits_only = TRUE"
"character FASTQ input path is handled and joined back to sequences"
# karaktersti -> dekker readFastq + header-rydding
"alignment accepts FASTQ tibble as database (covers writeFastq branch)"