"error when input is fasta and output_format is fastq"
"Invalid output_format when input tibble is of type 'fasta'"
"error if neither sample_size or sample_pct is specified"
"Either sample_size or sample_pct must be specified."
"error if both sample_size and sample_pct are specified"
"Only specify one of the following parameters, not both: sample_size, sample_pct "
"error when fastx_input has incorrect columns if input is fastq tibble"
"error when fastx_input has incorrect columns if input is fasta tibble"
"subsample fastq file with size, and return fastq file"
"subsample fastq file with size, and return fastq tibble"
"subsample fasta file with pct, and return fasta file"
"subsample fasta file with pct, and return fasta tibble"
"subsample fastq file with size, and return fastq file with relabeling"
"subsample fastq file with size, and return fastq file with sha1 relabeling"
"subsample fastq tibble with size, and return fastq tibble"
"subsample fasta tibble with size, and return fasta tibble"
"subsample fastq file with size, and return fastq tibble with vsearch_options"

error when input is fasta and output_format is fastq

error if neither sample_size or sample_pct is specified

error if both sample_size and sample_pct are specified

error when fastx_input has incorrect columns if input is fastq tibble

error when fastx_input has incorrect columns if input is fasta tibble

subsample fastq file with size, and return fastq file

subsample fastq file with size, and return fastq tibble

subsample fasta file with pct, and return fasta file

subsample fasta file with pct, and return fasta tibble

subsample fastq file with size, and return fastq file with relabeling

subsample fastq file with size, and return fastq file with sha1 relabeling

subsample fastq tibble with size, and return fastq tibble

subsample fasta tibble with size, and return fasta tibble

subsample fastq file with size, and return fastq tibble with vsearch_options

test_that("error when output_format is fastq, and fastaout and fastaout_rev are defined", {
"When output_format is defined as 'fastq', 'fastaout' and 'fastaout_rev' cannot be used. Use 'fastqout' and 'fastqout_rev' instead.")
test_that("error when output_format is 'fasta', and fastqout and fastqout_rev are defined", {
"When output_format is defined as 'fasta', 'fastqout' and 'fastqout_rev' cannot be used. Use 'fastaout' and 'fastaout_rev' instead.")
test_that("error when reverse is specified, but output files are not both NULL or both character strings", {
"When 'reverse' is specified and output_format is 'fasta', both 'fastaout' and 'fastaout_rev' must be NULL or both specified as character strings.")
"When 'reverse' is specified and output_format is 'fastq', both 'fastqout' and 'fastqout_rev' must be NULL or both specified as character strings.")
expect_error(vs_fastx_trim_filt(fastx_input = R1, reverse = R2),
test_that("error when reverse has incorrect columns if input is fastq tibble", {
R1 <- readRDS(test_path("testdata", "R1_fasta_df.rds")) |>
R2 <- readRDS(test_path("testdata", "R2_fasta_df.rds")) |>
test_that("error when input file does not exist when output_format is fastq", {
test_that("error when reverse file does not exist when output_format is fastq", {
paste("Cannot find reverse file:", reverse))
test_that("error when input file does not exist when output_format is fasta", {
test_that("error when reverse file does not exist when output_format is fasta", {
test_that("error if reverse input is of type fasta and output_format is fastq", {
test_that("trim/filter fastq sequences from two files, and return two fastq files", {
return_value <- vs_fastx_trim_filt(fastx_input = fastx_input,
test_that("trim/filter fastq sequences from two files, and return fastq tibble", {
trim_filt <- vs_fastx_trim_filt(fastx_input = fastx_input,
test_that("trim/filter fastq sequences from one file, and return fastq tibble", {
test_that("trim/filter fastq sequences from two tibbles, and return fastq tibble", {
test_that("trim/filter fasta sequences from two files, and return two fasta files", {
test_that("trim/filter fasta sequences from two tibbles, and return fasta tibble", {
test_that("trim/filter fastq sequences from two files, and return fastq tibble with stripping", {
test_that("trim/filter fastq sequences from one file with size values, and return fastq tibble", {
fastx_input <- test_path("testdata", "output", "R1_derep.fastq")
test_that("trim/filter fastq sequences from pe_df data frame", {
trim_filt <- vs_fastx_trim_filt(fastx_input = fastx_input)
"fastx_input has class 'pe_df' but no 'reverse' attribute found.")
test_that("trim/filter fasta sequences with wrong parameters", {
expect_true(any(grepl("maxee_rate is ignored for FASTA input", warnings)))
expect_true(any(grepl("truncqual is ignored for FASTA input", warnings)))
expect_true(any(grepl("truncee is ignored for FASTA input", warnings)))
expect_true(any(grepl("truncee_rate is ignored for FASTA input", warnings)))