error when lca_cutoff value is out of range

error when wrong columns in fastx_input fastq

error when wrong columns in fastx_input fasta

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

alignment accepts FASTQ tibble as database (covers writeFastq branch)

test_that("error when input fasta_input does not exist", {
paste("Cannot find input file:", fasta_input))
test_that("error when both outputs are specified", {
"Only one of 'centroids' or 'otutabout' can be specified.")
test_that("cluster sequences from fasta file, and return fasta file", {
return_value <- vs_cluster_size(fasta_input = fasta_input,
test_that("cluster sequences from fasta file, and return fasta tibble", {
cluster_sample1_R1 <- vs_cluster_size(fasta_input = fasta_input,
test_that("cluster sequences from fasta tibble, and return fasta file", {
test_that("cluster sequences from fasta tibble, and return fasta tibble", {
test_that("vs_cluster_size returns OTU table tibble when otutabout = TRUE", {
fasta_input <- microseq::readFasta(test_path("testdata", "R1.fasta")) |>
otu_tbl <- vs_cluster_size(fasta_input = fasta_input,
test_that("vs_cluster_size writes OTU table to file when otutabout is path", {
otutable_out <- withr::local_tempfile(fileext = ".tsv")
return_val <- vs_cluster_size(fasta_input = fasta_input,
test_that("cluster sequences from empty fasta tibble, and return fasta tibble", {
"No centroid sequences were returned by VSEARCH. Check input quality or parameters.")

"error when input fasta_input does not exist"
"Only one of 'centroids' or 'otutabout' can be specified."
"cluster sequences from fasta file, and return fasta file"
"cluster sequences from fasta file, and return fasta tibble"
"cluster sequences from fasta tibble, and return fasta file"
"cluster sequences from fasta tibble, and return fasta tibble"
"vs_cluster_size returns OTU table tibble when otutabout = TRUE"
"vs_cluster_size writes OTU table to file when otutabout is path"
"cluster sequences from empty fasta tibble, and return fasta tibble"
"No centroid sequences were returned by VSEARCH. Check input quality or parameters."