optimizing truncqual with default values and files as input

optimizing truncqual with tibbles as input

optimizing truncqual with pe_df tibble as input

vs_optimize_truncqual handles vs_fastq_mergepairs failure gracefully

"Only one of 'userout' or 'otutabout' can be specified.")
test_that("search with default values with fastq tibbles as input", {
db <- readRDS(test_path("testdata", "R1_fastq_df.rds"))[1:500, ]
return_value <- vs_search_exact(fastx_input = fastx_input,
colnames(actual) <- c("query", "target", "id", "alnlen",
test_that("search with default values with fasta files as input", {
test_that("search with default values with fasta file and tibble as input", {
db <- readRDS(test_path("testdata", "R1_fastq_df.rds"))[1:500, ] |>
test_that("vs_search_exact returns OTU table tibble when otutabout = TRUE", {
db <- fasta_input[1:10, ]  # ensure exact matches exist
otu_tbl <- vs_search_exact(fastx_input = fasta_input,
test_that("vs_search_exact writes OTU table to file when otutabout is path", {
otu_outfile <- withr::local_tempfile(fileext = ".tsv")
return_val <- vs_search_exact(fastx_input = fasta_input,
test_that("vs_search_exact returns alignment tibble with default userfields", {
out_tbl <- vs_search_exact(fastx_input = fasta_input,
expect_named(out_tbl, c("query", "target", "id", "alnlen", "mism", "opens",
"qlo", "qhi", "tlo", "thi", "evalue", "bits"))

"Only one of 'userout' or 'otutabout' can be specified."
"search with default values with fastq tibbles as input"
"search with default values with fasta files as input"
"search with default values with fasta file and tibble as input"
"vs_search_exact returns OTU table tibble when otutabout = TRUE"
"vs_search_exact writes OTU table to file when otutabout is path"
"vs_search_exact returns alignment tibble with default userfields"

search with default values with fastq tibbles as input

search with default values with fasta files as input

search with default values with fasta file and tibble as input

vs_search_exact returns OTU table tibble when otutabout = TRUE