inst/tinytest/test_munge_threading.R

In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

library(tinytest)
library(DBI)

test_munge_threading <- function() {
  con <- rduckhts_connect()
  on.exit(dbDisconnect(con, shutdown = TRUE))

  tmp_dir <- tempfile("duckhts_munge_threading_")
  dir.create(tmp_dir)

  fasta_ref <- file.path(tmp_dir, "munge.fa")
  writeLines(
    c(
      ">chrF",
      "ACGTACGTAA"
    ),
    fasta_ref
  )

  expect_true(rduckhts_fasta_index(
    con,
    fasta_ref,
    index_path = paste0(fasta_ref, ".fai")
  )$success[1])
  expect_silent(dbExecute(con, "PRAGMA threads=4"))

  out <- rduckhts_munge(
    con,
    query = paste(
      "SELECT 'chrF' AS CHR,",
      "2::BIGINT AS BP,",
      "CASE WHEN i % 2 = 0 THEN 'A' ELSE 'C' END AS A1,",
      "CASE WHEN i % 2 = 0 THEN 'C' ELSE 'A' END AS A2,",
      "'rs' || CAST(i AS VARCHAR) AS SNP,",
      "0.1::DOUBLE AS FRQ,",
      "1000::DOUBLE AS N",
      "FROM range(50000) t(i)"
    ),
    fasta_ref = fasta_ref,
    column_map = c(
      CHR = "CHR",
      BP = "BP",
      A1 = "A1",
      A2 = "A2",
      SNP = "SNP",
      FRQ = "FRQ",
      N = "N"
    )
  )

  expect_equal(nrow(out), 50000)
  expect_equal(sum(out$alleles_swapped), 25000)
  expect_equal(sum(is.na(out$filter)), 50000)
}

test_munge_threading()