library(tinytest)
library(DBI)

test_liftover_stress <- function() {
  drv <- duckdb::duckdb(config = list(allow_unsigned_extensions = "true"))
  con <- dbConnect(drv)
  on.exit(dbDisconnect(con, shutdown = TRUE))

  expect_silent(rduckhts_load(con))
  expect_silent(dbExecute(con, "PRAGMA threads=4"))

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

  src_fa <- file.path(tmp_dir, "liftover_src.fa")
  dst_fa <- file.path(tmp_dir, "liftover_dst.fa")
  chain_path <- file.path(tmp_dir, "liftover.chain")

  writeLines(c(
    ">chrF",
    "ACGTACGTAA",
    ">chrR",
    "AACCGGTTAA"
  ), src_fa)
  writeLines(c(
    ">chrLiftF",
    "ACGTACGTAA",
    ">chrLiftR",
    "TTAACCGGTT"
  ), dst_fa)
  writeLines(c(
    "chain 100 chrF 10 + 0 10 chrLiftF 10 + 0 10 1",
    "10",
    "",
    "chain 100 chrR 10 + 0 10 chrLiftR 10 - 0 10 2",
    "10"
  ), chain_path)

  expect_true(rduckhts_fasta_index(con, src_fa, index_path = paste0(src_fa, ".fai"))$success[1])
  expect_true(rduckhts_fasta_index(con, dst_fa, index_path = paste0(dst_fa, ".fai"))$success[1])

  expect_silent(dbExecute(
    con,
    paste(
      "CREATE TEMP TABLE stress_input AS",
      "SELECT CASE WHEN i % 2 = 0 THEN 'chrF' ELSE 'chrR' END AS chrom,",
      "2::BIGINT AS pos,",
      "CASE WHEN i % 2 = 0 THEN 'C' ELSE 'A' END AS ref,",
      "CASE WHEN i % 2 = 0 THEN 'T' ELSE 'G' END AS alt",
      "FROM range(1000000) t(i)"
    )
  ))

  out <- rduckhts_liftover(
    con,
    query = "stress_input",
    chain_path = chain_path,
    dst_fasta_ref = dst_fa,
    ref_col = "ref",
    alt_col = "alt",
    src_fasta_ref = src_fa
  )

  expect_equal(nrow(out), 1000000)
  expect_true(all(out$mapped))
  expect_equal(sum(out$reverse_complemented), 500000)
  expect_equal(sum(out$dest_chrom == "chrLiftF"), 500000)
  expect_equal(sum(out$dest_chrom == "chrLiftR"), 500000)
}

test_liftover_stress()
