x <- tibble::tribble(
  ~chrom , ~start , ~end , ~name ,
  "chr1" ,    100 ,  200 , "A"   ,
  "chr2" ,    300 ,  350 , "B"
)

# Window IDs are generated
test_that("window IDs are generated", {
  res <- bed_makewindows(x, win_size = 10)
  expect_true(".win_id" %in% colnames(res))
})

# Fixed win_size with foward numbering
test_that("win_size fwd", {
  res <- bed_makewindows(x, win_size = 10)
  # test number of windows
  expect_equal(nrow(res), 15)
  # test forward window numbering
  expect_true(all(res$.win_id == c(1:10, 1:5)))
  # test interval size
  expect_true(all(res$end - res$start == 10))
})

# Fixed win_size with reverse numbering
test_that("win_size rev", {
  res <- bed_makewindows(x, reverse = TRUE, win_size = 10)
  # test number of windows
  expect_equal(nrow(res), 15)
  # test forward window numbering
  expect_true(all(res$.win_id == c(10:1, 5:1)))
  # test interval size
  expect_true(all(res$end - res$start == 10))
})

# Fixed win_size +step_size with forward numbering
test_that("win_size +step_size fwd", {
  res <- bed_makewindows(x, win_size = 10, step_size = 5)
  # test number of windows
  expect_equal(nrow(res), 30)
  # test forward window numbering
  expect_true(all(res$.win_id == c(1:20, 1:10)))
  # test interval size
  expect_true(all(
    res[1:19, "end"] - res[1:19, "start"] == 10 &
      res$end[20] - res$start[20] == 5
  ))
  expect_true(all(
    res[21:29, "end"] - res[21:29, "start"] == 10 &
      res$end[30] - res$start[30] == 5
  ))
})

# Fixed win_size +step_size with reverse numbering
test_that("win_size +step_size rev", {
  res <- bed_makewindows(x, reverse = TRUE, win_size = 10, step_size = 5)
  # test number of windows
  expect_equal(nrow(res), 30)
  # test forward window numbering
  expect_true(all(res$.win_id == c(20:1, 10:1)))
  # test interval size
  expect_true(all(
    res[1:19, "end"] - res[1:19, "start"] == 10 &
      res$end[20] - res$start[20] == 5
  ))
  expect_true(all(
    res[21:29, "end"] - res[21:29, "start"] == 10 &
      res$end[30] - res$start[30] == 5
  ))
})

# Fixed number of windows with forward numbering
test_that("num_win fwd", {
  res <- bed_makewindows(x, num_win = 10)
  # test number of windows
  expect_equal(nrow(res), 20)
  # test forward window numbering
  expect_true(all(res$.win_id == c(1:10, 1:10)))
  # test interval size
  expect_true(all(res[1:10, "end"] - res[1:10, "start"] == 10))
  expect_true(all(res[11:20, "end"] - res[11:20, "start"] == 5))
})

# Fixed number of windows with reverse numbering
test_that("num_win rev", {
  res <- bed_makewindows(x, reverse = TRUE, num_win = 10)
  # test number of windows
  expect_equal(nrow(res), 20)
  # test forward window numbering
  expect_true(all(res$.win_id == c(10:1, 10:1)))
  # test interval size
  expect_true(all(res[1:10, "end"] - res[1:10, "start"] == 10))
  expect_true(all(res[11:20, "end"] - res[11:20, "start"] == 5))
})

test_that("interval is smaller than n windows", {
  # test warning
  expect_message(bed_makewindows(x, num_win = 150))
  # test that intervals are dropped if num_win > than interval size
  res <- suppressMessages(bed_makewindows(x, num_win = 150))
  expect_equal(nrow(res), 0)
})

# from https://github.com/arq5x/bedtools2/blob/master/test/makewindows/test-makewindows.sh
test_that("always get the number of requested windows. issue #322", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end , ~name ,
    "chr1" ,     11 ,   44 , "A"
  )
  res <- bed_makewindows(x, num_win = 10)
  expect_equal(nrow(res), 10)
  expect_equal(res$start[10], 38)
  expect_equal(res$end[10], 44)
})

test_that("report error if negative value win_size or num_win arguments supplied", {
  expect_error(bed_makewindows(x, num_win = -1))
  expect_error(bed_makewindows(x, win_size = -1))
})

test_that("check num_win reported correctly for additional intervals (related to #322)", {
  x <- tibble::tribble(
    ~chrom , ~start   , ~end     ,
    "chr1" ,  9437053 ,  9438070 ,
    "chr1" , 75360291 , 75368579 ,
    "chr1" , 86351980 , 86352127
  )
  res <- bed_makewindows(x, num_win = 100)
  expect_equal(max(res$.win_id), 100)
})

test_that("step_size creates correct overlapping windows (#438)", {
  bed <- tibble(
    chrom = "chr1",
    start = 0,
    end = 1000
  )

  # Test the reported bug case
  res <- bed_makewindows(bed, win_size = 200, step_size = 50)

  # Check that second window starts at 50, not 150 (this is the main bug fix)
  expect_equal(res$start[2], 50)
  expect_equal(res$end[2], 250)

  # Test that using step_size=10 generates windows starting every 10 bases (regression test for correct window stepping)
  res_10 <- bed_makewindows(bed, win_size = 100, step_size = 10)

  # Verify the step size is correct by checking differences
  start_diffs <- diff(res_10$start)
  expect_true(all(start_diffs == 10))

  # Verify first few windows are positioned correctly
  expect_equal(res_10$start[1:5], c(0, 10, 20, 30, 40))

  # Test that step_size = 0 behaves like no step_size (non-overlapping)
  res_no_step <- bed_makewindows(bed, win_size = 200)
  res_step_zero <- bed_makewindows(bed, win_size = 200, step_size = 0)
  expect_equal(res_no_step, res_step_zero)
})