# https://github.com/arq5x/bedtools2/blob/master/test/closest/test-closest.sh
test_that("1bp closer, check for off-by-one errors", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,     10 ,   20
  )

  y <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      9 ,   10 ,
    "chr1" ,     19 ,   20 ,
    "chr1" ,     20 ,   21
  )
  res <- bed_closest(x, y)
  expect_equal(nrow(res), 3)
  expect_true(all(c(-1, 0, 1) == res$.dist))
  expect_true(all(c(0, 1, 0) == res$.overlap))
})

test_that("reciprocal test of 1bp closer, check for off-by-one errors", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,     10 ,   20
  )

  y <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      9 ,   10 ,
    "chr1" ,     19 ,   20 ,
    "chr1" ,     20 ,   21
  )
  res <- bed_closest(y, x)
  expect_equal(nrow(res), 3)
  expect_true(all(c(1, 0, -1) == res$.dist))
  expect_true(all(c(0, 1, 0) == res$.overlap))
})

test_that("0bp apart closer, check for off-by-one errors", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,     10 ,   20
  )

  y <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      9 ,   10 ,
    "chr1" ,     19 ,   21 ,
    "chr1" ,     20 ,   21
  )
  res <- bed_closest(x, y)
  expect_equal(nrow(res), 3)
  expect_true(all(c(-1, 0, 1) == res$.dist))
  expect_true(all(c(0, 1, 0) == res$.overlap))
})

test_that("reciprocal of 0bp apart closer, check for off-by-one errors", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,     10 ,   20
  )

  y <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      9 ,   10 ,
    "chr1" ,     19 ,   21 ,
    "chr1" ,     20 ,   21
  )
  res <- bed_closest(y, x)
  res2 <- bed_closest(x, y)
  expect_equal(nrow(res), 3)
  expect_equal(nrow(res), 3)
  expect_true(all(c(1, 0, -1) == res$.dist))
  expect_true(all(c(0, 1, 0) == res$.overlap))
})

test_that("check that first left interval at index 0 is not lost", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,     10 ,   20
  )
  y <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      9 ,   10
  )
  res <- bed_closest(x, y)
  expect_equal(nrow(res), 1)
})

test_that("check that first right interval at index 0 is not lost", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,     10 ,   20
  )
  y <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,     20 ,   21
  )
  res <- bed_closest(x, y)
  expect_equal(nrow(res), 1)
})

test_that("check that strand closest works (strand = TRUE)", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end , ~name , ~score , ~strand ,
    "chr1" ,    100 ,  200 , "a"   ,     10 , "+"
  )

  y <- tibble::tribble(
    ~chrom , ~start , ~end , ~name , ~score , ~strand ,
    "chr1" ,     90 ,  120 , "b"   ,      1 , "-"
  )

  res <- bed_closest(group_by(x, strand), group_by(y, strand))
  # report NA
  expect_equal(nrow(res), 1)
  expect_equal(nrow(na.omit(res)), 0)
})

test_that("check that same strand is reported (strand = TRUE", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end , ~name , ~score , ~strand ,
    "chr1" ,     80 ,  100 , "q1"  ,      1 , "+"
  )

  y <- tibble::tribble(
    ~chrom , ~start , ~end , ~name  , ~score , ~strand ,
    "chr1" ,      5 ,   15 , "d1.1" ,      1 , "+"     ,
    "chr1" ,     20 ,   60 , "d1.2" ,      2 , "-"     ,
    "chr1" ,    200 ,  220 , "d1.3" ,      3 , "-"
  )

  pred <- tibble::tribble(
    ~chrom , ~start.x , ~end.x , ~name.x , ~score.x , ~strand.x , ~start.y , ~end.y , ~name.y , ~score.y , ~strand.y , ~.overlap , ~.distance ,
    "chr1" ,       80 ,    100 , "q1"    ,        1 , "+"       ,        5 ,     15 , "d1.1"  ,        1 , "+"       ,         0 ,        -66
  )

  res <- bed_closest(group_by(x, strand), group_by(y, strand))
  expect_true(all(pred == res))
})

test_that("check that different strand is reported (strand_opp = TRUE", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end , ~name , ~score , ~strand ,
    "chr1" ,     80 ,  100 , "q1"  ,      1 , "+"
  )

  y <- tibble::tribble(
    ~chrom , ~start , ~end , ~name  , ~score , ~strand ,
    "chr1" ,      5 ,   15 , "d1.1" ,      1 , "+"     ,
    "chr1" ,     20 ,   60 , "d1.2" ,      2 , "-"     ,
    "chr1" ,    200 ,  220 , "d1.3" ,      3 , "-"
  )

  pred <- tibble::tribble(
    ~chrom , ~start.x , ~end.x , ~name.x , ~score.x , ~strand.x , ~start.y , ~end.y , ~name.y , ~score.y , ~strand.y , ~.overlap , ~.dist ,
    "chr1" ,       80 ,    100 , "q1"    ,        1 , "+"       ,       20 ,     60 , "d1.2"  ,        2 , "+"       ,         0 ,    -21
  )

  res <- bed_closest(group_by(x, strand), group_by(flip_strands(y), strand))
  expect_true(all(pred == res))
})

test_that("check that reciprocal strand closest works (strand_opp = TRUE) ", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end , ~name , ~score , ~strand ,
    "chr1" ,    100 ,  200 , "a"   ,     10 , "+"
  )

  y <- tibble::tribble(
    ~chrom , ~start , ~end , ~name , ~score , ~strand ,
    "chr1" ,     80 ,   90 , "b"   ,      1 , "-"
  )

  res <- bed_closest(group_by(x, strand), group_by(flip_strands(y), strand))
  expect_equal(nrow(res), 1)
})

test_that("overlapping intervals are removed (overlap = F)", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,     10 ,   20
  )

  y <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      9 ,   10 ,
    "chr1" ,     19 ,   21 ,
    "chr1" ,     20 ,   21
  )

  res <- bed_closest(x, y, overlap = FALSE)
  expect_true(res[2, "start.y"] != 19)
})

test_that("duplicate intervals are not reported", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,    100 ,  200
  )

  y <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,    100 ,  200 ,
    "chr1" ,    150 ,  200 ,
    "chr1" ,    550 ,  580 ,
    "chr2" ,   7000 , 8500
  )
  res <- bed_closest(x, y)
  expect_false(any(duplicated(res)))
})

test_that("all overlapping features are reported", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,    100 ,  200
  )

  y <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,    100 ,  200 ,
    "chr1" ,    150 ,  200 ,
    "chr1" ,     50 ,  100 ,
    "chr1" ,    200 ,  300
  )
  exp <- tibble::tribble(
    ~chrom , ~start.x , ~start.y ,
    "chr1" ,      100 ,      200
  )
  res <- bed_closest(x, y)
  expect_true(nrow(res) == 4)
})

test_that("test reporting of first overlapping feature and
           overlap = F excludes overlapping intervals", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end   ,
    "chr1" ,    100 ,    101 ,
    "chr1" ,    200 ,    201 ,
    "chr1" ,    300 ,    301 ,
    "chr1" , 100000 , 100010 ,
    "chr1" , 100020 , 100040 ,
    "chr2" ,      1 ,     10 ,
    "chr2" ,     20 ,     30
  )

  y <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,    100 ,  101 ,
    "chr1" ,    150 ,  201 ,
    "chr1" ,    175 ,  375
  )
  pred <- tibble::tribble(
    ~chrom , ~start.x , ~end.x , ~start.y , ~end.y , ~.dist ,
    "chr1" ,      100 ,    101 ,      150 ,    201 ,     50 ,
    "chr1" ,      200 ,    201 ,      100 ,    101 ,   -100 ,
    "chr1" ,      300 ,    301 ,      150 ,    201 ,   -100 ,
    "chr1" ,   100000 , 100010 ,      175 ,    375 , -99626 ,
    "chr1" ,   100020 , 100040 ,      175 ,    375 , -99646 ,
    "chr2" ,        1 ,     10 , NA       , NA     , NA     ,
    "chr2" ,       20 ,     30 , NA       , NA     , NA
  )
  res <- bed_closest(x, y, overlap = F)
  expect_equal(res, pred)
})

### test distance reporting conditions ###

### tbls to test
d_q1 <- tibble::tribble(
  ~chrom , ~start , ~end , ~name    , ~score , ~strand ,
  "chr1" ,     80 ,  100 , "d_q1.1" ,      5 , "+"
)

d_q2 <- tibble::tribble(
  ~chrom , ~start , ~end , ~name    , ~score , ~strand ,
  "chr1" ,     80 ,  100 , "d_q2.1" ,      5 , "-"
)

d_d1F <- tibble::tribble(
  ~chrom , ~start , ~end , ~name   , ~score , ~strand ,
  "chr1" ,     40 ,   60 , "d1F.1" ,     10 , "+"
)

d_d1R <- tibble::tribble(
  ~chrom , ~start , ~end , ~name   , ~score , ~strand ,
  "chr1" ,     40 ,   60 , "d1R.1" ,     10 , "-"
)

d_d2F <- tibble::tribble(
  ~chrom , ~start , ~end , ~name   , ~score , ~strand ,
  "chr1" ,    140 ,  160 , "d2F.1" ,     10 , "+"
)

d_d2R <- tibble::tribble(
  ~chrom , ~start , ~end , ~name   , ~score , ~strand ,
  "chr1" ,    140 ,  160 , "d2R.1" ,     10 , "-"
)

test_that("default distance reporting works for forward hit on left, forward query", {
  pred <- tibble::tribble(
    ~chrom , ~start.x , ~end.x , ~name.x  , ~score.x , ~strand.x , ~start.y , ~end.y , ~name.y , ~score.y , ~strand.y , ~.overlap , ~.dist ,
    "chr1" ,       80 ,    100 , "d_q1.1" ,        5 , "+"       ,       40 ,     60 , "d1F.1" ,       10 , "+"       ,         0 ,    -21
  )
  res <- bed_closest(d_q1, d_d1F)
  expect_true(all(pred == res))
})

test_that("default distance reporting works for reverse hit on left, forward query", {
  pred <- tibble::tribble(
    ~chrom , ~start.x , ~end.x , ~name.x  , ~score.x , ~strand.x , ~start.y , ~end.y , ~name.y , ~score.y , ~strand.y , ~.overlap , ~.dist ,
    "chr1" ,       80 ,    100 , "d_q1.1" ,        5 , "+"       ,       40 ,     60 , "d1R.1" ,       10 , "-"       ,         0 ,    -21
  )
  res <- bed_closest(d_q1, d_d1R)
  expect_true(all(pred == res))
})

test_that("default distance reporting works for forward hit on left, reverse query", {
  pred <- tibble::tribble(
    ~chrom , ~start.x , ~end.x , ~name.x  , ~score.x , ~strand.x , ~start.y , ~end.y , ~name.y , ~score.y , ~strand.y , ~.overlap , ~.dist ,
    "chr1" ,       80 ,    100 , "d_q2.1" ,        5 , "-"       ,       40 ,     60 , "d1F.1" ,       10 , "+"       ,         0 ,    -21
  )
  res <- bed_closest(d_q2, d_d1F)
  expect_true(all(pred == res))
})

test_that("default distance reporting works for reverse hit on left, reverse query", {
  pred <- tibble::tribble(
    ~chrom , ~start.x , ~end.x , ~name.x  , ~score.x , ~strand.x , ~start.y , ~end.y , ~name.y , ~score.y , ~strand.y , ~.overlap , ~.dist ,
    "chr1" ,       80 ,    100 , "d_q2.1" ,        5 , "-"       ,       40 ,     60 , "d1R.1" ,       10 , "-"       ,         0 ,    -21
  )
  res <- bed_closest(d_q2, d_d1R)
  expect_true(all(pred == res))
})

test_that("default distance reporting works for forward hit on right, forward query", {
  pred <- tibble::tribble(
    ~chrom , ~start.x , ~end.x , ~name.x  , ~score.x , ~strand.x , ~start.y , ~end.y , ~name.y , ~score.y , ~strand.y , ~.overlap , ~.dist ,
    "chr1" ,       80 ,    100 , "d_q1.1" ,        5 , "+"       ,      140 ,    160 , "d2F.1" ,       10 , "+"       ,         0 ,     41
  )
  res <- bed_closest(d_q1, d_d2F)
  expect_true(all(pred == res))
})

test_that("default distance reporting works for reverse hit on right, forward query", {
  pred <- tibble::tribble(
    ~chrom , ~start.x , ~end.x , ~name.x  , ~score.x , ~strand.x , ~start.y , ~end.y , ~name.y , ~score.y , ~strand.y , ~.overlap , ~.dist ,
    "chr1" ,       80 ,    100 , "d_q1.1" ,        5 , "+"       ,      140 ,    160 , "d2R.1" ,       10 , "-"       ,         0 ,     41
  )
  res <- bed_closest(d_q1, d_d2R)
  expect_true(all(pred == res))
})

test_that("default distance reporting works for forward hit on right, reverse query", {
  pred <- tibble::tribble(
    ~chrom , ~start.x , ~end.x , ~name.x  , ~score.x , ~strand.x , ~start.y , ~end.y , ~name.y , ~score.y , ~strand.y , ~.overlap , ~.dist ,
    "chr1" ,       80 ,    100 , "d_q2.1" ,        5 , "-"       ,      140 ,    160 , "d2F.1" ,       10 , "+"       ,         0 ,     41
  )
  res <- bed_closest(d_q2, d_d2F)
  expect_true(all(pred == res))
})

test_that("default distance reporting works for reverse hit on right, reverse query", {
  pred <- tibble::tribble(
    ~chrom , ~start.x , ~end.x , ~name.x  , ~score.x , ~strand.x , ~start.y , ~end.y , ~name.y , ~score.y , ~strand.y , ~.overlap , ~.dist ,
    "chr1" ,       80 ,    100 , "d_q2.1" ,        5 , "-"       ,      140 ,    160 , "d2R.1" ,       10 , "-"       ,         0 ,     41
  )
  res <- bed_closest(d_q2, d_d2R)
  expect_true(all(pred == res))
})

### additional tbls for tests ###
a2 <- tibble::tribble(
  ~chrom , ~start , ~end , ~name , ~score , ~strand ,
  "chr1" ,     10 ,   20 , "a1"  ,      1 , "-"
)

b2 <- tibble::tribble(
  ~chrom , ~start , ~end , ~name , ~score , ~strand ,
  "chr1" ,      8 ,    9 , "b1"  ,      1 , "+"     ,
  "chr1" ,     21 ,   22 , "b2"  ,      1 , "-"
)

test_that("Make sure non-overlapping ties are reported ", {
  pred <- tibble::tribble(
    ~chrom , ~start.x , ~end.x , ~name.x , ~score.x , ~strand.x , ~start.y , ~end.y , ~name.y , ~score.y , ~strand.y , ~.overlap , ~.dist ,
    "chr1" ,       10 ,     20 , "a1"    ,        1 , "-"       ,       21 ,     22 , "b2"    ,        1 , "-"       ,         0 ,      2 ,
    "chr1" ,       10 ,     20 , "a1"    ,        1 , "-"       ,        8 ,      9 , "b1"    ,        1 , "+"       ,         0 ,     -2
  )
  res <- bed_closest(a2, b2)
  expect_equal(pred, res)
})

test_that("Make sure non-overlapping ties are reported with strand = T ", {
  pred <- tibble::tribble(
    ~chrom , ~start.x , ~end.x , ~name.x , ~score.x , ~strand.x , ~start.y , ~end.y , ~name.y , ~score.y , ~strand.y , ~.overlap , ~.dist ,
    "chr1" ,       10 ,     20 , "a1"    ,        1 , "-"       ,       21 ,     22 , "b2"    ,        1 , "-"       ,         0 ,      2
  )
  res <- bed_closest(group_by(a2, strand), group_by(b2, strand))
  expect_true(all(pred == res))
})

test_that("Make sure non-overlapping ties are reported with strand_opp = T ", {
  pred <- tibble::tribble(
    ~chrom , ~start.x , ~end.x , ~name.x , ~score.x , ~strand.x , ~start.y , ~end.y , ~name.y , ~score.y , ~strand.y , ~.overlap , ~.dist ,
    "chr1" ,       10 ,     20 , "a1"    ,        1 , "-"       ,        8 ,      9 , "b1"    ,        1 , "-"       ,         0 ,     -2
  )
  res <- bed_closest(group_by(a2, strand), group_by(flip_strands(b2), strand))
  expect_true(all(pred == res))
})

test_that("Make sure that closest intervals are captured when intervals span multiple interval tree nodes issue #105", {
  # when the y tbl has >= 64 intervals two nodes of the interval tree will be generated
  snps <- read_bed(valr_example("hg19.snps147.chr22.bed.gz"), n_max = 10)
  genes_one_node <- read_bed(
    valr_example("genes.hg19.chr22.bed.gz"),
    n_max = 63
  )
  genes_two_nodes <- read_bed(
    valr_example("genes.hg19.chr22.bed.gz"),
    n_max = 64
  )

  res_expt_one_node <- bed_closest(snps, genes_one_node)
  res_expt_two_nodes <- bed_closest(snps, genes_two_nodes)
  # adding one extra interval should not result in doubling the reported intervals
  expect_false(nrow(res_expt_two_nodes) >= 2 * nrow(res_expt_one_node))
})

test_that("test that a max of two duplicated x ivls are returned, assuming non-overlapping, and non-duplicate y ivls #105", {
  snps <- read_bed(valr_example("hg19.snps147.chr22.bed.gz"), n_max = 10)
  genes <- read_bed(valr_example("genes.hg19.chr22.bed.gz"), n_max = 64)
  # make sure there are no repeated y ivls (otherwise more than 2 x ivls should be reported)
  genes <- group_by(genes, chrom, start, end)
  genes <- mutate(genes, ivl_count = n())
  genes <- filter(genes, ivl_count == 1)
  genes <- select(genes, -ivl_count)
  genes <- group_by(genes, chrom)

  res <- bed_closest(snps, genes, overlap = FALSE)
  res <- group_by(res, chrom, start.x, end.x)
  res <- summarize(res, n = n(), .groups = "keep")
  # there should not be more than 2 possible closest ivls.
  expect_true(all(res$n <= 2))

  genome <- tibble::tribble(
    ~chrom , ~size    ,
    "chr1" , 10000000 ,
    "chr2" , 50000000 ,
    "chr3" , 60000000 ,
    "chrX" ,  5000000
  )

  x <- bed_random(genome, n = 1e5, seed = 1)
  y <- bed_random(genome, n = 1e5, seed = 2)

  x$idx <- seq_len(nrow(x))
  y$idx <- seq_len(nrow(y))

  res <- bed_closest(x, y, overlap = FALSE)
  res <- group_by(res, idx.x)
  res_grps <- summarize(res, n = n(), .groups = "keep")

  # if more than 1 x ivl reported, then it is due to duplicated y ivls in input
  multi_grps <- res_grps[res_grps$n > 1, ]
  if (nrow(multi_grps) > 0) {
    grps <- res[res$idx.x %in% multi_grps$idx.x, ]
    grps <- group_by(grps, idx.x)
    res <- summarize(
      grps,
      n_res = n(),
      same_abs_dist = length(unique(abs(.dist))) == 1,
      idx_y_distinct = length(unique(idx.y)) == n_res
    )
    expect_true(all(res$same_abs_dist & res$idx_y_distinct))
  }
})


test_that("ensure that subtraction is done with respect to input tbls issue#108", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end , ~group ,
    "chr1" ,    100 ,  200 , "A"    ,
    "chr1" ,    200 ,  400 , "A"    ,
    "chr1" ,    300 ,  500 , "A"    ,
    "chr1" ,    125 ,  175 , "C"    ,
    "chr1" ,    150 ,  200 , "B"
  )
  y <- tibble::tribble(
    ~chrom , ~start , ~end , ~group ,
    "chr1" ,    100 ,  200 , "A"    ,
    "chr1" ,    200 ,  400 , "B"    ,
    "chr1" ,    300 ,  500 , "A"    ,
    "chr1" ,    125 ,  175 , "C"    ,
    "chr2" ,    150 ,  200 , "A"
  )
  x_grouped <- arrange(x, chrom, start) |>
    group_by(group, chrom)
  y_grouped <- arrange(y, chrom, start) |>
    group_by(group, chrom)
  res <- bed_closest(x_grouped, y_grouped)
  expect_true(all(res$group.x == res$group.y))
})

# from https://github.com/arq5x/bedtools2/blob/master/test/closest/test-closest.sh
test_that("test closest forcing -s yet no matching strands on chrom", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end , ~group , ~score , ~strand ,
    "chr1" ,    100 ,  200 , "a"    ,     10 , "+"
  )
  y <- tibble::tribble(
    ~chrom , ~start , ~end , ~group , ~score , ~strand ,
    "chr1" ,     90 ,  120 , "b"    ,      1 , "-"
  )
  res <- bed_closest(group_by(x, strand), group_by(y, strand))
  expect_true(nrow(res) == 1)
  expect_true(nrow(na.omit(res)) == 0)
})

test_that("test closest forcing -S with only an opp strands on chrom", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end , ~group , ~score , ~strand ,
    "chr1" ,    100 ,  200 , "a"    ,     10 , "+"
  )
  y <- tibble::tribble(
    ~chrom , ~start , ~end , ~group , ~score , ~strand ,
    "chr1" ,     90 ,  120 , "b"    ,      1 , "-"
  )
  res <- bed_closest(group_by(x, strand), group_by(flip_strands(y), strand))
  expect_true(nrow(res) == 1)
})

test_that("Make sure non-overlapping ties are reported", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end , ~group , ~score , ~strand ,
    "chr1" ,     10 ,   20 , "a1"   ,      1 , "-"
  )
  y <- tibble::tribble(
    ~chrom , ~start , ~end , ~group , ~score , ~strand ,
    "chr1" ,      8 ,    9 , "b1"   ,      1 , "+"     ,
    "chr1" ,     21 ,   22 , "b2"   ,      1 , "-"
  )
  res <- bed_closest(x, y)
  expect_true(nrow(res) == 2)
})

test_that("Make sure non-overlapping ties are reported, with strand option", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end , ~group , ~score , ~strand ,
    "chr1" ,     10 ,   20 , "a1"   ,      1 , "-"
  )
  y <- tibble::tribble(
    ~chrom , ~start , ~end , ~group , ~score , ~strand ,
    "chr1" ,      8 ,    9 , "b1"   ,      1 , "+"     ,
    "chr1" ,     21 ,   22 , "b2"   ,      1 , "-"
  )
  res <- bed_closest(group_by(x, strand), group_by(y, strand))
  expect_true(nrow(res) == 1)
})

test_that("Make sure non-overlapping ties are reported, with strand-oppo option", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end , ~group , ~score , ~strand ,
    "chr1" ,     10 ,   20 , "a1"   ,      1 , "-"
  )
  y <- tibble::tribble(
    ~chrom , ~start , ~end , ~group , ~score , ~strand ,
    "chr1" ,      8 ,    9 , "b1"   ,      1 , "+"     ,
    "chr1" ,     21 ,   22 , "b2"   ,      1 , "-"
  )
  res <- bed_closest(group_by(x, strand), group_by(flip_strands(y), strand))
  expect_true(nrow(res) == 1)
})

test_that("check ties, single db", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end , ~group , ~score , ~strand ,
    "chr1" ,     10 ,   20 , "a1"   ,      1 , "-"
  )
  y <- tibble::tribble(
    ~chrom , ~start , ~end , ~group , ~score , ~strand ,
    "chr1" ,      8 ,    9 , "b1"   ,      1 , "+"     ,
    "chr1" ,     21 ,   22 , "b2"   ,      1 , "-"
  )
  res <- bed_closest(x, y)
  expect_true(nrow(res) == 2)
})

test_that("check reporting of adjacent intervals issue #348", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,     10 ,   20
  )

  y <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      8 ,    9 ,
    "chr1" ,      9 ,   10 ,
    "chr1" ,     20 ,   21 ,
    "chr1" ,     21 ,   22
  )
  res <- bed_closest(x, y)
  expect_true(nrow(res) == 2)
})