test_that("merge on 1 chrom", {
  bed_df <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,    100 ,  200 ,
    "chr1" ,    150 ,  250 ,
    "chr1" ,    200 ,  350
  )

  res <- bed_merge(bed_df)
  expect_equal(nrow(res), 1)
})

test_that("merge with interval at start", {
  bed_df <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      1 ,   50 ,
    "chr1" ,    100 ,  200 ,
    "chr1" ,    150 ,  250
  )

  res <- bed_merge(bed_df)
  expect_equal(nrow(res), 2)
})

test_that("merge with two chroms", {
  bed_df <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      1 ,   50 ,
    "chr1" ,     25 ,   75 ,
    "chr2" ,    100 ,  200 ,
    "chr2" ,    150 ,  250
  )

  res <- bed_merge(bed_df)
  expect_equal(nrow(res), 2)
})

test_that("book-ended intervals are merged", {
  bed_df <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      1 ,   50 ,
    "chr1" ,     50 ,  100
  )

  res <- bed_merge(bed_df)
  expect_equal(nrow(res), 1)
})

test_that("max_dist is enforced", {
  bed_df <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      1 ,   50 ,
    "chr1" ,     50 ,  100
  )

  res <- bed_merge(bed_df, max_dist = 1)
  expect_equal(nrow(res), 1)
})

test_that("max_dist is a positive value", {
  bed_df <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      1 ,   50 ,
    "chr1" ,     50 ,  100
  )

  expect_snapshot(bed_merge(bed_df, max_dist = -1), error = TRUE)
})

test_that("input groups are maintained in the output tbl 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"
  )

  x <- arrange(x, chrom, start)
  x <- group_by(x, group)
  res <- bed_merge(x)
  expect_true(all(x$group %in% res$group))
})

test_that("intervals can be merged by strand", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end , ~strand ,
    "chr1" ,    100 ,  200 , "+"     ,
    "chr1" ,    200 ,  400 , "+"     ,
    "chr1" ,    300 ,  500 , "+"     ,
    "chr1" ,    125 ,  175 , "-"     ,
    "chr1" ,    150 ,  200 , "-"
  )

  x <- group_by(x, strand)
  res <- bed_merge(x)
  expect_equal(nrow(res), 2)
})

test_that("summaries can be computed issue #132", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end , ~value , ~strand ,
    "chr1" ,      1 ,   50 ,      1 , "+"     ,
    "chr1" ,    100 ,  200 ,      2 , "+"     ,
    "chr1" ,    150 ,  250 ,      3 , "-"     ,
    "chr2" ,      1 ,   25 ,      4 , "+"     ,
    "chr2" ,    200 ,  400 ,      5 , "-"     ,
    "chr2" ,    400 ,  500 ,      6 , "+"     ,
    "chr2" ,    450 ,  550 ,      7 , "+"
  )

  res <- bed_merge(x, .value = sum(value))
  expect_true(all(res$.value != "."))
  expect_true(all(res$.value == c(1, 5, 4, 18)))
})

test_that("multiple summaries can be computed issue #132", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end , ~value , ~strand ,
    "chr1" ,      1 ,   50 ,      1 , "+"     ,
    "chr1" ,    100 ,  200 ,      2 , "+"     ,
    "chr1" ,    150 ,  250 ,      3 , "-"     ,
    "chr2" ,      1 ,   25 ,      4 , "+"     ,
    "chr2" ,    200 ,  400 ,      5 , "-"     ,
    "chr2" ,    400 ,  500 ,      6 , "+"     ,
    "chr2" ,    450 ,  550 ,      7 , "+"
  )

  res <- bed_merge(x, .value = sum(value), .min = min(value))
  expect_true(all(res$.value != "."))
  expect_true(all(res$.value == c(1, 5, 4, 18)))
  expect_true(all(res$.min == c(1, 2, 4, 5)))
})

test_that("contained intervals are merged issue #176", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      1 ,   10 ,
    "chr1" ,      2 ,    5 ,
    "chr1" ,      7 ,    9
  )

  res <- bed_merge(x)
  expect_true(nrow(res) == 1)
})

# from https://github.com/arq5x/bedtools2/blob/master/test/merge/test-merge.sh
test_that("Test that precision default is high enough for formatting not to give scientific notation", {
  x <- tibble::tribble(
    ~chrom , ~start   , ~end     , ~name   , ~score , ~strand , ~val1    , ~val2    ,
    "chr1" , 5333587L , 5344172L , "line1" , 0L     , "-"     , 5334680L , 5344172L ,
    "chr1" , 5481008L , 5484749L , "line2" , 0L     , "-"     , 5481796L , 5484749L ,
    "chr1" , 5481008L , 5484749L , "line3" , 0L     , "-"     , 5481796L , 5484749L ,
    "chr1" , 5481008L , 5484749L , "line4" , 0L     , "-"     , 5481796L , 5484749L ,
    "chr1" , 6763278L , 6766882L , "line5" , 0L     , "-"     , 7766544L , 6766882L
  )

  res <- bed_merge(x, .value = sum(val2))
  expect_equal(res$.value, c(5344172, 16454247, 6766882))
})

test_that("Test stranded merge with bedPlus files that have strand", {
  skip_if(packageVersion("readr") <= "1.4.0")

  expect_warning(
    x <- read_bed(valr_example("bug254_e.bed"), skip = 1, lazy = FALSE)
  )
  x <- x |> group_by(strand)
  res <- bed_merge(x, 200) |> arrange(end)
  expect_equal(res$end, c(20000, 25000))
})


test_that("check for off by one errors, related to issue #401 @kcamnairb ", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      1 ,   10 ,
    "chr1" ,      5 ,   20 ,
    "chr1" ,     30 ,   40
  )
  res <- bed_merge(x, max_dist = 10)
  ex <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      1 ,   40
  )
  expect_equal(res, ex)

  x <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      1 ,    3 ,
    "chr1" ,      2 ,    4 ,
    "chr1" ,      5 ,   10 ,
    "chr1" ,     12 ,   14
  )

  ex <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      1 ,    4 ,
    "chr1" ,      5 ,   10 ,
    "chr1" ,     12 ,   14
  )
  res <- bed_merge(x, max_dist = 0)
  expect_equal(res, ex)

  ex <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      1 ,   10 ,
    "chr1" ,     12 ,   14
  )
  res <- bed_merge(x, max_dist = 1)
  expect_equal(res, ex)

  x <- tibble::tribble(
    ~chrom        , ~start , ~end  ,
    "scaffold_66" ,  27262 , 70396 ,
    "scaffold_66" ,  66594 , 67647 ,
    "scaffold_66" ,  82218 , 85280 ,
    "scaffold_66" ,  85878 , 87553 ,
    "scaffold_66" ,  87831 , 89885 ,
    "scaffold_66" ,  90498 , 91996
  )

  ex <- tibble::tribble(
    ~chrom        , ~start , ~end  ,
    "scaffold_66" ,  27262 , 91996
  )
  res <- bed_merge(x, max_dist = 20000)
  expect_equal(res, ex)
})