# https://github.com/arq5x/bedtools2/blob/master/test/cluster/test-cluster.sh

x <- tibble::tribble(
  ~chrom , ~start  , ~end    , ~name , ~id , ~strand ,
  "chr1" ,   72017 ,  884436 , "a"   ,   1 , "+"     ,
  "chr1" ,   72017 ,  844113 , "b"   ,   2 , "+"     ,
  "chr1" ,  939517 , 1011278 , "c"   ,   3 , "+"     ,
  "chr1" , 1142976 , 1203168 , "d"   ,   4 , "+"     ,
  "chr1" , 1153667 , 1298845 , "e"   ,   5 , "-"     ,
  "chr1" , 1153667 , 1219633 , "f"   ,   6 , "+"     ,
  "chr1" , 1155173 , 1200334 , "g"   ,   7 , "-"     ,
  "chr1" , 1229798 , 1500664 , "h"   ,   8 , "-"     ,
  "chr1" , 1297735 , 1357056 , "i"   ,   9 , "+"     ,
  "chr1" , 1844181 , 1931789 , "j"   ,  10 , "-"
)

test_that("basic cluster works", {
  res <- bed_cluster(x)
  # test number of groups in output
  expect_equal(length(unique(res$.id)), 4)
  expect_equal(res$.id, c(1, 1, 2, 3, 3, 3, 3, 3, 3, 4))
})

test_that("stranded cluster works", {
  res <- bed_cluster(group_by(x, strand))
  # test number of groups in output
  expect_equal(length(unique(res$.id)), 6)
  expect_equal(res$.id, c(1, 1, 2, 3, 3, 4, 4, 4, 5, 6))
})

x <- tibble::tribble(
  ~chrom , ~start , ~end    , ~name , ~id , ~strand ,
  "chr1" ,  72017 ,  884436 , "a"   ,   1 , "+"     ,
  "chr1" ,  72017 ,  844113 , "b"   ,   2 , "+"     ,
  "chr1" , 939517 , 1011278 , "c"   ,   3 , "+"     ,
  "chr2" , 940000 ,  990000 , "d"   ,   4 , "-"
)

test_that("cluster ids are not repeated per group issue #171", {
  res <- bed_cluster(x)
  # test that groups have unique ids
  chr1_ids <- filter(res, chrom == "chr1") |>
    select(.id) |>
    unique() |>
    unlist()
  chr2_ids <- filter(res, chrom == "chr2") |>
    select(.id) |>
    unique() |>
    unlist()
  shared_ids <- intersect(chr1_ids, chr2_ids)
  expect_equal(length(shared_ids), 0)
})


test_that("guard against max_dist argument preventing clustering first interval in contig issue #388", {
  x <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "a"    ,      1 ,   10 ,
    "a"    ,     20 ,   50 ,
    "b"    ,     20 ,   50 ,
    "c"    ,    100 ,  100
  )

  res <- bed_cluster(x, max_dist = 0)
  expect_equal(res$.id, 1L:4L)

  res <- bed_cluster(x, max_dist = 100)
  expect_equal(res$.id, c(1, 1, 2, 3))

  res <- bed_cluster(x, max_dist = 10)
  expect_equal(res$.id, c(1, 1, 2, 3))

  res <- bed_cluster(x, max_dist = 9)
  expect_equal(res$.id, 1L:4L)
})

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_cluster(x, max_dist = 10)
  expect_equal(res$.id, c(1L, 1L, 1L))

  x <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      1 ,    3 ,
    "chr1" ,      2 ,    4 ,
    "chr1" ,      5 ,   10 ,
    "chr1" ,     12 ,   14
  )
  res <- bed_cluster(x, max_dist = 0)
  expect_equal(res$.id, c(1L, 1L, 2L, 3L))

  res <- bed_cluster(x, max_dist = 1)
  expect_equal(res$.id, c(1L, 1L, 1L, 2L))
})

test_that("check for additional errors, related to issue #401 @kcamnairb ", {
  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
  )
  res <- bed_cluster(x, max_dist = 20000)
  expect_true(all(res$.id == 1))

  x <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      1 ,   10 ,
    "chr1" ,      1 ,   11 ,
    "chr1" ,      1 ,    9 ,
    "chr1" ,      1 ,    9 ,
    "chr1" ,      3 ,    4 ,
    "chr1" ,      3 ,   12 ,
    "chr1" ,     10 ,   14 ,
    "chr1" ,    100 ,  200 ,
    "chr2" ,      1 ,   10 ,
    "chr2" ,      1 ,   11 ,
    "chr2" ,      1 ,    9 ,
    "chr2" ,      1 ,    9 ,
    "chr2" ,      3 ,    4 ,
    "chr2" ,      3 ,   12 ,
    "chr2" ,     10 ,   14 ,
    "chr2" ,    100 ,  200
  )

  res <- bed_cluster(x, max_dist = 0)
  expect_true(max(res$.id) == 4)

  res <- bed_cluster(x, max_dist = 100)
  expect_equal(res$.id, c(rep(1, 8), rep(2, 8)))

  res <- bed_cluster(x, max_dist = -3)
  expect_true(max(res$.id) == 6)
})