x <- tibble::tribble(
  ~chrom , ~start , ~end , ~strand ,
  "chr1" ,     20 ,   70 , "+"     ,
  "chr1" ,     50 ,  100 , "-"     ,
  "chr1" ,    200 ,  250 , "+"     ,
  "chr1" ,    220 ,  250 , "+"
)
genome <- tibble::tribble(
  ~chrom , ~size ,
  "chr1" ,   500 ,
  "chr2" ,  1000
)
test_that("bed_genomecov works", {
  ex <- tibble::tribble(
    ~chrom , ~start , ~end , ~.depth ,
    "chr1" ,  20L   ,  50L , 1L      ,
    "chr1" ,  50L   ,  70L , 2L      ,
    "chr1" ,  70L   , 100L , 1L      ,
    "chr1" , 200L   , 220L , 1L      ,
    "chr1" , 220L   , 250L , 2L
  )
  obs <- bed_genomecov(x, genome)
  expect_equal(obs, ex)

  res <- bed_genomecov(x, genome, zero_depth = TRUE)
  expect_true(sum(res$.depth == 0) > 0)
})

test_that("groups are respected", {
  ex <- tibble::tribble(
    ~chrom , ~start , ~end , ~strand , ~.depth ,
    "chr1" ,  20L   ,  70L , "+"     , 1L      ,
    "chr1" , 200L   , 220L , "+"     , 1L      ,
    "chr1" , 220L   , 250L , "+"     , 2L      ,
    "chr1" ,  50L   , 100L , "-"     , 1L
  )
  obs <- bed_genomecov(group_by(x, strand), genome)
  expect_equal(obs, ex)

  res <- bed_genomecov(group_by(x, strand), genome, zero_depth = TRUE)
  expect_equal(sum(res$chrom == "chr2"), 2L)
})

test_that("grouping is retained for zero depth intervals", {
  xx <- tibble::tribble(
    ~chrom , ~start , ~end , ~strand , ~grp ,
    "chr1" ,  20L   ,  70L , "+"     ,    1 ,
    "chr1" , 200L   , 220L , "-"     ,    1 ,
    "chr1" ,  20L   ,  70L , "+"     ,    2 ,
    "chr1" , 200L   , 220L , "-"     ,    2
  ) |>
    group_by(strand, grp)

  many_chroms_genome <- tibble(
    chrom = c("chr1", LETTERS),
    size = 500
  )

  res <- bed_genomecov(xx, many_chroms_genome, zero_depth = TRUE)
  expect_equal(length(setdiff(many_chroms_genome$chrom, res$chrom)), 0L)
  ex <- tibble::tribble(
    ~strand , ~grp , ~n  ,
    "+"     ,    1 , 26L ,
    "+"     ,    2 , 26L ,
    "-"     ,    1 , 26L ,
    "-"     ,    2 , 26L
  )

  lr <- res[res$chrom %in% LETTERS, ]
  nlr <- lr |>
    group_by(strand, grp) |>
    summarize(n = n()) |>
    ungroup()
  expect_identical(nlr, ex)
})

test_that("chroms in bed, not in genome, are dropped", {
  xx <- tibble::tribble(
    ~chrom  , ~start , ~end , ~strand , ~.depth ,
    "hello" ,  20L   ,  70L , "+"     , 1L      ,
    "world" , 200L   , 220L , "+"     , 1L      ,
    "chr1"  , 220L   , 250L , "+"     , 2L
  )
  expect_warning(res <- bed_genomecov(xx, genome))
  expect_true(all(res$chrom == "chr1"))
})

test_that("zero length input is handled", {
  xx <- tibble::tribble(
    ~chrom  , ~start , ~end , ~strand , ~.depth ,
    "hello" , 20L    , 70L  , "+"     , 1L      ,
  )

  expect_warning(res <- bed_genomecov(xx, genome))
  expect_true(nrow(res) == 0)

  xx <- xx[xx$chrom != "hello", ]

  res <- bed_genomecov(xx, genome)
  expect_true(nrow(res) == 0)
})

test_that("check edge cases with 1 bp intervals", {
  # base-level coverage equals number of basepairs in input intervals
  genome <- tribble(
    ~chrom , ~size ,
    "chr1" ,   1e5
  )
  seed <- 1010486
  ivls <- bed_random(genome, length = 1, n = 1e3, seed = seed)

  res <- bed_genomecov(ivls, genome)
  expect_true(sum(res$.depth) == 1e3)

  ivls <- tibble(
    chrom = "chr1",
    start = seq(0, 999),
    end = start + 2
  )
  res <- bed_genomecov(ivls, genome)
  expect_true(sum(res$.depth) == (1e3 * 2))

  set.seed(seed)
  ivls <- tibble(
    chrom = "chr1",
    start = seq(0, 999),
    end = start + sample(1:100, length(start), replace = TRUE)
  )

  res <- bed_genomecov(ivls, genome)
  n_bp <- sum(ivls$end - ivls$start)
  n_cov <- sum(res$.depth * (res$end - res$start))
  expect_equal(n_bp, n_cov)
})

test_that("check edge cases at beginning and end", {
  genome <- tribble(
    ~chrom , ~size ,
    "chr1" ,  1000
  )
  ex <- tibble::tribble(
    ~chrom , ~start , ~end  , ~.depth ,
    "chr1" ,   0L   ,    1L , 3L      ,
    "chr1" ,   1L   ,    2L , 1L      ,
    "chr1" , 999L   , 1000L , 1L
  )

  # oob intervals are ignored with a warning
  ivls <- tibble(
    chrom = "chr1",
    start = c(rep(0, 3), 1, 999, 1000),
    end = start + 1
  )

  expect_warning(res <- bed_genomecov(ivls, genome))
  expect_true(all(res$start < 1000))

  expect_equal(res, ex)
})

# bed related tests from #https://github.com/arq5x/bedtools2/blob/master/test/genomecov/test-genomecov.sh
y <- tibble::tribble(
  ~chrom , ~start , ~end , ~group , ~score , ~strand ,
  "1"    , 15L    , 20L  , "y1"   , 1L     , "+"     ,
  "1"    , 17L    , 22L  , "y2"   , 2L     , "+"
)
genome <- tibble::tribble(
  ~chrom , ~size ,
  "1"    , 100L  ,
  "2"    , 100L  ,
  "3"    , 100L
)

test_that("Test with chroms that have no coverage", {
  ex <- tibble::tribble(
    ~chrom , ~start , ~end , ~.depth ,
    "1"    , 15L    , 17L  , 1L      ,
    "1"    , 17L    , 20L  , 2L      ,
    "1"    , 20L    , 22L  , 1L
  )
  obs <- bed_genomecov(y, genome)
  expect_equal(ex, obs)
})

test_that("Test with chroms that have no coverage", {
  ex <- tibble::tribble(
    ~chrom , ~start , ~end , ~.depth ,
    "1"    ,  0L    ,  15L , 0L      ,
    "1"    , 15L    ,  17L , 1L      ,
    "1"    , 17L    ,  20L , 2L      ,
    "1"    , 20L    ,  22L , 1L      ,
    "1"    , 22L    , 100L , 0L      ,
    "2"    ,  0L    , 100L , 0L      ,
    "3"    ,  0L    , 100L , 0L
  )

  obs <- bed_genomecov(y, genome, zero_depth = TRUE)
  expect_equal(ex, obs)
})