test_that("complement with covering interval", {
  genome <- tibble::tribble(
    ~chrom , ~size ,
    "chr1" ,   500
  )
  bed <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      0 ,  500
  )
  res <- bed_complement(bed, genome)
  expect_equal(nrow(res), 0)
})

test_that("complement with middle interval", {
  genome <- tibble::tribble(
    ~chrom , ~size ,
    "chr1" ,   500
  )
  bed <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,    100 ,  200
  )
  expect <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      0 ,  100 ,
    "chr1" ,    200 ,  500
  )
  res <- bed_complement(bed, genome)
  expect_true(all(res == expect))
})

test_that("complement adds final interval", {
  genome <- tibble::tribble(
    ~chrom , ~size ,
    "chr1" ,   500
  )
  bed <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      0 ,   50 ,
    "chr1" ,    100 ,  200
  )
  expect <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,     50 ,  100 ,
    "chr1" ,    200 ,  500
  )
  res <- bed_complement(bed, genome)
  expect_true(all(res == expect))
})

test_that("multiple chroms", {
  genome <- tibble::tribble(
    ~chrom , ~size ,
    "chr1" ,   500 ,
    "chr2" ,   500
  )
  bed <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,    100 ,  500 ,
    "chr2" ,    100 ,  500
  )
  expect <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      0 ,  100 ,
    "chr2" ,      0 ,  100
  )
  res <- bed_complement(bed, genome)
  expect_true(all(res == expect))
})

test_that("multiple chroms, chr1 is covered", {
  genome <- tibble::tribble(
    ~chrom , ~size ,
    "chr1" ,   500 ,
    "chr2" ,   500
  )
  bed <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      0 ,  500 ,
    "chr2" ,    100 ,  500
  )
  expect <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr2" ,      0 ,  100
  )
  res <- bed_complement(bed, genome)
  expect_true(all(res == expect))
})

test_that("record exceeds chrom length", {
  genome <- tibble::tribble(
    ~chrom , ~size ,
    "chr1" ,   100
  )
  bed <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,     90 ,  110
  )
  expect <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      0 ,   90
  )
  res <- bed_complement(bed, genome)
  expect_true(all(res == expect))
})

test_that("test complement only on left side", {
  genome <- tibble::tribble(
    ~chrom , ~size ,
    "chr1" ,   100
  )
  bed <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,     90 ,  100
  )
  expect <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      0 ,   90
  )
  res <- bed_complement(bed, genome)
  expect_true(all(res == expect))
})

test_that("overlapping intervals", {
  genome <- tibble::tribble(
    ~chrom , ~size ,
    "chr1" ,   100
  )
  bed <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,     10 ,  100 ,
    "chr1" ,     20 ,   80
  )
  expect <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      0 ,   10
  )
  res <- bed_complement(bed, genome)
  expect_true(all(res == expect))
})

test_that("starting intervals are complemented (#78)", {
  genome <- tibble::tribble(
    ~chrom , ~size ,
    "chr1" ,   100
  )
  bed <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      0 ,   20
  )
  res <- bed_complement(bed, genome)
  expect_equal(nrow(res), 1)
  expect_equal(res$start, 20)
  expect_equal(res$end, 100)
})

test_that("non-overlapping genome chroms are in output (#78)", {
  genome <- tibble::tribble(
    ~chrom , ~size ,
    "chr1" ,   100 ,
    "chr2" ,   100
  )
  bed <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,     10 ,  100
  )
  expected <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      0 ,   10 ,
    "chr2" ,      0 ,  100
  )
  res <- bed_complement(bed, genome)
  expect_true(all(res == expected))
})

test_that("`x` intervals not in genome are ignored (#78)", {
  genome <- tibble::tribble(
    ~chrom , ~size ,
    "chr1" ,   500
  )
  bed <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr2" ,     10 ,  100
  )
  expected <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      0 ,  500
  )
  res <- bed_complement(bed, genome)
  expect_true(all(res == expected))
})

# from https://github.com/arq5x/bedtools2/blob/master/test/complement/test-complement.sh
test_that("ends are covered", {
  genome <- tibble::tribble(
    ~chrom , ~size ,
    "chr1" ,    20
  )
  bed <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      0 ,    1 ,
    "chr1" ,     19 ,   20
  )
  expected <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      1 ,   19
  )
  res <- bed_complement(bed, genome)
  expect_true(all(res == expected))
})

test_that("entirety is covered", {
  genome <- tibble::tribble(
    ~chrom , ~size ,
    "chr1" ,    20
  )
  bed <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      0 ,   20
  )
  res <- bed_complement(bed, genome)
  expect_true(nrow(res) == 0)
})

test_that("nothing is covered", {
  genome <- tibble::tribble(
    ~chrom , ~size ,
    "chr1" ,    20 ,
    "chr2" ,    20
  )
  bed <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr2" ,      0 ,   20
  )
  expected <- tibble::tribble(
    ~chrom , ~start , ~end ,
    "chr1" ,      0 ,   20
  )
  res <- bed_complement(bed, genome)
  expect_true(all(res == expected))
})

test_that("Issue #356", {
  genome <- tibble::tribble(
    ~chrom , ~size     ,
    "chr1" , 249250621
  )
  bed <- tibble::tribble(
    ~chrom , ~start , ~end  , ~name      ,
    "chr1" ,      0 , 10000 , "telomere"
  )
  expected <- tibble::tribble(
    ~chrom , ~start , ~end      ,
    "chr1" ,  10000 , 249250621
  )
  res <- bed_complement(bed, genome)
  expect_true(all(res == expected))
})