x <- matrix(c(1,3,1,1,2,3), ncol = 2, byrow = TRUE)
y <- matrix(c(2,1,10,9,20,18,19,15), ncol = 2, byrow = TRUE)

mnn <- Canek:::GetMnnPairs(t(x), t(y), kNN = 1)

test_that("GetMnnPairs works", {
  expect_true(!is.null(mnn))
  expect_named(mnn, "Pairs")
  expect_equal(dim(mnn$Pairs), c(1,2))
  expect_equal(colnames(mnn$Pairs), c("queBatch-Cells-Index", "refBatch-Cells-Index"))
  expect_equal(unname(mnn$Pairs[1,]), c(1,2))
})

mnn <- Canek:::GetMnnPairs(t(x), t(y), kNN = 2)

test_that("Get_MNN_Pairs works", {
  expect_true(!is.null(mnn))
  expect_named(mnn, "Pairs")
  expect_equal(dim(mnn$Pairs), c(4, 2))
  expect_equal(colnames(mnn$Pairs), c("queBatch-Cells-Index", "refBatch-Cells-Index"))
  expect_equal(unname(mnn$Pairs[1,]), c(1,2))
  expect_equal(unname(mnn$Pairs[2,]), c(1,3))
  expect_equal(unname(mnn$Pairs[3,]), c(2,1))
  expect_equal(unname(mnn$Pairs[4,]), c(2,3))

})