skip_if_not_installed("chromVAR")
skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg19")
if (requireNamespace("chromVAR", quietly = TRUE) & 
    requireNamespace("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE)) {
  test_that("testCoAccessibleLinks works on a 1 sample test dataset", {
    cellPopulations <- c("C2", "C5")
    capture.output(
      SampleTileMatrix <- MOCHA::getSampleTileMatrix(
        MOCHA:::testTileResults,
        cellPopulations = cellPopulations,
        threshold = 0
      )
    )
  
    cellPopulation <- "C2"
    regions <- MOCHA::StringsToGRanges(c(
      "chr1:10003000-10003499"
    ))
    capture.output(
      links <- MOCHA::getCoAccessibleLinks(SampleTileMatrix,
        cellPopulation,
        regions,
        verbose = FALSE
      )
    )
  
    capture.output(
      results <- MOCHA::testCoAccessibility(
        SampleTileMatrix,
        tile1 = links$Tile1,
        tile2 = links$Tile2,
        numCores = 1,
        ZI = TRUE,
        backNumber = 1000,
        verbose = FALSE
      )
    )
  
    expect_snapshot(
      results,
      variant = "1sample"
    )
  })
  
  test_that("testCoAccessibleLinks works on a 3 sample test dataset", {
    cellPopulations <- c("C2", "C3")
    capture.output(
      SampleTileMatrix <- MOCHA::getSampleTileMatrix(
        MOCHA:::testTileResultsMultisample,
        cellPopulations = cellPopulations,
        threshold = 0
      )
    )
  
    cellPopulation <- "C2"
    regions <- MOCHA::StringsToGRanges(c(
      "chr1:10009500-10009999"
    ))
  
    capture.output(
      links <- MOCHA::getCoAccessibleLinks(SampleTileMatrix,
        cellPopulation,
        regions,
        verbose = FALSE
      )
    )
  
    capture.output(
      results <- MOCHA::testCoAccessibility(
        SampleTileMatrix,
        tile1 = links$Tile1,
        tile2 = links$Tile2,
        numCores = 1,
        ZI = TRUE,
        backNumber = 1000,
        verbose = FALSE
      )
    )
  
    expect_snapshot(
      results,
      variant = "3sample"
    )
    
  })
}