setwd(file.path(getwd(), "testdata"))
 
 context("Test that annotateRepeats() function works correctly")
 test_that("annotateRepeats() generates the correct data structure", {
 
     gtf <- formatGTF(pathToGTF = "gencodeVM16.gtf")
     # Retrieve back-spliced junctions coordinates
     backSplicedJunctions <- getBackSplicedJunctions(gtf)
     mergedBSJunctions <- mergeBSJunctions(backSplicedJunctions, gtf)
 
     # Retrieve the genomic features of the circRNAs
     annotatedBSJs <- annotateBSJs(mergedBSJunctions[1, ], gtf)
 
     if (requireNamespace("BSgenome.Mmusculus.UCSC.mm10", quietly = TRUE)){
         # Get BSgenome object
         genome <- BSgenome::getBSgenome("BSgenome.Mmusculus.UCSC.mm10")
 
         # Retrieve sequences type = "ie"
         targets <-
             getSeqsFromGRs(
                 annotatedBSJs,
                 genome,
                 lIntron = 500,
                 lExon = 10,
                 type = "ie"
 
             )
 
         # Retrieve overlapping repeats
 
         # repeats <-
         #     annotateRepeats(
         #         targets,
         #         annotationHubID  = "AH6075",
         #         complementary = TRUE
         #     )
         # 
         # expect_is(repeats, "list")
         # expect_equal(length(repeats), 2)
     }else{
         cat(
             "Missing package BSgenome.Mmusculus.UCSC.mm10.
             Use BiocManager to install it."
         )
     }
 
 
 
 
 
 })