test_that("Artifical errors are denoised properly.", {
    
  #PACBB5941-16
  #deleted bp at position 60
  toy_example1 = 'ACAATGTATTTCATCCTAGGAATATGATCAGGAATATTAGGAATAATATTAAGAATATTATTCGAATTGAACTAGCACAACCAGGACCATTAATAAGAAATGACCAAATTTATAATGTAATTGTTACATCTCATGCATTCATTATAATTTTTATGGTAATACCAATTATAATCGGAGGATTCGGAAATTGATTAGTACCATTAATAATTGGAGCACCAGATATAGCATTCCCACGAATAAATAATATAAGATTTTGACTTCTTCCACCCTCACTTACATTGTTAATTTCAAGATCAATAGTAGAAATAGGACCAGGAACAGGATGAACACTATATCCACCGCTATCGTCAAATATTGCACATTCGGGAGGAAGTGTAGACTTAAGAATTTTTTCATTACACTTAGCCGGTGTATCATCAATCCTAGGAGCAATTAACTTTATTACAACAATTCTAAATATACGAACACTAGGAATATCATTAGACCGAACCCCCTTATTCGTATGATCAGTAATAATTACTGCAATTTTACTACTTCTATCTCTACCAGTACTAGCTGGAGCAATCACGATA'
  toy1_expected = "ACAATGTATTTCATCCTAGGAATATGATCAGGAATATTAGGAATAATATTAAGAATANNNNNNNGAATTGAACTAGCACAACCAGGACCATTAATAAGAAATGACCAAATTTATAATGTAATTGTTACATCTCATGCATTCATTATAATTTTTATGGTAATACCAATTATAATCGGAGGATTCGGAAATTGATTAGTACCATTAATAATTGGAGCACCAGATATAGCATTCCCACGAATAAATAATATAAGATTTTGACTTCTTCCACCCTCACTTACATTGTTAATTTCAAGATCAATAGTAGAAATAGGACCAGGAACAGGATGAACACTATATCCACCGCTATCGTCAAATATTGCACATTCGGGAGGAAGTGTAGACTTAAGAATTTTTTCATTACACTTAGCCGGTGTATCATCAATCCTAGGAGCAATTAACTTTATTACAACAATTCTAAATATACGAACACTAGGAATATCATTAGACCGAACCCCCTTATTCGTATGATCAGTAATAATTACTGCAATTTTACTACTTCTATCTCTACCAGTACTAGCTGGAGCAATCACGATA"
  
  test_toy1_out = denoise(toy_example1, 
                          name = "example1",
                      		ambig_char = "N",
                      		censor_length = 3,
                      		aa_check = FALSE, 
                      		to_file = FALSE)
  
  #test_toy1_out$outseq == toy1_expected
  expect_equal(test_toy1_out$outseq, toy1_expected)
  #test_toy1_out$adjustment_count ==  1
  expect_equal(test_toy1_out$adjustment_count, 1)
  #nchar(test_toy1_out$outseq) == nchar(toy_example1) + 1
  expect_equal(nchar(test_toy1_out$outseq), nchar(toy_example1) + 1 )
  
    
  #PACBB858-16
  #567 length sequence and it has the starting point that seems to be causing the issue with alignment
  toy_example2 = 'TTTTTGGTGCATGATCTAGAATAGTAGGAACTTCCTTAAGAATATTAATTCGTGCAGAATTAGGAACCCCTAATGCATTAATTGGAGATGATCAAATTTATAATGTAATTGTAACAGCCCATGCATTCATTATAATTTTCTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCACTGATATTAAGAGCCCCTGATATAGCTTTCCACGATTAAATAATATAAGATTTTGACTTTTACCTCCATCTTTAACATTATTGTTAACTAGAAGTTTAGTAGAAAGAGGAACCGGTACAGGATGAACAGTTTACCCCCCACTGTCATCTACATTAAGGCATTCCGGAGCATCTGTAGATTTATCTATTTTTTCTTTGCATTTAGCAGGGATTTCCTCTATTCTAGGAGCAGTAAATTTTATTTCAACAATTATTAATATACGGGCCCCAGGAATAACTTTTGATAAAATACCTTTATTTGTGTGATCAGTATTAATTACTGCAGTATTACTATTATTATCTTTACCAGTTCTAGCTGGAGCAATTACTATA'
  
  #first two bases are dropped from the sequence prior to adjustment, but reattached b/c keep_edges = TRUE
  #single deletion at position 221, so character added to lengthen by 1.
  toy2_expected = unlist(strsplit(toy_example2, ""))
  toy2_expected = c(toy2_expected[1:221] ,  c("N") ,  toy2_expected[222:length(toy2_expected)])
  
  toy2_expected[(212):(232)] = "N"
  toy2_expected = paste(toy2_expected, collapse="")
  
  test_toy2_out = denoise(x = toy_example2,
  						            name = "toy_example2-short_and_messy",
                      		ambig_char = "N",
                      		censor_length = 10,
                      		aa_check = FALSE, 
                      		to_file = FALSE)
  
  #test_toy2_out$outseq == toy2_expected
  expect_equal(test_toy2_out$outseq, toy2_expected)
  #nchar(test_toy2_out$outseq) == (nchar(toy_example2)+1)
  expect_equal(nchar(test_toy2_out$outseq), (nchar(toy_example2)+1))
  
  
  #character 70 is added to this string
  #should be removed and a censor of 1bp in either direction is applied
  toy_example3 = 'ACACTTTACTTTATTTTTGGTATTTGAGCAGGTATATTAGGGACTTCATTAAGTTTATTAATTCGAGCAGAAATTAGGTAATCCAGGTTCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTTATGCCAATTATAATTGGAGGTTTTGGTAATTGACTAGTTCCTTTAATACTAGGAGCCCCTGATATAGCTTTCCCCCGAATAAATAATATAAGTTTCTGACTTTTACCTCCCTCTCTTACCTTATTAATTTCAAGAAGAATTGTAGAAAATGGTGCAGGAACTGGATGAACAGTTTACCCTCCTCTTTCTTCTAATATCGCTCATAGAGGAAGATCAGTAGATTTAGCTATTTTTTCTTTACATTTAGCTGGTATTTCATCAATTTTAGGGGCTATTAATTTTATTACTACAATTATTAACATACGATTAAATAGACTAATATTTGATCAAATACCTTTATTCGTATGAGCTGTAGGGATTACTGCTTTTCTTTTA'
  
  toy3_expected = strsplit(toy_example3, "")[[1]]
  
  toy3_expected = c(toy3_expected[1:69], toy3_expected[71:length(toy3_expected)])
  toy3_expected[69] = "N"
  toy3_expected[70] = "N"
  toy3_expected = paste(toy3_expected, collapse = "")
  
  test_toy3_out = denoise(x = toy_example3,
                          name = "toy_example3-long_and_messy",
                          ambig_char = "N",
                          censor_length = 1,
                          aa_check = FALSE, 
                          to_file = FALSE)
  
  #test_toy3_out$outseq == toy3_expected
  expect_equal(test_toy3_out$outseq, toy3_expected)

  #nchar(test_toy3_out$outseq)==(nchar(toy_example3)-1)
  expect_equal(nchar(test_toy3_out$outseq), (nchar(toy_example3)-1))
  
  
  #no errors, but a reverse compliment
  toy_example_4 = "TAAGTGTTGATAGAGAATTGGGTCCCCTCCCCCTGCGGGGTCAAAGAATGTAGTGTTGAGGTTGCGGTCTGTTAATAATATTGTAATTCCGGCTGCAAGAACAGGGAGAGCAAGGAGTAGAAGAACAGTGGTGATAAGAATAGATCAAACAAATAATGGTGTTTGATATTGAGAAATAGTTGGGGGTTTTATATTAATAATAGTTGTAATAAAATTAATAGAGGCTAAAATTGATGAGATACCGGCCAAATGAAGGGAAAAGATGGCTAAATCAACAGAGGGGCCAGCATGTGCTAAATTACCTGCTAAAGGAGGATATACAGTTCATCCGGTTCCTGCTCCAGCTTCTACTCCTGCGGAGGCCAGGAGAAGTAAGAACGAAGGAGGAAGAAGCCAGAAACTTATATTATTTATTCGAGGGAATGCTATATCTGGTGCACCAATTATTAAAGGAACAAGTCAATTGCCAAAGCCACCAATTATTACAGGTATAACCATAAAAAAGATTATTACAAAGGCATGGGCGGTTACGATCACATTATAAATCTGATCATCCCCTAAAAGAGATCCGGGTTGACCTAGTTCAGCGCGAATTAGTAAACTTAAAGCTATTCCAACTATTCCTGCTCATGCACCAAAAATCAAGTAGAG"
  
  test_toy4_out = denoise(x = toy_example_4,
                          name = "toy_example3-long_and_messy",
                          ambig_char = "N",
                          censor_length = 10,
                          aa_check = FALSE, 
                          to_file = FALSE)
  
  test_toy4_out$outseq == toupper(rev_comp(toy_example_4))
  expect_equal(test_toy4_out$outseq, toupper(rev_comp(toy_example_4)))
  
  })