new_contents: import unittest
  import sliding_window_tree
  
  # For now, use a *.remap.sam file (paired end reads aligned to a consensus sequence with indels removed).
  SAM_FILENAME = "./data/TestSample-RT_S17.HIV1B-vif.remap.sam"
  MAPQ_CUTOFF = 0  # alignment quality cutoff
  MAX_PROP_N = 0  # maximum proportion of N bases in MSA-aligned sequence
  READ_QUAL_CUTOFF = 20   # Phred quality score cutoff [0,40]
  REFERENCE_FASTA = "./data/TestSample-RT_S17.HIV1B-vif.10.conseq"
  
  MIN_WINDOW_BREADTH_COV_FRACTION = 0.5
  MIN_WINDOW_DEPTH_COV = 2
  
  class TestSlidingWindowTree(unittest.TestCase):
  
      def test_process_windows(self):
          sliding_window_tree.process_windows(sam_filename=SAM_FILENAME,
                                              ref_fasta_filename=REFERENCE_FASTA,
                                              mapping_cutoff=MAPQ_CUTOFF,
                                              read_qual_cutoff=READ_QUAL_CUTOFF,
                                              max_prop_N=MAX_PROP_N,
                                              window_breadth_thresh=MIN_WINDOW_BREADTH_COV_FRACTION,
                                              window_depth_thresh=MIN_WINDOW_DEPTH_COV)
  
  
  if __name__ == '__main__':
      unittest.main()
  
subject: Add unit test for full pipeline to get sliding window dn/ds