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from absl.testing import absltest
from deepvariant.realigner.python import ssw

REF = 'CAGCCTTTCTGACCCGGAAATCAAAATAGGCACAACAAA'
QUERY = 'CTGAGCCGGTAAATC'

# Expected alignment:
#   CAGCCTTTCTGACCCGG-AAATCAAAATAGGCACAACAAA
#           ||||*|||| |||||
#           CTGAGCCGGTAAATC


class SswWrapTest(absltest.TestCase):
  """Basic tests for the wrapped SSW aligner."""

  def test_Align(self):
    """Tests the Align method."""
    aligner = ssw.Aligner()
    filter_ = ssw.Filter()
    length = aligner.set_reference_sequence(REF)
    self.assertLen(REF, length)
    alignment = aligner.align(QUERY, filter_)
    self.assertEqual(21, alignment.sw_score)
    self.assertEqual(8, alignment.sw_score_next_best)
    self.assertEqual(8, alignment.ref_begin)
    self.assertEqual(21, alignment.ref_end)
    self.assertEqual(0, alignment.query_begin)
    self.assertEqual(14, alignment.query_end)
    self.assertEqual(4, alignment.ref_end_next_best)
    self.assertEqual(2, alignment.mismatches)
    self.assertEqual(b'4=1X4=1I5=', alignment.cigar_string)

  def test_Align2_reversed(self):
    """Tests the Align method, reversing query and ref from above."""
    aligner = ssw.Aligner()
    filter_ = ssw.Filter()
    aligner.set_reference_sequence(QUERY)
    alignment = aligner.align(REF, filter_)
    self.assertEqual(21, alignment.sw_score)
    self.assertEqual(8, alignment.query_begin)
    self.assertEqual(21, alignment.query_end)
    self.assertEqual(0, alignment.ref_begin)
    self.assertEqual(14, alignment.ref_end)
    self.assertEqual(2, alignment.mismatches)
    self.assertEqual(b'8S4=1X4=1D5=17S', alignment.cigar_string)


if __name__ == '__main__':
  absltest.main()
