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


def p(obj):
  for x in dir(obj):
    if not x.startswith('_'):
      print(x + ':' + repr(getattr(obj, x, '')))


class SswGccTest(absltest.TestCase):
  """Tests for the wrapped SSW aligner in a way that fails with gcc5.4."""

  def test_short(self):
    """Test very short strings."""
    ref = 'tttt'
    query = 'ttAtt'
    match = 4
    mismatch = 2
    gap_extend_penalty = 2
    gap_open_penalty = 4

    aligner = ssw.Aligner.construct(
        match_score=match,
        mismatch_penalty=mismatch,
        gap_opening_penalty=gap_open_penalty,
        gap_extending_penalty=gap_extend_penalty)
    filter_ = ssw.Filter()
    length = aligner.set_reference_sequence(ref)
    self.assertLen(ref, length)
    alignment = aligner.align(query, filter_)
    p(alignment)
    self.assertEqual(b'2=1I2=', alignment.cigar_string)

  def test_longer(self):
    """Test longer strings, so the second-best alignment is considered."""
    ref = 'TTTTGGGGGGGGGGGGG'
    query = 'TTATTGGGGGGGGGGGGG'
    match = 4
    mismatch = 2
    gap_extend_penalty = 2
    gap_open_penalty = 4

    aligner = ssw.Aligner.construct(
        match_score=match,
        mismatch_penalty=mismatch,
        gap_opening_penalty=gap_open_penalty,
        gap_extending_penalty=gap_extend_penalty)
    filter_ = ssw.Filter()
    length = aligner.set_reference_sequence(ref)
    self.assertLen(ref, length)
    alignment = aligner.align(query, filter_)
    p(alignment)
    self.assertEqual(b'2=1I15=', alignment.cigar_string)


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