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"""Tests for deepvariant .very_sensitive_caller."""

from unittest import mock

from absl.testing import absltest
from absl.testing import parameterized

from deepvariant import very_sensitive_caller
from deepvariant.protos import deepvariant_pb2
from third_party.nucleus.testing import test_utils


def _reference_model_options(p_error, max_gq, gq_resolution=1):
  return deepvariant_pb2.VariantCallerOptions(
      sample_name='UNKNOWN',
      p_error=p_error,
      max_gq=max_gq,
      gq_resolution=gq_resolution,
      ploidy=2,
  )


class VerySensitiveCallerTests(parameterized.TestCase):

  def make_test_caller(self, p_error, max_gq, gq_resolution=1):
    options = _reference_model_options(p_error, max_gq, gq_resolution)
    return very_sensitive_caller.VerySensitiveCaller(
        options, use_cache_table=False
    )

  def fake_allele_counter(self, start_pos, counts):
    allele_counter = mock.Mock()
    # pylint: disable=g-complex-comprehension
    allele_counter.summary_counts.return_value = [
        deepvariant_pb2.AlleleCountSummary(
            ref_supporting_read_count=n_ref,
            total_read_count=n_ref + n_alt,
            ref_base=ref,
            reference_name='chr1',
            position=start_pos + i,
        )
        for i, (n_alt, n_ref, ref) in enumerate(counts)
    ]
    # pylint: enable=g-complex-comprehension
    allele_counter.counts.return_value = counts
    return allele_counter

  def test_calls_from_allele_counts(self):
    # Our test AlleleCounts are 5 positions:
    #
    # 10: A ref [no reads]
    # 11: G/C variant
    # 12: G ref [no reads]
    # 13: G ref [no reads]
    # 14: T/C variant
    #
    # The ref sites have no reads for ref or any alt simply because it
    # simplifies comparing them with the expected variant genotype likelihoods.
    # We aren't testing the correctness of the gvcf calculation here (that's
    # elsewhere) but rather focusing here on the separation of variants from
    # gvcf records, and the automatic merging of the gvcf blocks.
    allele_counter = self.fake_allele_counter(
        10,
        [
            (0, 0, 'A'),
            (10, 10, 'G'),
            (0, 0, 'G'),
            (0, 0, 'G'),
            (10, 10, 'T'),
        ],
    )
    fake_candidates = [
        deepvariant_pb2.DeepVariantCall(
            variant=test_utils.make_variant(alleles=['G', 'C'], start=11)
        ),
        deepvariant_pb2.DeepVariantCall(
            variant=test_utils.make_variant(alleles=['T', 'C'], start=14)
        ),
    ]

    caller = self.make_test_caller(0.01, 100)
    with mock.patch.object(caller, 'cpp_variant_caller') as mock_cpp:
      mock_cpp.calls_from_allele_counts.return_value = fake_candidates

      allele_counters = {'SAMPLE_ID': allele_counter}
      candidates, _ = caller.calls_and_gvcfs(
          allele_counters=allele_counters,
          target_sample='SAMPLE_ID',
          include_gvcfs=False,
      )

    expected_allele_counts_param = {}
    expected_allele_counts_param['SAMPLE_ID'] = allele_counter
    mock_cpp.calls_from_allele_counts.assert_called_once_with(
        expected_allele_counts_param, 'SAMPLE_ID'
    )
    self.assertEqual(candidates, fake_candidates)


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