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"""Tests for VariantCalling CLIF python wrappers."""



from absl.testing import absltest

from third_party.nucleus.io import fasta
from third_party.nucleus.io import sam
from third_party.nucleus.util import ranges
from deepvariant import testdata

from deepvariant.protos import deepvariant_pb2
from deepvariant.python import allelecounter as _allelecounter
from deepvariant.python import variant_calling


def setUpModule():
  testdata.init()


class WrapVariantCallingTest(absltest.TestCase):

  def test_call_from_allele_counter(self):
    ref = fasta.IndexedFastaReader(testdata.CHR20_FASTA)
    sam_reader = sam.SamReader(testdata.CHR20_BAM)
    size = 1000
    region = ranges.make_range('chr20', 10000000, 10000000 + size)
    allele_counter = _allelecounter.AlleleCounter(
        ref.c_reader, region, [],
        deepvariant_pb2.AlleleCounterOptions(partition_size=size))
    caller = variant_calling.VariantCaller(
        deepvariant_pb2.VariantCallerOptions(
            min_count_snps=2,
            min_count_indels=2,
            min_fraction_snps=0.12,
            min_fraction_indels=0.12,
            sample_name='sample_name',
            p_error=0.001,
            max_gq=50,
            gq_resolution=1,
            ploidy=2))

    # Grab all of the reads in our region and add them to the allele_counter.
    reads = list(sam_reader.query(region))
    self.assertNotEmpty(reads)
    for read in reads:
      allele_counter.add(read, 'sample_id')

    # Get the candidates records for this whole region.
    candidates = caller.calls_from_allele_counter(allele_counter)

    # We should have at least some candidates and some gvcf records.
    self.assertNotEmpty(candidates)

    # Each candidate should be a DeepVariantCall.
    for candidate in candidates:
      self.assertIsInstance(candidate, deepvariant_pb2.DeepVariantCall)


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