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"""Tests for AlleleCounter 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


def setUpModule():
  testdata.init()


class WrapAlleleCounterTest(absltest.TestCase):

  def test_wrap(self):
    ref = fasta.IndexedFastaReader(testdata.CHR20_FASTA)
    sam_reader = sam.SamReader(testdata.CHR20_BAM)
    size = 100
    region = ranges.make_range('chr20', 10000000, 10000000 + size)
    options = deepvariant_pb2.AlleleCounterOptions(partition_size=size)
    allele_counter = _allelecounter.AlleleCounter(ref.c_reader, region, [],
                                                  options)
    reads = list(sam_reader.query(region))
    self.assertGreater(len(reads), 0)
    for read in reads:
      allele_counter.add(read, 'sample_id')
    counts = allele_counter.counts()
    self.assertLen(counts, size)


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