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"""Tests for third_party.nucleus.io.tabix."""

from __future__ import absolute_import
from __future__ import division
from __future__ import print_function

import os
import shutil

from absl.testing import absltest

from etils import epath
from third_party.nucleus.io import tabix
from third_party.nucleus.io import vcf
from third_party.nucleus.testing import test_utils
from third_party.nucleus.util import ranges


class TabixTest(absltest.TestCase):
  """Test the functionality of tabix.build_index."""

  def setUp(self):
    super(TabixTest, self).setUp()
    self.input_file = test_utils.genomics_core_testdata('test_samples.vcf.gz')
    self.output_file = test_utils.test_tmpfile('test_samples.vcf.gz')
    shutil.copyfile(self.input_file, self.output_file)
    self.tbx_index_file = self.output_file + '.tbi'
    self.csi_index_file = self.output_file + '.csi'

  def tearDown(self):
    super(TabixTest, self).tearDown()
    os.remove(self.output_file)
    try:
      os.remove(self.tbx_index_file)
    except OSError:
      pass
    try:
      os.remove(self.csi_index_file)
    except OSError:
      pass

  def test_build_index_tbx(self):
    self.assertFalse(epath.Path(self.tbx_index_file).exists())
    tabix.build_index(self.output_file)
    self.assertTrue(epath.Path(self.tbx_index_file).exists())

  def test_build_index_csi(self):
    min_shift = 14
    self.assertFalse(epath.Path(self.csi_index_file).exists())
    tabix.build_csi_index(self.output_file, min_shift)
    self.assertTrue(epath.Path(self.csi_index_file).exists())

  def test_vcf_query_tbx(self):
    tabix.build_index(self.output_file)
    self.input_reader = vcf.VcfReader(self.input_file)
    self.output_reader = vcf.VcfReader(self.output_file)

    range1 = ranges.parse_literal('chr3:100,000-500,000')
    self.assertEqual(
        list(self.input_reader.query(range1)),
        list(self.output_reader.query(range1)))

  def test_vcf_query_csi(self):
    min_shift = 14
    tabix.build_csi_index(self.output_file, min_shift)
    self.input_reader = vcf.VcfReader(self.input_file)
    self.output_reader = vcf.VcfReader(self.output_file)

    range1 = ranges.parse_literal('chr3:100,000-500,000')
    self.assertEqual(
        list(self.input_reader.query(range1)),
        list(self.output_reader.query(range1)))

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