def test_report_malformed_records(self):
header_definitions = merge_header_definitions.VcfHeaderDefinitions()
inferred_headers = VcfHeader()
records = [vcfio.MalformedVcfRecord('file1',
'rs6054257 G A 29 PASS',
'Invalid literal')]
expected = [
'No Header Conflicts Found.\n',
'\n',
'No Undefined Headers Found.\n',
'\n',
preprocess_reporter._InconsistencyType.MALFORMED_RECORDS + '\n',
preprocess_reporter._HeaderLine.MALFORMED_RECORDS_HEADER + '\n',
(preprocess_reporter._DELIMITER).join([
'file1', 'rs6054257 G A 29 PASS', 'Invalid literal\n']),
'\n'
]
self._generate_report_and_assert_contents_equal(
expected, header_definitions, inferred_headers=inferred_headers,
malformed_records=records)
from __future__ import absolute_import
import unittest
from apache_beam.testing.test_pipeline import TestPipeline
from apache_beam.testing.util import assert_that
from apache_beam.transforms import Create
from gcp_variant_transforms.beam_io import vcfio
from gcp_variant_transforms.testing import asserts
from gcp_variant_transforms.testing.testdata_util import hash_name
from gcp_variant_transforms.transforms import filter_variants
# A sample MalformedVcfRecord.
MALFORMED_RECORD = vcfio.MalformedVcfRecord('FILE', 'LINE', 'ERROR')
class FilterVariantsTest(unittest.TestCase):
"""Test cases for ``FilterVariants`` transform."""
def setUp(self):
self.variants = self._get_sample_variants()
self.pipeline = TestPipeline()
def _get_sample_variants(self):
variant_1 = vcfio.Variant(
reference_name='19',
start=11,
end=12,
reference_bases='C',
alternate_bases=['A', 'TT'],
