def test_add_read(self):
fh = MockBamFileHandle()
b = BamCache(fh)
r = MockRead('name')
b.add_read(r)
self.assertEqual(1, len(b.cache.values()))
self.assertEqual(set([r]), b.cache['name'])
def test_add_invalid_read(self, log_patcher):
bad_read = mock.Mock(
is_unmapped=False, reference_start=0, reference_end=0, query_name='BAD_READ'
)
cache = BamCache(MockBamFileHandle())
cache.add_read(bad_read)
self.assertEqual(0, len(cache.cache))
log_patcher.assert_called_with('ignoring invalid read', 'BAD_READ', level=logging.DEBUG)
def test_add_invalid_read(self, log_patcher):
bad_read = mock.Mock(
is_unmapped=False, reference_start=0, reference_end=0, query_name='BAD_READ'
)
cache = BamCache(MockBamFileHandle())
cache.add_read(bad_read)
assert len(cache.cache) == 0
log_patcher.method_calls[0].assert_called_with('ignoring invalid read: BAD_READ')
def test_add_read(self):
fh = MockBamFileHandle()
b = BamCache(fh)
r = mock.MagicMock(query_name='name', query_sequence='')
b.add_read(r)
self.assertEqual(1, len(b.cache.values()))
b.add_read(r)
self.assertEqual(1, len(b.cache.values()))
r.reference_start = 0
b.add_read(r)
self.assertEqual(1, len(b.cache.values()))