Beispiel #1
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 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'])
Beispiel #2
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 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)
Beispiel #3
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 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')
Beispiel #4
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 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()))