def test_write_sam_pairs(self): reader = ["line1\n", "line2\n"] read1 = MockSplitRead("key1", "L") read2 = MockSplitRead("key2", "R") builder = MockSplitReadBuilder({'line1': read1, 'line2' : read2}, set(["@header1", "@header2"])) read_group_pairs = {} _write_sam_pairs(read_group_pairs, reader, builder, MockWriter(), MockLogger()) self.assertEqual(1, read1.write_sam_pairs_called) self.assertEqual(1, read2.write_sam_pairs_called)
def test_write_sam_pairs_headersPassThrough(self): reader = ["@header1\n","@header2\n"] builder = MockSplitReadBuilder({}, set(["@header1", "@header2"])) writer = MockWriter() read_group_pairs = {} _write_sam_pairs(read_group_pairs, reader, builder, writer, MockLogger()) actual_lines = writer.lines() self.assertEqual(2, len(actual_lines)) self.assertEqual("@header1", actual_lines[0]) self.assertEqual("@header2", actual_lines[1])