test_aggregate.py 文件源码

def test_aggregate_reads_5():
    "it should drop reads that has too much mismatch"

    o = Namespace(verbos=False, qual=20, mismatch_limit=2)

    reads = (
        ("r1", 'C', 60, 2, 11, 1, 4, 11,  False, True),
        ("r1", 'C', 60, 4, 13, 1, 2, -11, True, True),
        ("r2", 'C', 60, 3, 12, 3, 5, 11,  False, True),
        ("r2", 'C', 60, 5, 14, 1, 3, -11, True, True),
        ("r3", 'C', 60, 6, 14, 3, 0, 0, True, False),
        ("r4", 'C', 60, 7, 14, 1, 0, 0, True, False)
    )

    unique_pairs, unique_single, *_, nlowq, ninconsis = aggregate_reads(o, reads)

    assert len(unique_pairs) == 1
    assert len(unique_single) == 1
    assert nlowq == 3