test_bam.py 文件源码

def test_pad_softclip_3(tmpdir):
    "it should pad softclipped bases"

    make_bam(tmpdir.strpath, """
             123456789_123
        r1 + __.*.......
        r1 -   .*.........
        r2 - ...*.......
        r2 +   .*.......__
    """)

    o = Namespace(verbos=False, mismatch_limit=-1)
    sam = AlignmentFile(tmpdir.join("test.bam").strpath)

    adjusted_pos = pad_softclip(sam)

    assert adjusted_pos["r1"] == (0, 13) # 0-based position
    assert adjusted_pos["r2"] == (0, 13)