test_bam.py 文件源码

def test_pad_softclip_2(tmpdir):
    "it should ignore more than two reads which share the same name"

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

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

    adjusted_pos = pad_softclip(sam)

    assert sum(1 for startpos, length in adjusted_pos.values() if startpos != -1) == 1