test_bam.py 文件源码

def test_get_reads_2(tmpdir):
    "it should read properties correctly"

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

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

    r = next(get_reads(o, sam, 'ref', '4'))

    assert r[0] == "r1" # name
    assert r[3] == 0 # 0-based pos
    assert r[4] == 11 # length
    assert r[5] == -1 # mismatch, not caculated
    assert r[6] == 2 # mate pos
    assert r[7] == 13 # template length
    assert r[8] == False # is_reverse
    assert r[9] == True # paired and mapped