test_bam.py 文件源码

def test_get_reads_1(tmpdir):
    "it should get all but only the reads that covers the given position"

    make_bam(tmpdir.strpath, """
             123456789_123456789_12
        r1 + ...........
        r1 -      ......*....
        r2 +   .........*.
        r2 -       .....*.......
        r3 +       ...........
        r3 -            ....*......
        r4 +       ...........
        r4 -            ...........
             123456789_123456789_12
    """)

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

    assert sum( 1 for _ in get_reads(o, sam, 'ref', '4') )  == 2
    assert sum( 1 for _ in get_reads(o, sam, 'ref', '12') ) == 7
    assert sum( 1 for _ in get_reads(o, sam, 'ref', '20') ) == 2