Add additional flags for pysamstats.load_pileup

[nrkssa]

Include optional flags to pileup.py/load_pileup

• min_mapq=0
• min_baseq=0
• no_del=False
• no_dup=False

This allows for the use of these flags in all pysamsstats.load_* calls

[alimanfoo]

Great, thank you!

For a test, something like this added to the pysamstats/test/test_pileup.py module would be fine I think:

def test_pileup_kwargs():
    # check that keyword arguments are being passed through
    kwargs = {
        'chrom': 'Pf3D7_01_v3',
        'start': 2000,
        'end': 2100,
        'min_mapq': 1,
        'min_baseq': 1,
        'no_del': True,
        'no_dup': True
    }
    for f, needs_ref in pileup_functions:
        if needs_ref:
            a = f(Samfile('fixture/test.bam'), Fastafile('fixture/ref.fa'), **kwargs)
        else:
            a = f(Samfile('fixture/test.bam'), **kwargs)
        assert isinstance(a, np.ndarray)
        assert a.dtype.names is not None

[nrkssa]

Great, thank you!

For a test, something like this added to the pysamstats/test/test_pileup.py module would be fine I think:

def test_pileup_kwargs():
    # check that keyword arguments are being passed through
    kwargs = {
        'chrom': 'Pf3D7_01_v3',
        'start': 2000,
        'end': 2100,
        'min_mapq': 1,
        'min_baseq': 1,
        'no_del': True,
        'no_dup': True
    }
    for f, needs_ref in pileup_functions:
        if needs_ref:
            a = f(Samfile('fixture/test.bam'), Fastafile('fixture/ref.fa'), **kwargs)
        else:
            a = f(Samfile('fixture/test.bam'), **kwargs)
        assert isinstance(a, np.ndarray)
        assert a.dtype.names is not None

Thanks. I have included this function in test/test_pileup.py. The latest commit contains this change.

[alimanfoo]

Awesome, thanks!