temp-call-test-near-opt-aln.py

def test_alignment_score_threshold():
    """Test for "report all near optimal alignments" strategy.

    """
    contigfile = data_file('aln_scr_thresh.contig.augfasta')
    contigstream = kevlar.parse_augmented_fastx(kevlar.open(contigfile, 'r'))
    contigs = list(contigstream)

    gdnafile = data_file('aln_scr_thresh.gdna.fa')
    gdnastream = kevlar.reference.load_refr_cutouts(kevlar.open(gdnafile, 'r'))
    targets = list(gdnastream)

    calls = list(call(targets, contigs))
    assert len(calls) == 1
    assert calls[0].position == 23232242 - 1
    assert calls[0].filterstr == 'PASS'