def test_chunk_pairs(self):
poss = [5, 7, 8, 10, 11, 12]
chroms = ['c1'] * len(poss)
poss = numpy.array(poss)
chroms = numpy.array(chroms)
varis = VariationsArrays()
varis[POS_FIELD] = poss
varis[CHROM_FIELD] = chroms
pairs = list(varis.iterate_chunk_pairs(max_dist=3, chunk_size=2))
pos_pairs = [(pair['chunk1'][POS_FIELD][0], pair['chunk2'][POS_FIELD][0]) for pair in pairs]
expected = [(5, 5), (5, 8), (8, 8), (8, 11), (11, 11)]
assert pos_pairs == expected
pairs = list(varis.iterate_chunk_pairs(max_dist=4, chunk_size=2))
pos_pairs = [(pair['chunk1'][POS_FIELD][0], pair['chunk2'][POS_FIELD][0]) for pair in pairs]
expected = [(5, 5), (5, 8), (5, 11), (8, 8), (8, 11), (11, 11)]
assert pos_pairs == expected
