def test_index(self):
snps = VariationsArrays()
chroms = [1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4]
pos = [1, 2, 3, 1, 2, 3, 1, 2, 3, 2, 4, 6]
snps['/variations/chrom'] = numpy.array(chroms)
snps['/variations/pos'] = numpy.array(pos)
index = PosIndex(snps)
assert index.index_pos(1, 1) == 0
assert index.index_pos(2, 1) == 3
assert index.index_pos(3, 1) == 6
assert index.index_pos(4, 1) == 9
assert index.index_pos(4, 2) == 9
assert index.index_pos(4, 3) == 10
assert index.index_pos(4, 4) == 10
assert index.get_chrom_range_index(1) == (0, 2)
assert index.get_chrom_range_pos(1) == (1, 3)
assert index.covered_length == 10
