Bug fix for issue 132

[zlian1758]

singletons are a list of tuples that have None in it. Python cannot perform sorted([(3, None), (2, None), (1, None)])

[joshfactorial]

The only problem with this solution is that it leaves singletons unsorted, which changes the result. I believe changing

                properly_paired_reads.append((read_1, read_2))
            elif read1_is_singleton:
                # This will be the choice for all single-ended reads
                singletons.append((read_1, None))
            else:
                singletons.append((None, read_2))

to

                properly_paired_reads.append((read_1, read_2))
            elif read1_is_singleton:
                # This will be the choice for all single-ended reads
                singletons.append((read_1, None))
            else:
                singletons.append((read_2, None))

would preserve the order of the records, while enabling a sort. I'm testing this fix out in another branch.